Updated on 2024/10/07

Information

 

写真a

 
SUYAMA MIKITA
 
Organization
Medical Institute of Bioregulation Research Center for Systems Immunology Professor
Graduate School of Systems Life Sciences Department of Systems Life Sciences（Concurrent）
Graduate School of Medical Sciences Department of Medical Sciences（Concurrent）
Title
Professor
Profile
We are mainly analyzing genomic sequences and epigenomic data to get much insight into gene regulation by computational biological approaches. The current research topics include, (1) genome-wide identification of transcription factor binding sites. (2) molecular evolutionary analysis of cis-elements for splicing. (3) comparative genome analyses of gene duplications and genome rearrangements. (4) genome informatics analysis of sex differences. (5) development of tools for bioinformatics analyses.
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Research Areas

  • Life Science / System genome science

Degree

  • Agriculture

Research Interests・Research Keywords

  • Research theme：Analysis of regulatory mechanisms for gene expression by comparative genomic approach.

    Keyword：comparative genomics, bioinformatics

    Research period： 2012.1 - 2013.3

Papers

  • Mechanistic insights into mutually exclusive splicing in dynamin 1. Reviewed International journal

    Mikita Suyama

    Bioinformatics   29 ( 17 )   2084 - 2087   2013.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/btt368

  • A network of conserved co-occurring motifs for the regulation of alternative splicing. Reviewed International journal

    Suyama M, Harrington ED, Vinokourova S, von Knebel Doeberitz M, Ohara O, Bork P.

    Nucleic Acids Res.   38 ( 22 )   2010.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/nar/gkq705

  • Identification and analysis of short indels inducing exon extension/shrinkage events Reviewed

    Qu, Z; Sakaguchi, N; Kikutake, C; Suyama, M

    FEBS OPEN BIO   2024.7   （ ISSN:2211-5463 ）

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    Authorship：Last author,　Corresponding author   Language：English   Publisher：FEBS Open Bio  

    The search for genetic variants that act as causative factors in human diseases by disrupting the normal splicing process has primarily focused on single nucleotide variants (SNVs). It is worth noting that insertions or deletions (indels) have also been sporadically reported as causative disease variants through their potential impact on the splicing process. In this study, to perform identification of indels inducing exon extension/shrinkage events, we used individual-specific genomes and RNA sequencing (RNA-seq) data pertaining to the corresponding individuals and identified 12 exon extension/shrinkage events that were potentially induced by indels that disrupted authentic splice sites or created novel splice sites in 235 normal individuals. By evaluating the impact of these abnormal splicing events on the resulting transcripts, we found that five events led to the generation of premature termination codons (PTCs), including those occurring within genes associated with genetic disorders. Our analysis revealed that the potential functions of indels have been underexamined, and it is worth considering the possibility that indels may affect splice site usage, using RNA-seq data to discover novel potentially disease-associated mutations.

    DOI： 10.1002/2211-5463.13871

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  • The anti-tumor effect of trifluridine via induction of aberrant mitosis is unaffected by mutations modulating p53 activity Reviewed

    Wakasa, T; Nonaka, K; Harada, A; Ohkawa, Y; Kikutake, C; Suyama, M; Kobunai, T; Tsunekuni, K; Matsuoka, K; Kataoka, Y; Ochiiwa, H; Miyadera, K; Sagara, T; Oki, E; Ohdo, S; Maehara, Y; Iimori, M; Kitao, H

    CELL DEATH DISCOVERY   10 ( 1 )   307   2024.7   （ ISSN:2058-7716 eISSN:2058-7716 ）

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    Language：English   Publisher：Cell Death Discovery  

    The fluorinated thymidine analog trifluridine (FTD) is a chemotherapeutic drug commonly used to treat cancer; however, the mechanism by which FTD induces cytotoxicity is not fully understood. In addition, the effect of gain-of-function (GOF) missense mutations of the TP53 gene (encoding p53), which promote cancer progression and chemotherapeutic drug resistance, on the chemotherapeutic efficacy of FTD is unclear. Here, we revealed the mechanisms by which FTD-induced aberrant mitosis and contributed to cytotoxicity in both p53-null and p53-GOF missense mutant cells. In p53-null mutant cells, FTD-induced DNA double-stranded breaks, single-stranded DNA accumulation, and the associated DNA damage responses during the G2 phase. Nevertheless, FTD-induced DNA damage and the related responses were not sufficient to trigger strict G2/M checkpoint arrest. Thus, these features were carried over into mitosis, resulting in chromosome breaks and bridges, and subsequent cytokinesis failure. Improper mitotic exit eventually led to cell apoptosis, caused by the accumulation of extensive DNA damage and the presence of micronuclei encapsulated in the disrupted nuclear envelope. Upon FTD treatment, the behavior of the p53-GOF-missense mutant, isogenic cell lines, generated by CRISPR/Cas9 genome editing, was similar to that of p53-null mutant cells. Thus, our data suggest that FTD treatment overrode the effect on gene expression induced by p53-GOF mutants and exerted its anti-tumor activity in a manner that was independent of the p53 function.

    DOI： 10.1038/s41420-024-02083-3

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  • Subtype-specific alternative splicing events in breast cancer identified by large-scale data analysis Reviewed

    Deguchi, Y; Kikutake, C; Suyama, M

    SCIENTIFIC REPORTS   14 ( 1 )   14158   2024.6   （ ISSN:2045-2322 ）

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    Authorship：Last author,　Corresponding author   Language：English   Publisher：Scientific Reports  

    Genome analysis in cancer has focused mainly on elucidating the function and regulatory mechanisms of genes that exhibit differential expression or mutation in cancer samples compared to normal samples. Recently, transcriptome analysis revealed that abnormal splicing events in cancer samples could contribute to cancer pathogenesis. Moreover, splicing variants in cancer reportedly generate diverse cancer antigens. Although abnormal splicing events are expected to be potential targets in cancer immunotherapy, the exploration of such targets and their biological significance in cancer have not been fully understood. In this study, to explore subtype-specific alternative splicing events, we conducted a comprehensive analysis of splicing events for each breast cancer subtype using large-scale splicing data derived from The Cancer Genome Atlas and found subtype-specific alternative splicing patterns. Analyses indicated that genes that produce subtype-specific alternative splicing events are potential novel targets for immunotherapy against breast cancer. The subtype-specific alternative splicing events identified in this study, which were not identified by mutation or differential expression analysis, bring new significance to previously overlooked splicing events.

    DOI： 10.1038/s41598-024-65035-y

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  • MUC1-C Is a Common Driver of Acquired Osimertinib Resistance in NSCLC. Reviewed International journal

    Naoki Haratake, Hiroki Ozawa, Yoshihiro Morimoto, Nami Yamashita, Tatsuaki Daimon, Atrayee Bhattacharya, Keyi Wang, Ayako Nakashoji, Hideko Isozaki, Mototsugu Shimokawa, Chie Kikutake, Mikita Suyama, Asato Hashinokuchi, Kazuki Takada, Tomoyoshi Takenaka, Tomoharu Yoshizumi, Tetsuya Mitsudomi, Aaron N Hata, Donald Kufe

    Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer   19 ( 3 )   434 - 450   2024.3   （ ISSN:1556-0864 eISSN:1556-1380 ）

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    INTRODUCTION: Osimertinib is an irreversible EGFR tyrosine kinase inhibitor approved for the first-line treatment of patients with metastatic NSCLC harboring EGFR exon 19 deletions or L858R mutations. Patients treated with osimertinib invariably develop acquired resistance by mechanisms involving additional EGFR mutations, MET amplification, and other pathways. There is no known involvement of the oncogenic MUC1-C protein in acquired osimertinib resistance. METHODS: H1975/EGFR (L858R/T790M) and patient-derived NSCLC cells with acquired osimertinib resistance were investigated for MUC1-C dependence in studies of EGFR pathway activation, clonogenicity, and self-renewal capacity. RESULTS: We reveal that MUC1-C is up-regulated in H1975 osimertinib drug-tolerant persister cells and is necessary for activation of the EGFR pathway. H1975 cells selected for stable osimertinib resistance (H1975-OR) and MGH700-2D cells isolated from a patient with acquired osimertinib resistance are found to be dependent on MUC1-C for induction of (1) phospho (p)-EGFR, p-ERK, and p-AKT, (2) EMT, and (3) the resistant phenotype. We report that MUC1-C is also required for p-EGFR, p-ERK, and p-AKT activation and self-renewal capacity in acquired osimertinib-resistant (1) MET-amplified MGH170-1D #2 cells and (2) MGH121 Res#2/EGFR (T790M/C797S) cells. Importantly, targeting MUC1-C in these diverse models reverses osimertinib resistance. In support of these results, high MUC1 mRNA and MUC1-C protein expression is associated with a poor prognosis for patients with EGFR-mutant NSCLCs. CONCLUSIONS: Our findings reveal that MUC1-C is a common effector of osimertinib resistance and is a potential target for the treatment of osimertinib-resistant NSCLCs.

    DOI： 10.1016/j.jtho.2023.10.017

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  • The impact of selective HDAC inhibitors on the transcriptome of early mouse embryos. Reviewed International journal

    Ruiqi Shao, Takayoshi Suzuki, Mikita Suyama, Yuichi Tsukada

    BMC genomics   25 ( 1 )   143 - 143   2024.2   （ ISSN:1471-2164 ）

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    Authorship：Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    BACKGROUND: Histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), plays a crucial role in the control of gene expression. HDAC inhibitors (HDACi) have shown potential in cancer therapy; however, the specific roles of HDACs in early embryos remain unclear. Moreover, although some pan-HDACi have been used to maintain cellular undifferentiated states in early embryos, the specific mechanisms underlying their effects remain unknown. Thus, there remains a significant knowledge gap regarding the application of selective HDACi in early embryos. RESULTS: To address this gap, we treated early embryos with two selective HDACi (MGCD0103 and T247). Subsequently, we collected and analyzed their transcriptome data at different developmental stages. Our findings unveiled a significant effect of HDACi treatment during the crucial 2-cell stage of zygotes, leading to a delay in embryonic development after T247 and an arrest at 2-cell stage after MGCD0103 administration. Furthermore, we elucidated the regulatory targets underlying this arrested embryonic development, which pinpointed the G2/M phase as the potential period of embryonic development arrest caused by MGCD0103. Moreover, our investigation provided a comprehensive profile of the biological processes that are affected by HDACi, with their main effects being predominantly localized in four aspects of zygotic gene activation (ZGA): RNA splicing, cell cycle regulation, autophagy, and transcription factor regulation. By exploring the transcriptional regulation and epigenetic features of the genes affected by HDACi, we made inferences regarding the potential main pathways via which HDACs affect gene expression in early embryos. Notably, Hdac7 exhibited a distinct response, highlighting its potential as a key player in early embryonic development. CONCLUSIONS: Our study conducted a comprehensive analysis of the effects of HDACi on early embryonic development at the transcriptional level. The results demonstrated that HDACi significantly affected ZGA in embryos, elucidated the distinct actions of various selective HDACi, and identified specific biological pathways and mechanisms via which these inhibitors modulated early embryonic development.

    DOI： 10.1186/s12864-024-10029-3

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  • Modeling embryo-endometrial interface recapitulating human embryo implantation Reviewed

    Shun Shibata, Shun Endo, Luis A. E. Nagai, Eri H. Kobayashi, Akira Oike, Norio Kobayashi, Akane Kitamura, Takeshi Hori, Yuji Nashimoto, Ryuichiro Nakato, Hirotaka Hamada, Hirokazu Kaji, Chie Kikutake, Mikita Suyama, Masatoshi Saito, Nobuo Yaegashi, Hiroaki Okae, Takahiro Arima

    Science Advances   10 ( 8 )   eadi4819   2024.2   （ ISSN:2375-2548 eISSN:2375-2548 ）

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    Language：Others   Publishing type：Research paper (scientific journal)   Publisher：American Association for the Advancement of Science (AAAS)  

    The initiation of human pregnancy is marked by the implantation of an embryo into the uterine environment; however, the underlying mechanisms remain largely elusive. To address this knowledge gap, we developed hormone-responsive endometrial organoids (EMO), termed apical-out (AO)–EMO, which emulate the in vivo architecture of endometrial tissue. The AO-EMO comprise an exposed apical epithelium surface, dense stromal cells, and a self-formed endothelial network. When cocultured with human embryonic stem cell–derived blastoids, the three-dimensional feto-maternal assembloid system recapitulates critical implantation stages, including apposition, adhesion, and invasion. Endometrial epithelial cells were subsequently disrupted by syncytial cells, which invade and fuse with endometrial stromal cells. We validated this fusion of syncytiotrophoblasts and stromal cells using human blastocysts. Our model provides a foundation for investigating embryo implantation and feto-maternal interactions, offering valuable insights for advancing reproductive medicine.

    DOI： 10.1126/sciadv.adi4819

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  • CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development. Reviewed International journal

    Takanori Shimizu, Akira Oike, Eri H Kobayashi, Asato Sekiya, Norio Kobayashi, Shun Shibata, Hirotaka Hamada, Masatoshi Saito, Nobuo Yaegashi, Mikita Suyama, Takahiro Arima, Hiroaki Okae

    Proceedings of the National Academy of Sciences of the United States of America   120 ( 51 )   e2311372120   2023.12   （ ISSN:0027-8424 eISSN:1091-6490 ）

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    The placenta serves as the interface between the mother and fetus, facilitating the exchange of gases and nutrients between their separate blood circulation systems. Trophoblasts in the placenta play a central role in this process. Our current understanding of mammalian trophoblast development relies largely on mouse models. However, given the diversification of mammalian placentas, findings from the mouse placenta cannot be readily extrapolated to other mammalian species, including humans. To fill this knowledge gap, we performed CRISPR knockout screening in human trophoblast stem cells (hTSCs). We targeted genes essential for mouse placental development and identified more than 100 genes as critical regulators in both human hTSCs and mouse placentas. Among them, we further characterized in detail two transcription factors, DLX3 and GCM1, and revealed their essential roles in hTSC differentiation. Moreover, a gene function-based comparison between human and mouse trophoblast subtypes suggests that their relationship may differ significantly from previous assumptions based on tissue localization or cellular function. Notably, our data reveal that hTSCs may not be analogous to mouse TSCs or the extraembryonic ectoderm (ExE) in which in vivo TSCs reside. Instead, hTSCs may be analogous to progenitor cells in the mouse ectoplacental cone and chorion. This finding is consistent with the absence of ExE-like structures during human placental development. Our data not only deepen our understanding of human trophoblast development but also facilitate cross-species comparison of mammalian placentas.

    DOI： 10.1073/pnas.2311372120

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  • Homologous Recombination Repair Gene Alterations Are Associated with Tumor Mutational Burden and Survival of Immunotherapy. Reviewed International journal

    Mamoru Ito, Makoto Kubo, Hitomi Kawaji, Yoshiki Otsubo, Kanako Kurata, Hikaru Abutani, Mikita Suyama, Yoshinao Oda, Tomoharu Yoshizumi, Masafumi Nakamura, Eishi Baba

    Cancers   15 ( 23 )   2023.11   （ ISSN:2072-6694 eISSN:2072-6694 ）

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    BACKGROUND: Comprehensive genomic profiling (CGP) has become generally accepted practice in cancer care since CGP has become reimbursed by national healthcare insurance in Japan in 2019. However, its usefulness for cancer patients is insufficient for several reasons. METHODS: In an observational clinical study of FoundationOne® CDx, potential biomarkers were explored and the cause of testing failure was investigated. A total of 220 cancer patients were enrolled in the study during the period from 2018 to 2019 at Kyushu University Hospital. RESULTS: The primary tumor sites of the 220 cases were breast (115), colon (29), stomach (19), and pancreas (20). The present dataset suggested that homologous recombination repair (HRR) gene alterations were positively associated with tumor mutational burden-high (TMB-high) (p = 0.0099). A public dataset confirmed that patients with HRR gene alterations had a higher TMB and showed significantly longer survival of immunotherapy. In the present study, 18 cases failed sequencing. A lower percentage of tumor cell nuclei was the most common reason for testing failures (p = 0.037). Cases that received neoadjuvant chemotherapy before sampling tended to fail testing. CONCLUSIONS: HRR gene alterations can be a potential biomarker predicting TMB-high and a good response to immunotherapy. For successful sequencing, samples with lower percentages of tumor cell nuclei and previous neoadjuvant chemotherapy should be avoided.

    DOI： 10.3390/cancers15235608

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  • Exome-wide benchmark of difficult-to-sequence regions using short-read next-generation dna sequencing. Reviewed International journal

    Atsushi Hijikata, Mikita Suyama, Shingo Kikugawa, Ryo Matoba, Takuya Naruto, Yumi Enomoto, Kenji Kurosawa, Naoki Harada, Kumiko Yanagi, Tadashi Kaname, Keisuke Miyako, Masaki Takazawa, Hideo Sasai, Junichi Hosokawa, Sakae Itoga, Tomomi Yamaguchi, Tomoki Kosho, Keiko Matsubara, Yoko Kuroki, Maki Fukami, Kaori Adachi, Eiji Nanba, Naomi Tsuchida, Yuri Uchiyama, Naomichi Matsumoto, Kunihiro Nishimura, Osamu Ohara

    Nucleic acids research   52 ( 1 )   114 - 124   2023.11   （ ISSN:0305-1048 eISSN:1362-4962 ）

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    Next-generation DNA sequencing (NGS) in short-read mode has recently been used for genetic testing in various clinical settings. NGS data accuracy is crucial in clinical settings, and several reports regarding quality control of NGS data, primarily focusing on establishing NGS sequence read accuracy, have been published thus far. Variant calling is another critical source of NGS errors that remains unexplored at the single-nucleotide level despite its established significance. In this study, we used a machine-learning-based method to establish an exome-wide benchmark of difficult-to-sequence regions at the nucleotide-residue resolution using 10 genome sequence features based on real-world NGS data accumulated in The Genome Aggregation Database (gnomAD) of the human reference genome sequence (GRCh38/hg38). The newly acquired metric, designated the 'UNMET score,' along with additional lines of structural information from the human genome, allowed us to assess the sequencing challenges within the exonic region of interest using conventional short-read NGS. Thus, the UNMET score could provide a basis for addressing potential sequential errors in protein-coding exons of the human reference genome sequence GRCh38/hg38 in clinical sequencing.

    DOI： 10.1093/nar/gkad1140

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  • Pan-cancer analysis of whole-genome doubling and its association with patient prognosis. Reviewed International journal

    Chie Kikutake, Mikita Suyama

    BMC cancer   23 ( 1 )   619 - 619   2023.7   （ eISSN:1471-2407 ）

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    BACKGROUND: Whole-genome doubling (WGD) is a common mutation in cancer. Various studies have suggested that WGD is associated with a poor prognosis in cancer. However, the detailed association between WGD occurrence and prognosis remains unclear. In this study, we aimed to elucidate the mechanism by which WGD affects prognosis using sequencing data from the Pan-Cancer Analysis of Whole Genomes (PCAWG) and The Cancer Genome Atlas. METHODS: Whole-genome sequencing data of 23 cancer types were downloaded from PCAWG project. We defined the WGD event in each sample using the WGD status annotated using PCAWG. We used MutationTimeR to predict the relative timings of mutations and loss of heterozygosity (LOH) in WGD, thus evaluating their association with WGD. We also analyzed the association between WGD-associated factors and patient prognosis. RESULTS: WGD was associated with several factors, e.g., length of LOH regions. Survival analysis using WGD-associated factors revealed that longer LOH regions and LOH in chr17 were associated with poor prognosis in samples with WGD (WGD samples) and samples without WGD (nWGD samples). In addition to these two factors, nWGD samples showed that the number of mutations in tumor suppressor genes was associated with prognosis. Moreover, we explored the genes associated with prognosis in both samples separately. CONCLUSION: The prognosis-related factors in WGD samples differed significantly compared with those in nWGD samples. This study emphasizes the need for different treatment strategies for WGD and nWGD samples.

    DOI： 10.1186/s12885-023-11132-6

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  • Possible involvement of silent mutations in cancer pathogenesis and evolution. Reviewed International journal

    Chie Kikutake, Mikita Suyama

    Scientific reports   13 ( 1 )   7593 - 7593   2023.5   （ ISSN:2045-2322 ）

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    Authorship：Last author,　Corresponding author   Language：English   Publishing type：Research paper (scientific journal)  

    Recent studies have shown that some silent mutations can be harmful to various processes. In this study, we performed a comprehensive in silico analysis to elucidate the effects of silent mutations on cancer pathogenesis using exome sequencing data derived from the Cancer Genome Atlas. We focused on the codon optimality scores of silent mutations, which were defined as the difference between the optimality of synonymous codons, calculated using the codon usage table. The relationship between cancer evolution and silent mutations showed that the codon optimality score of the mutations that occurred later in carcinogenesis was significantly higher than of those that occurred earlier. In addition, mutations with higher scores were enriched in genes involved in the cell cycle and cell division, while those with lower scores were enriched in genes involved in apoptosis and cellular senescence. Our results demonstrate that some silent mutations can be involved in cancer pathogenesis.

    DOI： 10.1038/s41598-023-34452-w

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  • Genome-wide identification of copy neutral loss of heterozygosity reveals its possible association with spatial positioning of chromosomes. Reviewed International journal

    Hyeonjeong Kim, Mikita Suyama

    Human Molecular Genetics   32 ( 7 )   1175 - 1183   2023.3   （ ISSN:0964-6906 eISSN:1460-2083 ）

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    Loss of heterozygosity (LOH) is a genetic alteration that results from the loss of one allele at a heterozygous locus. In particular, copy neutral LOH (CN-LOH) events are generated, for example, by mitotic homologous recombination after monoallelic defection or gene conversion, resulting in novel homozygous locus having two copies of the normal counterpart allele. This phenomenon can serve as a source of genome diversity and is associated with various diseases. To clarify the nature of the CN-LOH such as the frequency, genomic distribution and inheritance pattern, we made use of whole-genome sequencing data of the three-generation CEPH/Utah family cohort, with the pedigree consisting of grandparents, parents and offspring. We identified an average of 40.7 CN-LOH events per individual taking advantage of 285 healthy individuals from 33 families in the cohort. On average 65% of them were classified as gonosomal-mosaicism-associated CN-LOH, which exists in both germline and somatic cells. We also confirmed that the incidence of the CN-LOH has little to do with the parents' age and sex. Furthermore, through the analysis of the genomic region including the CN-LOH, we found that the chance of the occurrence of the CN-LOH tends to increase at the GC-rich locus and/or on the chromosome having a relatively close inter-homolog distance. We expect that these results provide significant insights into the association between genetic alteration and spatial position of chromosomes as well as the intrinsic genetic property of the CN-LOH.

    DOI： 10.1093/hmg/ddac278

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    Repository Public URL： https://hdl.handle.net/2324/7181969

  • Increased neutrophils in inflammatory bowel disease accelerate the accumulation of amyloid plaques in the mouse model of Alzheimer's disease. Reviewed International journal

    Ryusei Kaneko, Ako Matsui, Mahiro Watanabe, Yoshihiro Harada, Mitsuhiro Kanamori, Natsumi Awata, Mio Kawazoe, Tomoaki Takao, Yutaro Kobayashi, Chie Kikutake, Mikita Suyama, Takashi Saito, Takaomi C Saido, Minako Ito

    Inflammation and regeneration   43 ( 1 )   20 - 20   2023.3   （ ISSN:1880-9693 eISSN:1880-8190 ）

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    BACKGROUND: Alzheimer's disease (AD) is one of the neurodegenerative diseases and characterized by the appearance and accumulation of amyloid-β (Aβ) aggregates and phosphorylated tau with aging. The aggregation of Aβ, which is the main component of senile plaques, is closely associated with disease progression. AppNL-G-F mice, a mouse model of AD, have three familial AD mutations in the amyloid-β precursor gene and exhibit age-dependent AD-like symptoms and pathology. Gut-brain interactions have attracted considerable attention and inflammatory bowel disease (IBD) has been associated with a higher risk of dementia, especially AD, in humans. However, the underlying mechanisms and the effects of intestinal inflammation on the brain in AD remain largely unknown. Therefore, we aimed to investigate the effects of intestinal inflammation on AD pathogenesis. METHODS: Wild-type and AppNL-G-F mice at three months of age were fed with water containing 2% dextran sulfate sodium (DSS) to induce colitis. Immune cells in the brain were analyzed using single-cell RNA sequencing (scRNA-seq) analysis, and the aggregation of Aβ protein in the brain was analyzed via immunohistochemistry. RESULTS: An increase in aggregated Aβ was observed in the brains of AppNL-G-F mice with acute intestinal inflammation. Detailed scRNA-seq analysis of immune cells in the brain showed that neutrophils in the brain increased after acute enteritis. Eliminating neutrophils by antibodies suppressed the accumulation of Aβ, which increased because of intestinal inflammation. CONCLUSION: These results suggest that neutrophils infiltrate the AD brain parenchyma when acute colitis occurs, and this infiltration is significantly related to disease progression. Therefore, we propose that neutrophil-targeted therapies could reduce Aβ accumulation observed in early AD and prevent the increased risk of AD due to colitis.

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  • 遺伝性疾患の原因となる偽エクソン活性化の網羅的探索

    須山 幹太

    上原記念生命科学財団研究報告集   36   1 - 5   2022.12

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    Language：Japanese   Publisher：(公財)上原記念生命科学財団  

  • Drosophila transcription factor NF-Y suppresses transcription of the lipase 4 gene, a key gene for lipid storage. Reviewed International journal

    Yasuhide Yoshioka, Keisuke Anzai, Ryosuke Kowada, Ken Hiratsuka, Teppei Hirayabu, Masashi Yasuda, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Hideki Yoshida, Masamitsu Yamaguchi

    Experimental cell research   420 ( 1 )   113307 - 113307   2022.11   （ ISSN:0014-4827 eISSN:1090-2422 ）

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    The CCAAT motif-binding factor NF-Y consists of three different subunits, NF-YA, NF-YB, and NF-YC. Although it is suggested that NF-Y activity is essential for normal tissue homeostasis, survival, and metabolic function, its precise role in lipid metabolism is not clarified yet. In Drosophila, eye disc specific knockdown of Drosophila NF-YA (dNF-YA) induced aberrant morphology of the compound eye, the rough eye phenotype in adults and mutation of the lipase 4 (lip4) gene suppressed the rough eye phenotype. RNA-seq analyses with dNF-YA knockdown third instar larvae identified the lip4 gene as one of the genes that are up-regulated by the dNF-YA knockdown. We identified three dNF-Y-binding consensuses in the 5'flanking region of the lip4 gene, and a chromatin immunoprecipitation assay with the specific anti-dNF-YA IgG demonstrated dNF-Y binding to this genomic region. The luciferase transient expression assay with cultured Drosophila S2 cells and the lip4 promoter-luciferase fusion genes with and without mutations in the dNF-Y-binding consensuses showed that each of the three dNF-Y consensus sequences negatively regulated lip4 gene promoter activity. Consistent with these results, qRT-PCR analysis with the dNF-YA knockdown third instar larvae revealed that endogenous lip4 mRNA levels were increased by the knockdown of dNF-YA in vivo. The specific knockdown of dNF-YA in the fat body with the collagen-GAL4 driver resulted in smaller oil droplets in the fat body cells. Collectively, these results suggest that dNF-Y is involved in lipid storage through its negative regulation of lip4 gene transcription.

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  • Prostaglandin E2 receptor Ptger4b regulates female-specific peptidergic neurons and female sexual receptivity in medaka. Reviewed International journal

    Thomas Fleming, Yukiko Kikuchi, Mikoto Nakajo, Masaya Tachizawa, Tomoaki Inazumi, Soken Tsuchiya, Yukihiko Sugimoto, Daisuke Saito, Mikita Suyama, Yasuyuki Ohkawa, Takashi Baba, Ken-Ichirou Morohashi, Kataaki Okubo

    Communications biology   5 ( 1 )   1215 - 1215   2022.11   （ eISSN:2399-3642 ）

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    In vertebrates, female receptivity to male courtship is highly dependent on ovarian secretion of estrogens and prostaglandins. We recently identified female-specific neurons in the medaka (Oryzias latipes) preoptic area that express Npba, a neuropeptide mediating female sexual receptivity, in response to ovarian estrogens. Here we show by transcriptomic analysis that these neurons express a multitude of neuropeptides, in addition to Npba, in an ovarian-dependent manner, and we thus termed them female-specific, sex steroid-responsive peptidergic (FeSP) neurons. Our results further revealed that FeSP neurons express a prostaglandin E2 receptor gene, ptger4b, in an ovarian estrogen-dependent manner. Behavioral and physiological examination of ptger4b-deficient female medaka found that they exhibit increased sexual receptivity while retaining normal ovarian function and that their FeSP neurons have reduced firing activity and impaired neuropeptide release. Collectively, this work provides evidence that prostaglandin E2/Ptger4b signaling mediates the estrogenic regulation of FeSP neuron activity and female sexual receptivity.

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  • Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis. Reviewed International journal

    Chie Kikutake, Mikita Suyama

    Cancer medicine   11 ( 20 )   3902 - 3916   2022.10   （ ISSN:2045-7634 ）

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    BACKGROUND: Open chromatin is associated with gene transcription. Previous studies have shown that the density of mutations in open chromatin regions is lower than that in flanking regions because of the higher accessibility of DNA repair machinery. However, in several cancer types, open chromatin regions show an increased local density of mutations in activated regulatory regions. Although the mutation distribution within open chromatin regions in cancer cells has been investigated, only few studies have focused on their functional implications in cancer. To reveal the impact of highly mutated open chromatin regions on cancer, we investigated the association between mutations in open chromatin regions and their possible functions. METHODS: Whole-genome sequencing data of 18 cancer types were downloaded from the PanCancer Analysis of Whole Genomes and Catalog of Somatic Mutations in Cancer. We quantified the mutations located in open chromatin regions defined by The Cancer Genome Atlas and classified open chromatin regions into three categories based on the number of mutations. Then, we investigated the chromatin state, amplification, and possible target genes of the open chromatin regions with a high number of mutations. We also analyzed the association between the number of mutations in open chromatin regions and patient prognosis. RESULTS: In some cancer types, the proportion of promoter or enhancer chromatin state in open chromatin regions with a high number of mutations was significantly higher than that in the regions with a low number of mutations. The possible target genes of open chromatin regions with a high number of mutations were more strongly associated with cancer than those of other open chromatin regions. Moreover, a high number of mutations in open chromatin regions was significantly associated with a poor prognosis in some cancer types. CONCLUSIONS: These results suggest that highly mutated open chromatin regions play an important role in cancer pathogenesis and can be effectively used to predict patient prognosis.

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  • Tmsb10 triggers fetal Leydig differentiation by suppressing the RAS/ERK pathway. Reviewed International journal

    Miki Inoue, Takashi Baba, Fumiya Takahashi, Miho Terao, Shogo Yanai, Yuichi Shima, Daisuke Saito, Kei Sugihara, Takashi Miura, Shuji Takada, Mikita Suyama, Yasuyuki Ohkawa, Ken-Ichirou Morohashi

    Communications biology   5 ( 1 )   974 - 974   2022.9   （ eISSN:2399-3642 ）

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    Leydig cells in fetal testes play crucial roles in masculinizing fetuses through androgen production. Gene knockout studies have revealed that growth factors are implicated in fetal Leydig cell (FLC) differentiation, but little is known about the mechanisms regulating this process. We investigate this issue by characterizing FLC progenitor cells using single-cell RNA sequencing. The sequence datasets suggest that thymosin β10 (Tmsb10) is transiently upregulated in the progenitors. While studying the function of Tmsb10, we reveal that platelet-derived growth factor (PDGF) regulates ciliogenesis through the RAS/ERK and PI3K/AKT pathways, and thereby promotes desert hedgehog (DHH)-dependent FLC differentiation. Tmsb10 expressed in the progenitor cells induces their differentiation into FLCs by suppressing the RAS/ERK pathway. Through characterizing the transiently expressed Tmsb10 in the FLC progenitors, this study unveils the molecular process of FLC differentiation and shows that it is cooperatively induced by DHH and PDGF.

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  • Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing. Reviewed International journal

    Toru Masuda, Shojiro Haji, Yasuhiro Nakashima, Mariko Tsuda, Daisaku Kimura, Akiko Takamatsu, Norifusa Iwahashi, Hironobu Umakoshi, Motoaki Shiratsuchi, Chie Kikutake, Mikita Suyama, Yasuyuki Ohkawa, Yoshihiro Ogawa

    iScience   25 ( 8 )   104781 - 104781   2022.8   （ eISSN:2589-0042 ）

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    Despite recent therapeutic advances for multiple myeloma (MM), relapse is very common. Here, we conducted longitudinal single-cell transcriptome sequencing (scRNA-seq) of MM cells from a patient with relapsed MM, treated with multiple anti-myeloma drugs. We observed five subclusters of MM cells, which appeared and/or disappeared in response to the therapeutic pressure, and identified cluster 3 which emerged during lenalidomide treatment and disappeared after proteasome inhibitor (PI) treatment. Among the differentially expressed genes in cluster 3, we found a candidate drug-response gene; pellino E3 ubiquitin-protein ligase family member 2 (PELI2), which is responsible for PI-induced cell death in in vitro assay. Kaplan-Meier survival analysis of database revealed that higher expression of PELI2 is associated with a better prognosis. Our integrated strategy combining longitudinal scRNA-seq analysis, in vitro functional assay, and database analysis would facilitate the understanding of clonal dynamics of MM in response to anti-myeloma drugs and identification of drug-response genes.

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  • Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits. Reviewed International journal

    Naoto Kubota, Mikita Suyama

    PLoS computational biology   18 ( 8 )   e1010436   2022.8   （ ISSN:1553-734X eISSN:1553-7358 ）

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    Genomic variations are associated with gene expression levels, which are called expression quantitative trait loci (eQTL). Most eQTL may affect the total gene expression levels by regulating transcriptional activities of a specific promoter. However, the direct exploration of genomic loci associated with promoter activities using RNA-seq data has been challenging because eQTL analyses treat the total expression levels estimated by summing those of all isoforms transcribed from distinct promoters. Here we propose a new method for identifying genomic loci associated with promoter activities, called promoter usage quantitative trait loci (puQTL), using conventional RNA-seq data. By leveraging public RNA-seq datasets from the lymphoblastoid cell lines of 438 individuals from the GEUVADIS project, we obtained promoter activity estimates and mapped 2,592 puQTL at the 10% FDR level. The results of puQTL mapping enabled us to interpret the manner in which genomic variations regulate gene expression. We found that 310 puQTL genes (16.1%) were not detected by eQTL analysis, suggesting that our pipeline can identify novel variant-gene associations. Furthermore, we identified genomic loci associated with the activity of "hidden" promoters, which the standard eQTL studies have ignored. We found that most puQTL signals were concordant with at least one genome-wide association study (GWAS) signal, enabling novel interpretations of the molecular mechanisms of complex traits. Our results emphasize the importance of the re-analysis of public RNA-seq datasets to obtain novel insights into gene regulation by genomic variations and their contributions to complex traits.

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  • In Vitro Generation of Brain Regulatory T Cells by Co-culturing With Astrocytes. Reviewed International journal

    Shinichi Yamamoto, Ako Matsui, Masaki Ohyagi, Chie Kikutake, Yoshihiro Harada, Mana Iizuka-Koga, Mikita Suyama, Akihiko Yoshimura, Minako Ito

    Frontiers in immunology   13   960036 - 960036   2022.7   （ ISSN:1664-3224 ）

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    Regulatory T cells (Tregs) are normally born in the thymus and activated in secondary lymphoid tissues to suppress immune responses in the lymph node and at sites of inflammation. Tregs are also resident in various tissues or accumulate in damaged tissues, which are now called tissue Tregs, and contribute to homeostasis and tissue repair by interacting with non-immune cells. We have shown that Tregs accumulate in the brain during the chronic phase in a mouse cerebral infarction model, and these Tregs acquire the characteristic properties of brain Tregs and contribute to the recovery of neurological damage by interacting with astrocytes. However, the mechanism of tissue Treg development is not fully understood. We developed a culture method that confers brain Treg characteristics in vitro. Naive Tregs from the spleen were activated and efficiently amplified by T-cell receptor (TCR) stimulation in the presence of primary astrocytes. Furthermore, adding IL-33 and serotonin could confer part of the properties of brain Tregs, such as ST2, peroxisome proliferator-activated receptor γ (PPARγ), and serotonin receptor 7 (Htr7) expression. Transcriptome analysis revealed that in vitro generated brain Treg-like Tregs (induced brain Tregs; iB-Tregs) showed similar gene expression patterns as those in in vivo brain Tregs, although they were not identical. Furthermore, in Parkinson's disease models, in which T cells have been shown to be involved in disease progression, iB-Tregs infiltrated into the brain more readily and ameliorated pathological symptoms more effectively than splenic Tregs. These data indicate that iB-Tregs contribute to our understanding of brain Treg development and could also be therapeutic for inflammatory brain diseases.

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  • The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells. Reviewed International journal

    Norio Kobayashi, Hiroaki Okae, Hitoshi Hiura, Naoto Kubota, Eri H Kobayashi, Shun Shibata, Akira Oike, Takeshi Hori, Chie Kikutake, Hirotaka Hamada, Hirokazu Kaji, Mikita Suyama, Marie-Line Bortolin-Cavaillé, Jérôme Cavaillé, Takahiro Arima

    Nature communications   13 ( 1 )   3071 - 3071   2022.6   （ eISSN:2041-1723 ）

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    The first cell fate commitment during mammalian development is the specification of the inner cell mass and trophectoderm. This irreversible cell fate commitment should be epigenetically regulated, but the precise mechanism is largely unknown in humans. Here, we show that naïve human embryonic stem (hES) cells can transdifferentiate into trophoblast stem (hTS) cells, but primed hES cells cannot. Our transcriptome and methylome analyses reveal that a primate-specific miRNA cluster on chromosome 19 (C19MC) is active in naïve hES cells but epigenetically silenced in primed ones. Moreover, genome and epigenome editing using CRISPR/Cas systems demonstrate that C19MC is essential for hTS cell maintenance and C19MC-reactivated primed hES cells can give rise to hTS cells. Thus, we reveal that C19MC activation confers differentiation potential into trophoblast lineages on hES cells. Our findings are fundamental to understanding the epigenetic regulation of human early development and pluripotency.

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  • Pervasive occurrence of splice-site-creating mutations and their possible involvement in genetic disorders Reviewed

    Sakaguchi Narumi, Suyama Mikita

    npj Genomic Medicine   7 ( 1 )   2022.3   （ eISSN:20567944 ）

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    The search for causative mutations in human genetic disorders has mainly focused on mutations that disrupt coding regions or splice sites. Recently, however, it has been reported that mutations creating splice sites can also cause a range of genetic disorders. In this study, we identified 5656 candidate splice-site-creating mutations (SCMs), of which 3942 are likely to be pathogenic, in 4054 genes responsible for genetic disorders. Reanalysis of exome data obtained from ciliopathy patients led us to identify 38 SCMs as candidate causative mutations. We estimate that, by focusing on SCMs, the increase in diagnosis rate is approximately 5.9–8.5% compared to the number of already known pathogenic variants. This finding suggests that SCMs are mutations worth focusing on in the search for causative mutations of genetic disorders.

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  • Kastor and Polluks polypeptides encoded by a single gene locus cooperatively regulate VDAC and spermatogenesis. Reviewed International journal

    Shintaro Mise, Akinobu Matsumoto, Keisuke Shimada, Toshiaki Hosaka, Masatomo Takahashi, Kazuya Ichihara, Hideyuki Shimizu, Chisa Shiraishi, Daisuke Saito, Mikita Suyama, Tomoharu Yasuda, Toru Ide, Yoshihiro Izumi, Takeshi Bamba, Tomomi Kimura-Someya, Mikako Shirouzu, Haruhiko Miyata, Masahito Ikawa, Keiichi I Nakayama

    Nature communications   13 ( 1 )   1071 - 1071   2022.2   （ eISSN:2041-1723 ）

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    Although several long noncoding RNAs (lncRNAs) have recently been shown to encode small polypeptides, those in testis remain largely uncharacterized. Here we identify two sperm-specific polypeptides, Kastor and Polluks, encoded by a single mouse locus (Gm9999) previously annotated as encoding a lncRNA. Both Kastor and Polluks are inserted in the outer mitochondrial membrane and directly interact with voltage-dependent anion channel (VDAC), despite their different amino acid sequences. Male VDAC3-deficient mice are infertile as a result of reduced sperm motility due to an abnormal mitochondrial sheath in spermatozoa, and deficiency of both Kastor and Polluks also severely impaired male fertility in association with formation of a similarly abnormal mitochondrial sheath. Spermatozoa lacking either Kastor or Polluks partially recapitulate the phenotype of those lacking both. Cooperative function of Kastor and Polluks in regulation of VDAC3 may thus be essential for mitochondrial sheath formation in spermatozoa and for male fertility.

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  • Genome-wide identification of exon extension/shrinkage events induced by splice-site-creating mutations. Reviewed International journal

    Zhuo Qu, Narumi Sakaguchi, Chie Kikutake, Mikita Suyama

    RNA biology   19 ( 1 )   1143 - 1152   2022.1   （ ISSN:1547-6286 eISSN:1555-8584 ）

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    Mutations that affect phenotypes have been identified primarily as those that directly alter amino acid sequences or disrupt splice sites. However, some mutations not located in functionally important sites can also affect phenotypes, such as splice-site-creating mutations (SCMs). To investigate how frequent exon extension/shrinkage events induced by SCMs occur in normal individuals, we used personal genome sequencing data and transcriptome data of the corresponding individuals and identified 371 exon extension/shrinkage events in normal individuals. This number was about three times higher than the number of pseudo-exon activation events identified in the previous study. The average numbers of exon extension and exon shrinkage events in each sample were 3.3 and 11.2, respectively. We also evaluated the impact of exon extension/shrinkage events on the resulting transcripts and their protein products and found that 40.2% of the identified events may have possible functional impacts by either generating premature termination codons in transcripts or affecting protein domains. Our results indicated that a certain fraction of SCMs identified in this study can be pathogenic mutations by creating novel splice sites.

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  • Sex differences in metabolic pathways are regulated by Pfkfb3 and Pdk4 expression in rodent muscle. Reviewed International journal

    Antonius Christianto, Takashi Baba, Fumiya Takahashi, Kai Inui, Miki Inoue, Mikita Suyama, Yusuke Ono, Yasuyuki Ohkawa, Ken-Ichirou Morohashi

    Communications biology   4 ( 1 )   1264 - 1264   2021.11

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    DOI： 10.1038/s42003-021-02790-y

  • Identification of SLC38A7 as a Prognostic Marker and Potential Therapeutic Target of Lung Squamous Cell Carcinoma. Reviewed International journal

    Naoki Haratake, Qingjiang Hu, Tatsuro Okamoto, Tomoko Jogo, Gouji Toyokawa, Fumihiko Kinoshita, Tomoyoshi Takenaka, Tetsuzo Tagawa, Norifumi Iseda, Shinji Itoh, Yuichi Yamada, Yoshinao Oda, Mototsugu Shimokawa, Chie Kikutake, Mikita Suyama, Motoko Unoki, Hiroyuki Sasaki, Masaki Mori

    Annals of surgery   274 ( 3 )   500 - 507   2021.9

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    DOI： 10.1097/SLA.0000000000005001

  • A ubiquitin-like protein encoded by the "noncoding" RNA TINCR promotes keratinocyte proliferation and wound healing. Reviewed International journal

    Akihiro Nita, Akinobu Matsumoto, Ronghao Tang, Chisa Shiraishi, Kazuya Ichihara, Daisuke Saito, Mikita Suyama, Tomoharu Yasuda, Gaku Tsuji, Masutaka Furue, Bumpei Katayama, Toshiyuki Ozawa, Teruasa Murata, Teruki Dainichi, Kenji Kabashima, Atsushi Hatano, Masaki Matsumoto, Keiichi I Nakayama

    PLoS genetics   17 ( 8 )   e1009686   2021.8

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    DOI： 10.1371/journal.pgen.1009686

  • Sexual fate of murine external genitalia development: Conserved transcriptional competency for male-biased genes in both sexes. Reviewed International journal

    Daiki Kajioka, Kentaro Suzuki, Shoko Matsushita, Shinjiro Hino, Tetsuya Sato, Shuji Takada, Kyoichi Isono, Toru Takeo, Mizuki Kajimoto, Naomi Nakagata, Mitsuyoshi Nakao, Mikita Suyama, Tony DeFalco, Shinichi Miyagawa, Gen Yamada

    Proceedings of the National Academy of Sciences of the United States of America   118 ( 23 )   2021.6

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    DOI： 10.1073/pnas.2024067118

  • Pan-cancer analysis of non-coding recurrent mutations and their possible involvement in cancer pathogenesis. Reviewed International journal

    Chie Kikutake, Minako Yoshihara, Mikita Suyama

    NAR cancer   3 ( 1 )   zcab008   2021.3

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    DOI： 10.1093/narcan/zcab008

  • Functional variants in hematopoietic transcription factor footprints and their roles in the risk of immune system diseases

    Naoto Kubota, Mikita Suyama

    bioRxiv   2021.3

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    DOI： 10.1101/2021.03.22.436360

  • In silico identification of pseudo-exon activation events in personal genome and transcriptome data. Reviewed International journal

    Narumi Sakaguchi, Mikita Suyama

    RNA biology   18 ( 3 )   382 - 390   2021.3

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    DOI： 10.1080/15476286.2020.1809195

  • Augmented oxidative stress increases 8-oxoguanine preferentially in the transcriptionally active genomic regions. Reviewed International journal

    Shinya Akatsuka, Guang Hua Li, Shinichi Kawaguchi, Takashi Takahashi, Minako Yoshihara, Mikita Suyama, Shinya Toyokuni

    Free radical research   54 ( 11-12 )   872 - 882   2020.12

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    DOI： 10.1080/10715762.2020.1733548

  • Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells. Reviewed International journal

    Hiroki Inada, Miyako Udono, Kanae Matsuda-Ito, Kenichi Horisawa, Yasuyuki Ohkawa, Shizuka Miura, Takeshi Goya, Junpei Yamamoto, Masao Nagasaki, Kazuko Ueno, Daisuke Saitou, Mikita Suyama, Yoshihiko Maehara, Wataru Kumamaru, Yoshihiro Ogawa, Sayaka Sekiya, Atsushi Suzuki

    Nature communications   11 ( 1 )   5292 - 5292   2020.10

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    DOI： 10.1038/s41467-020-19041-z

  • Comparative genomic analysis of inbred rat strains reveals the existence of ancestral polymorphisms Reviewed

    Hyeonjeong Kim, Minako Yoshihara, Mikita Suyama

    Mammalian Genome   31 ( 3-4 )   86 - 94   2020.4

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    DOI： 10.1007/s00335-020-09831-7

  • 性染色体構成の差異がライディッヒ細胞の遺伝子発現に及ぼす影響

    柳井 翔吾, 高橋 史也, 戌亥 海, Han Soyun, 原口 省吾, 馬場 崇, Choi Man-Ho, 須山 幹太, 大川 恭行, 諸橋 憲一郎

    日本内分泌学会雑誌   95 ( 4 )   1557 - 1557   2020.2

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  • An integrated analysis of public genomic data unveils a possible functional mechanism of psoriasis risk via a long-range ERRFI1 enhancer. Reviewed International journal

    Naoto Kubota, Mikita Suyama

    BMC medical genomics   13 ( 1 )   8 - 8   2020.1

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    DOI： 10.1186/s12920-020-0662-9

  • CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors. Reviewed International journal

    Masami Miki, Takamasa Oono, Nao Fujimori, Takehiro Takaoka, Ken Kawabe, Yoshihiro Miyasaka, Takao Ohtsuka, Daisuke Saito, Masafumi Nakamura, Yasuyuki Ohkawa, Yoshinao Oda, Mikita Suyama, Tetsuhide Ito, Yoshihiro Ogawa

    Cancer medicine   8 ( 8 )   3748 - 3760   2019.7

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    DOI： 10.1002/cam4.2232

  • Zfp281 Shapes the Transcriptome of Trophoblast Stem Cells and Is Essential for Placental Development Reviewed

    Takashi Ishiuchi, Hiroaki Ohishi, Tetsuya Sato, Satoshi Kamimura, Masayoshi Yorino, Shusaku Abe, Atsushi Suzuki, Teruhiko Wakayama, Mikita Suyama, Hiroyuki Sasaki

    Cell Reports   27 ( 6 )   1742 - 1754.e6   2019.5

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    DOI： 10.1016/j.celrep.2019.04.028

  • Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones Reviewed

    Yuko Katoh-Fukui, Takashi Baba, Tetsuya Sato, Hiroyuki Otake, Yuko Nagakui-Noguchi, Miyuki Shindo, Mikita Suyama, Yasuyuki Ohkawa, Hideki Tsumura, Ken-Ichirou Morohashi, Maki Fukami

    Bone   120   219 - 231   2019.3

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    DOI： 10.1016/j.bone.2018.10.021

  • Novel components of germline sex determination acting downstream of foxl3 in medaka. Reviewed International journal

    Developmental biology   445 ( 1 )   80 - 89   2019.1

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    DOI： 10.1016/j.ydbio.2018.10.019

  • Fetal leydig cells dedifferentiate and serve as adult leydig stem cells Reviewed

    Yuichi Shima, Kanako Miyabayashi, Tetsuya Sato, Mikita Suyama, Yasuyuki Ohkawa, Masao Doi, Hitoshi Okamura, Kentaro Suzuki

    Development (Cambridge)   145 ( 23 )   2018.12

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    DOI： 10.1242/dev.169136

  • Ad4BP/SF-1 regulates cholesterol synthesis to boost the production of steroids Reviewed

    Takashi Baba, Hiroyuki Otake, Miki Inoue, Tetsuya Sato, Yasuhiro Ishihara, Ju Yeon Moon, Megumi Tsuchiya, Kanako Miyabayashi, Hidesato Ogawa, Yuichi Shima, Lixiang Wang, Ryuichiro Sato, Takeshi Yamazaki, Mikita Suyama, Masatoshi Nomura, Man Ho Choi, Yasuyuki Ohkawa, Ken ichirou Morohashi

    Communications Biology   1 ( 1 )   2018.12

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    DOI： 10.1038/s42003-018-0020-z

  • Pan-cancer analysis of intratumor heterogeneity associated with patient prognosis using multidimensional measures. Reviewed International journal

    Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama

    Oncotarget   9 ( 102 )   37689 - 37699   2018.12

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    DOI： 10.18632/oncotarget.26485

  • Intratumor heterogeneity of HMCN1 mutant alleles associated with poor prognosis in patients with breast cancer Reviewed

    Chie Nakashima, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama

    Oncotarget   9 ( 70 )   33337 - 33347   2018.9

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    DOI： 10.18632/oncotarget.26071

  • The Autism-Related Protein CHD8 Cooperates with C/EBPβ to Regulate Adipogenesis. Reviewed International journal

    23 ( 7 )   1988 - 2000   2018.5

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    The gene encoding the chromatin remodeler CHD8 is the most frequently mutated gene in individuals with autism spectrum disorder (ASD). Heterozygous mutations in CHD8 give rise to ASD that is often accompanied by macrocephaly, gastrointestinal complaints, and slender habitus. Whereas most phenotypes of CHD8 haploinsufficiency likely result from delayed neurodevelopment, the mechanism underlying slender habitus has remained unknown. Here, we show that CHD8 interacts with CCAAT/enhancer-binding protein β (C/EBPβ) and promotes its transactivation activity during adipocyte differentiation. Adipogenesis was impaired in Chd8-deleted preadipocytes, with the upregulation of C/EBPα and peroxisome-proliferator-activated receptor γ (PPARγ), two master regulators of this process, being attenuated in mutant cells. Furthermore, mice with CHD8 ablation in white preadipocytes had a markedly reduced white adipose tissue mass. Our findings reveal a mode of C/EBPβ regulation by CHD8 during adipogenesis, with CHD8 deficiency resulting in a defect in the development of white adipose tissue.

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  • DBTSS/DBKERO for integrated analysis of transcriptional regulation Reviewed

    Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki

    Nucleic Acids Research   46 ( D1 )   D229 - D238   2018.1

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    DOI： 10.1093/nar/gkx1001

  • Identification of a candidate enhancer for DMRT3 involved in spastic cerebral palsy pathogenesis. International journal

    Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama

    Biochemical and biophysical research communications   496 ( 1 )   133 - 139   2018.1

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    DOI： 10.1016/j.bbrc.2018.01.011

  • Derivation of Human Trophoblast Stem Cells. International journal

    Hiroaki Okae, Hidehiro Toh, Tetsuya Sato, Hitoshi Hiura, Sota Takahashi, Kenjiro Shirane, Yuka Kabayama, Mikita Suyama, Hiroyuki Sasaki, Takahiro Arima

    Cell stem cell   22 ( 1 )   50 - 63   2018.1

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    DOI： 10.1016/j.stem.2017.11.004

  • DBTSS/DBKERO for integrated analysis of transcriptional regulation. International journal

    Ayako Suzuki, Shin Kawano, Toutai Mitsuyama, Mikita Suyama, Yae Kanai, Katsuhiko Shirahige, Hiroyuki Sasaki, Katsushi Tokunaga, Katsuya Tsuchihara, Sumio Sugano, Kenta Nakai, Yutaka Suzuki

    Nucleic acids research   46 ( D1 )   D229-D238   2018.1

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    DOI： 10.1093/nar/gkx1001

  • Identification of a candidate enhancer for DMRT3 involved in spastic cerebral palsy pathogenesis Reviewed

    Naoto Kubota, Toshifumi Yokoyama, Nobuhiko Hoshi, Mikita Suyama

    Biochemical and Biophysical Research Communications   496 ( 1 )   133 - 139   2018.1

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    DOI： 10.1016/j.bbrc.2018.01.011

  • Histone methyltransferase G9a is a key regulator of the starvation-induced behaviors in Drosophila melanogaster Reviewed

    Kouhei Shimaji, Ryo Tanaka, Toru Maeda, Mamiko Ozaki, Hideki Yoshida, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Masamitsu Yamaguchi

    Scientific Reports   7 ( 1 )   2017.12

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    DOI： 10.1038/s41598-017-15344-2

  • 病態モデル動物からアプローチする発達障害の分子病態理解 クロマチンリモデリングの異常によって発症するASDの分子病態

    片山 雄太, 西山 正章, 昌子 浩孝, 大川 恭行, 川村 淳生, 佐藤 哲也, 須山 幹太, 内匠 透, 宮川 剛, 中山 敬一

    生命科学系学会合同年次大会   2017年度   [1AW21 - 2]   2017.12

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    Language：Japanese  

  • Identification of secretory leukoprotease inhibitor as an endogenous negative regulator in allergic effector cells Reviewed

    Shintaro Matsuba, Toshiki Yabe-Wada, Kazuya Takeda, Tetsuya Sato, Mikita Suyama, Toshiyuki Takai, Toshiaki Kikuchi, Toshihiro Nukiwa, Akira Nakamura

    Frontiers in Immunology   8 ( NOV )   2017.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.3389/fimmu.2017.01538

  • Identification of Candidate Genes for Generalized Tonic-Clonic Seizures in Noda Epileptic Rat. International journal

    Takashi Kuramoto, Birger Voigt, Satoshi Nakanishi, Kazuhiro Kitada, Tadashi Nakamura, Kaori Wakamatsu, Minako Yoshihara, Mikita Suyama, Risa Uemura, Miyuu Tanaka, Mitsuru Kuwamura, Saki Shimizu, Yukihiro Ohno, Masashi Sasa, Tadao Serikawa

    Behavior genetics   47 ( 6 )   609 - 619   2017.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/s10519-017-9870-2

  • Histone methyltransferase G9a is a key regulator of the starvation-induced behaviors in Drosophila melanogaster. International journal

    Kouhei Shimaji, Ryo Tanaka, Toru Maeda, Mamiko Ozaki, Hideki Yoshida, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Masamitsu Yamaguchi

    Scientific reports   7 ( 1 )   14763 - 14763   2017.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/s41598-017-15344-2

  • Alterations in Fetal Leydig Cell Gene Expression during Fetal and Adult Development Reviewed

    Kanako Miyabayashi, Yuichi Shima, Miki Inoue, Tetsuya Sato, Takashi Baba, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi

    Sexual Development   11 ( 2 )   53 - 63   2017.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1159/000453323

  • A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo Reviewed

    Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    BMC Genetics   18 ( 1 )   2017.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12863-017-0497-3

  • Role of Ad4-binding protein/steroidogenic factor 1 in regulating NADPH production in adrenocortical Y-1 cells.

    Bing Li, Takashi Baba, Kanako Miyabayashi, Tetsuya Sato, Yuichi Shima, Tomomi Ichinose, Daisuke Miura, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi

    Endocrine journal   64 ( 3 )   315 - 324   2017.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1507/endocrj.EJ16-0467

  • A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo. International journal

    Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    BMC genetics   18 ( 1 )   29 - 29   2017.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12863-017-0497-3

  • Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells. International journal

    Yurina Shishido, Takashi Baba, Tetsuya Sato, Yuichi Shima, Kanako Miyabayashi, Miki Inoue, Haruhiko Akiyama, Hiroshi Kimura, Yoshiakira Kanai, Yasuhiro Ishihara, Shogo Haraguchi, Akira Miyazaki, Damjana Rozman, Takeshi Yamazaki, Man-Ho Choi, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi

    Scientific reports   7   41912 - 41912   2017.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/srep41912

  • Control of tissue size and development by a regulatory element in the yorkie 3'UTR Reviewed

    Takanari Umegawachi, Hideki Yoshida, Hiromu Koshida, Momoko Yamada, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Henry M. Krause, Masamitsu Yamaguchi

    American Journal of Cancer Research   7 ( 3 )   673 - 687   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)  

  • Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing. International journal

    Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki

    BMC genomics   18 ( 1 )   31 - 31   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-016-3392-9

  • Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells Reviewed

    Yurin Shishido, Takashi Baba, Tetsuy Sato, Yuich Shima, Kanak Miyabayashi, Mik Inoue, Haruhik Akiyama, Hirosh Kimura, Yoshiakir Kanai, Yasuhir Ishihara, Shogo Haraguchi, Akir Miyazaki, Damjan Rozman, Takesh Yamazaki, Man Ho Choi, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi

    Scientific reports   7   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/srep41912

  • Software updates in the illumina hiseq platform affect whole-genome bisulfite sequencing Reviewed

    Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Katsuhiko Hayashi, Mitinori Saitou, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki

    BMC Genomics   18 ( 1 )   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-016-3392-9

  • Role of Ad4-binding protein/steroidogenic factor 1 in regulating NADPH production in adrenocortical Y-1 cells Reviewed

    Bing Li, Takashi Baba, Kanako Miyabayashi, Tetsuya Sato, Yuichi Shima, Tomomi Ichinose, Daisuke Miura, Yasuyuki Ohkawa, Mikita Suyama, Ken-Ichirou Morohashi

    Endocrine Journal   64 ( 3 )   315 - 324   2017.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1507/endocrj.EJ16-0467

  • Application of target capture sequencing of exons and conserved non-coding sequences to 20 inbred rat strains Reviewed

    Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    Genomics Data   10   155 - 157   2016.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.gdata.2016.11.010

  • Application of target capture sequencing of exons and conserved non-coding sequences to 20 inbred rat strains. International journal

    Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    Genomics data   10   155 - 157   2016.12

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  • Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta Reviewed

    Hirotaka Hamada, Hiroaki Okae, Hidehiro Toh, Hatsune Chiba, Hitoshi Hiura, Kenjiro Shirane, Tetsuya Sato, Mikita Suyama, Nobuo Yaegashi, Hiroyuki Sasaki, Takahiro Arima

    American Journal of Human Genetics   99 ( 5 )   1045 - 1058   2016.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.ajhg.2016.08.021

  • Allele-Specific Methylome and Transcriptome Analysis Reveals Widespread Imprinting in the Human Placenta. International journal

    Hirotaka Hamada, Hiroaki Okae, Hidehiro Toh, Hatsune Chiba, Hitoshi Hiura, Kenjiro Shirane, Tetsuya Sato, Mikita Suyama, Nobuo Yaegashi, Hiroyuki Sasaki, Takahiro Arima

    American journal of human genetics   99 ( 5 )   1045 - 1058   2016.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/j.ajhg.2016.08.021

  • CHD8 haploinsufficiency results in autistic-like phenotypes in mice. International journal

    Yuta Katayama, Masaaki Nishiyama, Hirotaka Shoji, Yasuyuki Ohkawa, Atsuki Kawamura, Tetsuya Sato, Mikita Suyama, Toru Takumi, Tsuyoshi Miyakawa, Keiichi I Nakayama

    Nature   537 ( 7622 )   675 - 679   2016.9

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/nature19357

  • INCOMPLETE REPROGRAMMING OF GERMLINE DNA METHYLATION IN THE HUMAN PLACENTA

    Hirotaka Hamada, Hiroaki Okae, Mikita Suyama, Hiroyuki Sasaki, Nobuo Yaegashi, Takahiro Arima

    PLACENTA   45   113 - 113   2016.9

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  • Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat Reviewed

    Minako Yoshihara, Daisuke Saito, Tetsuya Sato, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    BMC Genomics   17 ( 1 )   2016.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-016-2975-9

  • Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat. International journal

    Minako Yoshihara, Daisuke Saito, Tetsuya Sato, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    BMC genomics   17   593 - 593   2016.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-016-2975-9

  • Erratum Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome (Nature Communications (2015) 6 (7870) DOI: 10.1038/ncomms8870) Reviewed

    Nature Communications   7   2016.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/ncomms12003

  • Corrigendum: Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. International journal

    Nature communications   7   12003 - 12003   2016.6

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/ncomms12003

  • TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin Reviewed

    Toshiki Yabe-Wada, Shintaro Matsuba, Kazuya Takeda, Tetsuya Sato, Mikita Suyama, Yasuyuki Ohkawa, Toshiyuki Takai, Haifeng Shi, Caroline C. Philpott, Akira Nakamura

    Scientific Reports   6   2016.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/srep26566

  • TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin. International journal

    Toshiki Yabe-Wada, Shintaro Matsuba, Kazuya Takeda, Tetsuya Sato, Mikita Suyama, Yasuyuki Ohkawa, Toshiyuki Takai, Haifeng Shi, Caroline C Philpott, Akira Nakamura

    Scientific reports   6   26566 - 26566   2016.5

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/srep26566

  • Isolation and characterization of Fetal Leydig progenitor cells of male mice Reviewed

    Miki Inoue, Yuichi Shima, Kanako Miyabayashi, Kaori Tokunaga, Tetsuya Sato, Takashi Baba, Yasuyuki Ohkawa, Haruhiko Akiyama, Mikita Suyama, Ken-Ichirou Morohashi

    Endocrinology   157 ( 3 )   1222 - 1233   2016.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1210/en.2015-1773

  • Isolation and Characterization of Fetal Leydig Progenitor Cells of Male Mice. International journal

    Miki Inoue, Yuichi Shima, Kanako Miyabayashi, Kaori Tokunaga, Tetsuya Sato, Takashi Baba, Yasuyuki Ohkawa, Haruhiko Akiyama, Mikita Suyama, Ken-ichirou Morohashi

    Endocrinology   157 ( 3 )   1222 - 33   2016.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1210/en.2015-1773

  • Androgen regulates Mafb expression through its 3′UTR during mouse urethral masculinization Reviewed

    157 ( 2 )   844 - 857   2016.2

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    External genitalia are prominent organs showing hormone-dependent sexual differentiation. Androgen is an essential regulator of masculinization of the genital tubercle, which is the anlage of external genitalia. We have previously shown that v-maf avian musculoaponeurotic fibrosarcoma oncogene homolog B (MAFB) is an androgen-inducible regulator of embryonic urethral masculinization in mice. However, it remains unclear how androgen regulates Mafb expression. The current study suggests that the Mafb 3′ untranslated region (UTR) is an essential region for its regulation by androgen. We identified 2 functional androgen response elements (AREs) in Mafb 3′UTR. Androgen receptor is bound to such AREs in 3′UTR during urethral masculinization. In addition to 3′UTR, Mafb 5′UTR also showed androgen responsiveness. Moreover, we also demonstrated that β-catenin, one of genital tubercle masculinization factors, may be an additional regulator of Mafb expression during urethral masculinization. This study provides insights to elucidate mechanisms of gene regulation through AREs present in Mafb 3′UTR for a better understanding of the processes of urethral masculinization.

    DOI： 10.1210/en.2015-1586

  • Androgen Regulates Mafb Expression Through its 3'UTR During Mouse Urethral Masculinization. International journal

    Shoko Matsushita, Kentaro Suzuki, Yukiko Ogino, Shinjiro Hino, Tetsuya Sato, Mikita Suyama, Takahiro Matsumoto, Akiko Omori, Satoshi Inoue, Gen Yamada

    Endocrinology   157 ( 2 )   844 - 57   2016.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1210/en.2015-1586

  • CHD8 haploinsufficiency results in autistic-like phenotypes in mice Reviewed

    Yuta Katayama, Masaaki Nishiyama, Hirotaka Shoji, Yasuyuki Ohkawa, Atsuki Kawamura, Tetsuya Sato, Mikita Suyama, Toru Takumi, Tsuyoshi Miyakawa, Keiichi Nakayama

    Nature   537 ( 7622 )   675 - 679   2016.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/nature19357

  • ChromContact A web tool for analyzing spatial contact of chromosomes from Hi-C data Reviewed

    Tetsuya Sato, Mikita Suyama

    BMC Genomics   16 ( 1 )   2015.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-015-2282-x

  • 新生仔マウスの精原幹細胞の形成と分化における全ゲノムDNAメチル化およびトランスクリプトーム解析

    久保 直樹, 藤 英博, 白根 健次郎, 白川 峰征, 小林 久人, 佐藤 哲也, 曾根 秀利, 佐藤 康人, 富澤 信一, 鶴崎 美徳, 柴田 弘紀, 才津 浩智, 鈴木 穣, 松本 直通, 須山 幹太, 河野 友宏, 大保 和之, 佐々木 裕之

    日本生化学会大会・日本分子生物学会年会合同大会講演要旨集   88回・38回   [1P0606] - [1P0606]   2015.12

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  • ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data. International journal

    Tetsuya Sato, Mikita Suyama

    BMC genomics   16   1060 - 1060   2015.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-015-2282-x

  • Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation Reviewed

    Daisuke Saito, Mikita Suyama

    Epigenetics   10 ( 12 )   1093 - 1098   2015.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1080/15592294.2015.1115176

  • Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis Reviewed

    Kouhei Shimaji, Takahiro Konishi, Shintaro Tanaka, Hideki Yoshida, Yasuko Kato, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Hiroshi Kimura, Masamitsu Yamaguchi

    Genes to Cells   20 ( 11 )   902 - 914   2015.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1111/gtc.12281

  • Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus. International journal

    Toyoshi Yanagihara, Fumiyuki Sanematsu, Tetsuya Sato, Takehito Uruno, Xuefeng Duan, Takahiro Tomino, Yosuke Harada, Mayuki Watanabe, Yuqing Wang, Yoshihiko Tanaka, Yoichi Nakanishi, Mikita Suyama, Fukui Yoshinori

    Nature communications   6   8820 - 8820   2015.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/ncomms9820

  • Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis. International journal

    Kouhei Shimaji, Takahiro Konishi, Shintaro Tanaka, Hideki Yoshida, Yasuko Kato, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Hiroshi Kimura, Masamitsu Yamaguchi

    Genes to cells : devoted to molecular & cellular mechanisms   20 ( 11 )   902 - 14   2015.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1111/gtc.12281

  • Intronic regulation of Aire expression by Jmjd6 for self-tolerance induction in the thymus Reviewed

    Toyoshi Yanagihara, Fumiyuki Sanematsu, Tetsuya Sato, Takehito Uruno, Xuefeng Duan, Takahiro Tomino, Yosuke Harada, Mayuki Watanabe, Yuqing Wang, Yoshihiko Tanaka, Yoichi Nakanishi, Mikita Suyama, Fukui Yoshinori

    Nature communications   6   2015.11

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    DOI： 10.1038/ncomms9820

  • DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis Reviewed

    Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Tetsuya Sato, Hidetoshi Sone, Yasuyuki Sato, Shin Ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Mikita Suyama, Tomohiro Kono, Kazuyuki Ohbo, Hiroyuki Sasaki

    BMC genomics   16 ( 1 )   2015.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-015-1833-5

  • DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis. International journal

    Naoki Kubo, Hidehiro Toh, Kenjiro Shirane, Takayuki Shirakawa, Hisato Kobayashi, Tetsuya Sato, Hidetoshi Sone, Yasuyuki Sato, Shin-ichi Tomizawa, Yoshinori Tsurusaki, Hiroki Shibata, Hirotomo Saitsu, Yutaka Suzuki, Naomichi Matsumoto, Mikita Suyama, Tomohiro Kono, Kazuyuki Ohbo, Hiroyuki Sasaki

    BMC genomics   16 ( 1 )   624 - 624   2015.8

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1186/s12864-015-1833-5

  • Foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka Reviewed

    Toshiya Nishimura, Tetsuya Sato, Yasuhiro Yamamoto, Ikuko Watakabe, Yasuyuki Ohkawa, Mikita Suyama, Satoru Kobayashi, Minoru Tanaka

    Science   349 ( 6245 )   328 - 331   2015.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1126/science.aaa2657

  • Sex determination. foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka. International journal

    Toshiya Nishimura, Tetsuya Sato, Yasuhiro Yamamoto, Ikuko Watakabe, Yasuyuki Ohkawa, Mikita Suyama, Satoru Kobayashi, Minoru Tanaka

    Science (New York, N.Y.)   349 ( 6245 )   328 - 31   2015.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1126/science.aaa2657

  • Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome. International journal

    Nature communications   6   7870 - 7870   2015.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/ncomms8870

  • Mutations in CDCA7 and HELLS cause immunodeficiency-centromeric instability-facial anomalies syndrome Reviewed

    Nature communications   6   2015.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/ncomms8870

  • GenomeCons A web server for manipulating multiple genome sequence alignments and their consensus sequences Reviewed

    Tetsuya Sato, Mikita Suyama

    Bioinformatics   31 ( 8 )   1293 - 1295   2015.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/btu803

  • GenomeCons: a web server for manipulating multiple genome sequence alignments and their consensus sequences. International journal

    Tetsuya Sato, Mikita Suyama

    Bioinformatics (Oxford, England)   31 ( 8 )   1293 - 5   2015.4

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/btu803

  • Genome-Wide Analysis of DNA Methylation Dynamics during Early Human Development Reviewed

    Hiroaki Okae, Hatsune Chiba, Hitoshi Hiura, Hirotaka Hamada, Akiko Sato, Takafumi Utsunomiya, Hiroyuki Kikuchi, Hiroaki Yoshida, Atsushi Tanaka, Mikita Suyama, Takahiro Arima

    PLoS genetics   10 ( 12 )   2014.12

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    DOI： 10.1371/journal.pgen.1004868

  • Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. International journal

    Minako Yoshihara, Li Jiang, Shinya Akatsuka, Mikita Suyama, Shinya Toyokuni

    DNA research : an international journal for rapid publication of reports on genes and genomes   21 ( 6 )   603 - 12   2014.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/dsu023

  • Genome-wide analysis of DNA methylation dynamics during early human development. International journal

    Hiroaki Okae, Hatsune Chiba, Hitoshi Hiura, Hirotaka Hamada, Akiko Sato, Takafumi Utsunomiya, Hiroyuki Kikuchi, Hiroaki Yoshida, Atsushi Tanaka, Mikita Suyama, Takahiro Arima

    PLoS genetics   10 ( 12 )   e1004868   2014.12

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    DOI： 10.1371/journal.pgen.1004868

  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Reviewed

    Nature   423 ( 10 )   695 - 777   2014.12

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    DOI： 10.1038/nature03154

  • Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus Reviewed

    Minako Yoshihara, Li Jiang, Shinya Akatsuka, Mikita Suyama, Shinya Toyokuni

    DNA Research   21 ( 6 )   603 - 612   2014.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/dsu023

  • Genome-wide analysis of histone modifications in human endometrial stromal cells Reviewed

    Isao Tamura, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Kosuke Jozaki, Maki Okada, Lifa Lee, Ryo Maekawa, Hiromi Asada, Shun Sato, Yoshiaki Yamagata, Hiroshi Tamura, Norihiro Sugino

    Molecular Endocrinology   28 ( 10 )   1656 - 1669   2014.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1210/me.2014-1117

  • TLR9シグナルの新規制御分子Sortilinの機能解析

    和田 俊樹, 武田 和也, 松葉 慎太郎, 中村 晃, 佐藤 哲也, 須山 幹太, 大川 恭行, 高井 俊行

    金沢医科大学雑誌   39 ( 2 )   45 - 45   2014.10

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  • Genome-wide analysis of histone modifications in human endometrial stromal cells. International journal

    Isao Tamura, Yasuyuki Ohkawa, Tetsuya Sato, Mikita Suyama, Kosuke Jozaki, Maki Okada, Lifa Lee, Ryo Maekawa, Hiromi Asada, Shun Sato, Yoshiaki Yamagata, Hiroshi Tamura, Norihiro Sugino

    Molecular endocrinology (Baltimore, Md.)   28 ( 10 )   1656 - 69   2014.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1210/me.2014-1117

  • Characterization of common marmoset dysgerminoma-like tumor induced by the lentiviral expression of reprogramming factors Reviewed

    Saori Yamaguchi, Tomotoshi Marumoto, Takenobu Nii, Hirotaka Kawano, Jiyuan Liao, Yoko Nagai, Michiyo Okada, Atsushi Takahashi, Hiroyuki Inoue, Erika Sasaki, Hiroshi Fujii, Shinji Okano, Hayao Ebise, Tetsuya Sato, Mikita Suyama, Hideyuki Okano, Yoshie Miura, Kenzaburo Tani

    Cancer Science   105 ( 4 )   402 - 408   2014.4

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    DOI： 10.1111/cas.12367

  • Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1. International journal

    Takashi Baba, Hiroyuki Otake, Tetsuya Sato, Kanako Miyabayashi, Yurina Shishido, Chia-Yih Wang, Yuichi Shima, Hiroshi Kimura, Mikako Yagi, Yasuhiro Ishihara, Shinjiro Hino, Hidesato Ogawa, Mitsuyoshi Nakao, Takeshi Yamazaki, Dongchon Kang, Yasuyuki Ohkawa, Mikita Suyama, Bon-Chu Chung, Ken-Ichirou Morohashi

    Nature communications   5   3634 - 3634   2014.4

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    DOI： 10.1038/ncomms4634

  • Characterization of common marmoset dysgerminoma-like tumor induced by the lentiviral expression of reprogramming factors. International journal

    Saori Yamaguchi, Tomotoshi Marumoto, Takenobu Nii, Hirotaka Kawano, Jiyuan Liao, Yoko Nagai, Michiyo Okada, Atsushi Takahashi, Hiroyuki Inoue, Erika Sasaki, Hiroshi Fujii, Shinji Okano, Hayao Ebise, Tetsuya Sato, Mikita Suyama, Hideyuki Okano, Yoshie Miura, Kenzaburo Tani

    Cancer science   105 ( 4 )   402 - 8   2014.4

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    DOI： 10.1111/cas.12367

  • Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1 Reviewed

    Takashi Baba, Hiroyuki Otake, Tetsuya Sato, Kanako Miyabayashi, Yurina Shishido, Chia Yih Wang, Yuichi Shima, Hiroshi Kimura, Mikako Yagi, Yasuhiro Ishihara, Shinjiro Hino, Hidesato Ogawa, Mitsuyoshi Nakao, Takeshi Yamazaki, Dongchon Kang, Yasuyuki Ohkawa, Mikita Suyama, Bon Chu Chung, Ken Ichirou Morohashi

    Nature communications   5   2014.4

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    DOI： 10.1038/ncomms4634

  • Mechanistic insights into mutually exclusive splicing in dynamin 1. International journal

    Mikita Suyama

    Bioinformatics (Oxford, England)   29 ( 17 )   2084 - 7   2013.9

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    DOI： 10.1093/bioinformatics/btt368

  • β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation.

    32 ( 29 )   3477 - 3482   2013.7

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    DOI： 10.1038/onc.2012.376

  • C-type Lectin MCL Is an FcRγ-Coupled Receptor that Mediates the Adjuvanticity of Mycobacterial Cord Factor Reviewed

    38 ( 5 )   1050 - 1062   2013.5

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    Cord factor, also called trehalose-6,6'-dimycolate (TDM), is a potent mycobacterial adjuvant. We herein report that the C-type lectin MCL (also called Clec4d) is a TDM receptor that is likely to arise from gene duplication of Mincle (also called Clec4e). Mincle isknown to be an inducible receptor recognizing TDM, whereas MCL was constitutively expressed in myeloid cells. To examine the contribution of MCL in response to TDM adjuvant, we generated MCL-deficient mice. TDM promoted innate immune responses, such as granuloma formation, which was severely impaired in MCL-deficient mice. TDM-induced acquired immune responses, such as experimental autoimmune encephalomyelitis (EAE), was almost completely dependent on MCL, but not Mincle. Furthermore, by generating Clec4egfp reporter mice, we found that MCL was also crucial for driving Mincle induction upon TDM stimulation. These results suggest that MCL is an FcRγ-coupled activating receptor that mediates the adjuvanticity ofTDM. •MCL is an ITAM-coupled TDM receptor that arises from gene duplication of Mincle•Innate and acquired immunity induced by TDM are impaired in MCL-deficient mice•MCL drives Mincle expression in dendritic cells upon TDM stimulation•MCL, but not Mincle, is critically involved in EAE induced by TDM adjuvant.

    DOI： 10.1016/j.immuni.2013.03.010

  • C-type lectin MCL is an FcRγ-coupled receptor that mediates the adjuvanticity of mycobacterial cord factor. International journal

    38 ( 5 )   1050 - 62   2013.5

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    Cord factor, also called trehalose-6,6'-dimycolate (TDM), is a potent mycobacterial adjuvant. We herein report that the C-type lectin MCL (also called Clec4d) is a TDM receptor that is likely to arise from gene duplication of Mincle (also called Clec4e). Mincle is known to be an inducible receptor recognizing TDM, whereas MCL was constitutively expressed in myeloid cells. To examine the contribution of MCL in response to TDM adjuvant, we generated MCL-deficient mice. TDM promoted innate immune responses, such as granuloma formation, which was severely impaired in MCL-deficient mice. TDM-induced acquired immune responses, such as experimental autoimmune encephalomyelitis (EAE), was almost completely dependent on MCL, but not Mincle. Furthermore, by generating Clec4e(gfp) reporter mice, we found that MCL was also crucial for driving Mincle induction upon TDM stimulation. These results suggest that MCL is an FcRγ-coupled activating receptor that mediates the adjuvanticity of TDM.

    DOI： 10.1016/j.immuni.2013.03.010

  • β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation. Reviewed International journal

    2012.9

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    DOI： 10.1038/onc.2012.376

  • A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males. Reviewed International journal

    Chanavee Ratanajaraya, Hiroyuki Nishiyama, Meiko Takahashi, Takahisa Kawaguchi, Ryoichi Saito, Yoshiki Mikami, Mikita Suyama, Mark Lathrop, Ryo Yamada, Osamu Ogawa, Fumihiko Matsuda

    Journal of Human Genetics   56 ( 8 )   572 - 576   2011.8

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    DOI： 10.1038/jhg.2011.60

  • A polymorphism of the POLG2 gene is genetically associated with the invasiveness of urinary bladder cancer in Japanese males. International journal

    Chanavee Ratanajaraya, Hiroyuki Nishiyama, Meiko Takahashi, Takahisa Kawaguchi, Ryoichi Saito, Yoshiki Mikami, Mikita Suyama, Mark Lathrop, Ryo Yamada, Osamu Ogawa, Fumihiko Matsuda

    Journal of human genetics   56 ( 8 )   572 - 6   2011.8

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    DOI： 10.1038/jhg.2011.60

  • A network of conserved co-occurring motifs for the regulation of alternative splicing. International journal

    Mikita Suyama, Eoghan D Harrington, Svetlana Vinokourova, Magnus von Knebel Doeberitz, Osamu Ohara, Peer Bork

    Nucleic acids research   38 ( 22 )   7916 - 26   2010.12

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    DOI： 10.1093/nar/gkq705

  • Transcriptome complexity in a genome-reduced bacterium Reviewed

    Science   326 ( 5957 )   1268 - 1271   2009.11

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    DOI： 10.1126/science.1176951

  • Transcriptome complexity in a genome-reduced bacterium. International journal

    Science (New York, N.Y.)   326 ( 5957 )   1268 - 71   2009.11

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    DOI： 10.1126/science.1176951

  • Functional and comparative genomics analyses of pmp22 in medaka fish Reviewed

    Junji Itou, Mikita Suyama, Yukio Imamura, Tomonori Deguchi, Kazuhiro Fujimori, Shunsuke Yuba, Yutaka Kawarabayasi, Takashi Kawasaki

    BMC Neuroscience   10   2009.6

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    DOI： 10.1186/1471-2202-10-60

  • Functional and comparative genomics analyses of pmp22 in medaka fish. International journal

    Junji Itou, Mikita Suyama, Yukio Imamura, Tomonori Deguchi, Kazuhiro Fujimori, Shunsuke Yuba, Yutaka Kawarabayasi, Takashi Kawasaki

    BMC neuroscience   10   60 - 60   2009.6

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    DOI： 10.1186/1471-2202-10-60

  • Selective maintenance of Drosophila tandemly arranged duplicated genes during evolution Reviewed

    Carlos Quijano, Pavel Tomancak, Jesus Lopez-Marti, Mikita Suyama, Peer Bork, Marco Milan, David Torrents, Miguel Manzanares

    Genome biology   9 ( 12 )   2008.12

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    DOI： 10.1186/gb-2008-9-12-r176

  • Non-random retention of protein-coding overlapping genes in Metazoa Reviewed

    BMC genomics   9   2008.4

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    DOI： 10.1186/1471-2164-9-174

  • Non-random retention of protein-coding overlapping genes in Metazoa. International journal

    BMC genomics   9   174 - 174   2008.4

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    DOI： 10.1186/1471-2164-9-174

  • Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes Reviewed

    Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents

    PLoS Computational Biology   2 ( 6 )   627 - 636   2006.7

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    DOI： 10.1371/journal.pcbi.0020076

  • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. International journal

    Mikita Suyama, David Torrents, Peer Bork

    Nucleic acids research   34 ( Web Server issue )   W609-12   2006.7

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  • PAL2NAL Robust conversion of protein sequence alignments into the corresponding codon alignments Reviewed

    Mikita Suyama, David Torrents, Peer Bork

    Nucleic acids research   34 ( WEB. SERV. ISS. )   W609 - W612   2006.7

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    DOI： 10.1093/nar/gkl315

  • Identification and analysis of genes and pseudogenes within duplicated regions in the human and mouse genomes. International journal

    Mikita Suyama, Eoghan Harrington, Peer Bork, David Torrents

    PLoS computational biology   2 ( 6 )   e76   2006.6

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  • Molecular cloning and characterization of an enzyme hydrolyzing p-nitrophenyl α-D-glucoside from Bacillus stearothermophilus SA0301 Reviewed

    70 ( 2 )   495 - 499   2006.3

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    Bacillus stearothermophilus SA0301 produces an extracellular oligo-1,6-glucosidase (bsO16G) that also hydrolyzes p-nitrophenyl α-D-glucoside (Tonozuka et al., J. Appl. Glycosci., 45, 397-400 (1998)). We cloned a gene for an enzyme hydrolyzing p-nitrophenyl α-D-glucoside, which was different from the one mentioned above, from B. stearothermophilus SA0301. The k0/Km values of bsO16G for isomaltotriose and isomaltose were 13.2 and 1.39 s-1·mM-1 respectively, while the newly cloned enzyme did not hydrolyze isomaltotriose, and the k0/Km value for isomaltose was 0.81 s -1·mM-1. The primary structure of the cloned enzyme more closely resembled those of trehalose-6-phosphate hydrolases than those of oligo-1,6-glucosidases, and the cloned enzyme hydrolyzed trehalose 6-phosphate. An open reading frame encoding a protein homologous to the trehalose-specific IIBC component of the phopshotransferase system was also found upstream of the gene for this enzyme.

    DOI： 10.1271/bbb.70.495

  • Molecular cloning and characterization of an enzyme hydrolyzing p-nitrophenyl alpha-D-glucoside from Bacillus stearothermophilus SA0301. International journal

    Atsushi Kobayashi, Takashi Tonozuka, Kimihiko Sato, Mikita Suyama, Jun Sasaki, Batbold Nyamdawaa, Masayoshi Sakaguchi, Yoshiyuki Sakano

    Bioscience, biotechnology, and biochemistry   70 ( 2 )   495 - 9   2006.2

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  • Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii Reviewed

    Mikita Suyama, Warren C. Lathe, Peer Bork

    FEBS Letters   579 ( 24 )   5281 - 5286   2005.10

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    DOI： 10.1016/j.febslet.2005.08.051

  • Palindromic repetitive DNA elements with coding potential in Methanocaldococcus jannaschii. International journal

    Mikita Suyama, Warren C Lathe 3rd, Peer Bork

    FEBS letters   579 ( 24 )   5281 - 6   2005.10

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  • Initial sequence of the chimpanzee genome and comparison with the human genome Reviewed

    Nature   437 ( 7055 )   69 - 87   2005.9

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    DOI： 10.1038/nature04072

  • Generation and annotation of the DNA sequences of human chromosomes 2 and 4 Reviewed

    La Deana W. Hillier, Tina A. Graves, Robert S. Fulton, Lucinda A. Fulton, Kymberlie H. Pepin, Patrick Minx, Caryn Wagner-McPherson, Dan Layman, Kristine Wylie, Mandeep Sekhon, Michael C. Becker, Ginger A. Fewell, Kimberly D. Delehaunty, Tracie L. Miner, William E. Nash, Colin Kremitzki, Lachlan Oddy, Hui Du, Hui Sun, Holland Bradshaw-Cordum, Johar Ali, Jason Carter, Matt Cordes, Anthony Harris, Amber Isak, Andrew Van Brunt, Christine Nguyen, Feiyu Du, Laura Courtney, Joelle Kalicki, Philip Ozersky, Scott Abbott, Jon Armstrong, Edward A. Belter, Lauren Caruso, Maria Cedroni, Marc Cotton, Teresa Davidson, Anu Desai, Glendoria Elliott, Thomas Erb, Catrina Fronick, Tony Gaige, William Haakenson, Krista Haglund, Andrea Holmes, Richard Harkins, Kyung Kim, Scott S. Kruchowski, Cynthia Madsen Strong, Neenu Grewal, Ernest Goyea, Shunfang Hou, Andrew Levy, Scott Martinka, Kelly Mead, Michael D. McLellan, Rick Meyer, Jennifer Randall-Maher, Chad Tomlinson, Sara Dauphin-Kohlberg, Amy Kozlowicz-Reilly, Neha Shah, Sharhonda Swearengen-Shahid, Jacqueline Snider, Joseph T. Strong, Johanna Thompson, Martin Yoakum, Shawn Leonard, Charlene Pearman, Lee Trani, Maxim Radionenko, Jason E. Waligorski, Chunyan Wang, Susan M. Rock, Aye Mon Tin-Wollam, Rachel Maupin, Phil Latreille, Michael C. Wendl, Shiaw Pyng Yang, Craig Pohl, John W. Wallis, John Spieth, Tamberlyn A. Bieri, Nicolas Berkowicz, Joanne O. Nelson, John Osborne, Li Ding, Rekha Meyer, Aniko Sabo, Yoram Shotland, Prashant Sinha, Patricia E. Wohldmann, Lisa L. Cook, Matthew T. Hickenbotham, James Eldred, Donald Williams, Thomas A. Jones, Xinwei She, Francesca D. Ciccarelli, Elisa Izaurralde, James Taylor, Jeremy Schmutz, Richard M. Myers, David R. Cox, Xiaoqiu Huang, John D. McPherson, Elaine R. Mardis, Sandra W. Clifton, Wesley C. Warren, Asif T. Chinwalla, Sean R. Eddy, Marco A. Marra, Ivan Ovcharenko, Terrence S. Furey, Webb Miller, Evan E. Eichler, Peer Bork, Mikita Suyama, David Torrents, Robert H. Waterston, Richard K. Wilson

    Nature   434 ( 7034 )   724 - 731   2005.4

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    DOI： 10.1038/nature03466

  • Generation and annotation of the DNA sequences of human chromosomes 2 and 4. International journal

    Ladeana W Hillier, Tina A Graves, Robert S Fulton, Lucinda A Fulton, Kymberlie H Pepin, Patrick Minx, Caryn Wagner-McPherson, Dan Layman, Kristine Wylie, Mandeep Sekhon, Michael C Becker, Ginger A Fewell, Kimberly D Delehaunty, Tracie L Miner, William E Nash, Colin Kremitzki, Lachlan Oddy, Hui Du, Hui Sun, Holland Bradshaw-Cordum, Johar Ali, Jason Carter, Matt Cordes, Anthony Harris, Amber Isak, Andrew van Brunt, Christine Nguyen, Feiyu Du, Laura Courtney, Joelle Kalicki, Philip Ozersky, Scott Abbott, Jon Armstrong, Edward A Belter, Lauren Caruso, Maria Cedroni, Marc Cotton, Teresa Davidson, Anu Desai, Glendoria Elliott, Thomas Erb, Catrina Fronick, Tony Gaige, William Haakenson, Krista Haglund, Andrea Holmes, Richard Harkins, Kyung Kim, Scott S Kruchowski, Cynthia Madsen Strong, Neenu Grewal, Ernest Goyea, Shunfang Hou, Andrew Levy, Scott Martinka, Kelly Mead, Michael D McLellan, Rick Meyer, Jennifer Randall-Maher, Chad Tomlinson, Sara Dauphin-Kohlberg, Amy Kozlowicz-Reilly, Neha Shah, Sharhonda Swearengen-Shahid, Jacqueline Snider, Joseph T Strong, Johanna Thompson, Martin Yoakum, Shawn Leonard, Charlene Pearman, Lee Trani, Maxim Radionenko, Jason E Waligorski, Chunyan Wang, Susan M Rock, Aye-Mon Tin-Wollam, Rachel Maupin, Phil Latreille, Michael C Wendl, Shiaw-Pyng Yang, Craig Pohl, John W Wallis, John Spieth, Tamberlyn A Bieri, Nicolas Berkowicz, Joanne O Nelson, John Osborne, Li Ding, Rekha Meyer, Aniko Sabo, Yoram Shotland, Prashant Sinha, Patricia E Wohldmann, Lisa L Cook, Matthew T Hickenbotham, James Eldred, Donald Williams, Thomas A Jones, Xinwei She, Francesca D Ciccarelli, Elisa Izaurralde, James Taylor, Jeremy Schmutz, Richard M Myers, David R Cox, Xiaoqiu Huang, John D McPherson, Elaine R Mardis, Sandra W Clifton, Wesley C Warren, Asif T Chinwalla, Sean R Eddy, Marco A Marra, Ivan Ovcharenko, Terrence S Furey, Webb Miller, Evan E Eichler, Peer Bork, Mikita Suyama, David Torrents, Robert H Waterston, Richard K Wilson

    Nature   434 ( 7034 )   724 - 31   2005.4

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  • Complex genomic rearrangements lead to novel primate gene function Reviewed

    Francesca D. Ciccarelli, Christian von Mering, Mikita Suyama, Eoghan D. Harrington, Elisa Izaurralde, Peer Bork

    Genome Research   15 ( 3 )   343 - 351   2005.3

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    DOI： 10.1101/gr.3266405

  • Complex genomic rearrangements lead to novel primate gene function. International journal

    Francesca D Ciccarelli, Christian von Mering, Mikita Suyama, Eoghan D Harrington, Elisa Izaurralde, Peer Bork

    Genome research   15 ( 3 )   343 - 51   2005.3

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  • BLAST2GENE A comprehensive conversion of BLAST output into independent genes and gene fragments Reviewed

    Mikita Suyama, David Torrents, Peer Bork

    Bioinformatics   20 ( 12 )   1968 - 1970   2004.8

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    DOI： 10.1093/bioinformatics/bth172

  • [Genome database].

    Mikita Suyama

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   49 ( 11 Suppl )   1841 - 6   2004.8

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  • BLAST2GENE: a comprehensive conversion of BLAST output into independent genes and gene fragments. International journal

    Mikita Suyama, David Torrents, Peer Bork

    Bioinformatics (Oxford, England)   20 ( 12 )   1968 - 70   2004.8

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  • Genome database Reviewed

    Mikita Suyama

    Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme   49 ( 11 Suppl )   1841 - 1846   2004.8

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  • Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Reviewed International journal

    Hillier LW et al.

    Nature   432   2004.6

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  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution Reviewed

    Nature   428 ( 6982 )   493 - 520   2004.4

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    DOI： 10.1038/nature02426

  • Genome sequence of the Brown Norway rat yields insights into mammalian evolution. International journal

    Nature   428 ( 6982 )   493 - 521   2004.4

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  • A genome-wide survey of human pseudogenes Reviewed

    David Torrents, Mikita Suyama, Evgeny Zdobnov, Peer Bork

    Genome Research   13 ( 12 )   2559 - 2567   2003.12

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    DOI： 10.1101/gr.1455503

  • A genome-wide survey of human pseudogenes. International journal

    David Torrents, Mikita Suyama, Evgeny Zdobnov, Peer Bork

    Genome research   13 ( 12 )   2559 - 67   2003.12

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  • The DNA sequence of human chromosome 7 Reviewed

    La Deana W. Hillier, Robert S. Fulton, Lucinda A. Fulton, Tina A. Graves, Kymberlie H. Pepin, Caryn Wagner-McPherson, Dan Layman, Jason Maas, Sara Jaeger, Rebecca Walker, Kristine Wylie, Mandeep Sekhon, Michael C. Becker, Michelle D. O'Laughlin, Mark E. Schaller, Ginger A. Fewell, Kimberly D. Delehaunty, Tracie L. Miner, William E. Nash, Matt Cordes, Hui Du, Hui Sun, Jennifer Edwards, Holland Bradshaw-Cordum, Johar Ali, Stephanie Andrews, Amber Isak, Andrew Van Brunt, Christine Nguyen, Feiyu Du, Betty Lamar, Laura Courtney, Joelle Kalicki, Philip Ozersky, Lauren Bielicki, Kelsi Scott, Andrea Holmes, Richard Harkins, Anthony Harris, Cynthia Madsen Strong, Shunfang Hou, Chad Tomlinson, Sara Dauphin-Kohlberg, Amy Kozlowicz-Reilly, Shawn Leonard, Theresa Rohlfing, Susan M. Rock, Aye Mon Tin-Wollam, Amanda Abbott, Patrick Minx, Rachel Maupin, Catrina Strowmatt, Phil Latreille, Nancy Miller, Doug Johnson, Jennifer Murray, Jeffrey P. Woessner, Michael C. Wendl, Shiaw Pyng Yang, Brian R. Schultz, John W. Wallis, John Spieth, Tamberlyn A. Bieri, Joanne O. Nelson, Nicolas Berkowicz, Patricia E. Wohldmann, Lisa L. Cook, Matthew T. Hickenbotham, James Eldred, Donald Williams, Joseph A. Bedell, Elaine R. Mardis, Sandra W. Clifton, Stephanie L. Chissoe, Marco A. Marra, Christopher Raymond, Eric Haugen, Will Gillett, Yang Zhou, Rose James, Karen Phelps, Shawn Iadanoto, Kerry Bubb, Elizabeth Simms, Ruth Levy, James Clendenning, Rajinder Kaul, W. James Kent, Terrence S. Furey, Robert A. Baertsch, Michael R. Brent, Evan Keibler, Paul Flicek, Peer Borkk, Mikita Suyamak, Jeffrey A. Bailey, Matthew E. Portnoy, David Torrentsk, Asif T. Chinwalla, Warren R. Gish, Sean R. Eddy, John D. McPherson, Maynard V. Olson, Evan E. Eichler, Eric D. Green, Robert H. Waterston, Richard K. Wilson

    Nature   424 ( 6945 )   157 - 164   2003.7

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    DOI： 10.1038/nature01782

  • The DNA sequence of human chromosome 7. International journal

    Ladeana W Hillier, Robert S Fulton, Lucinda A Fulton, Tina A Graves, Kymberlie H Pepin, Caryn Wagner-McPherson, Dan Layman, Jason Maas, Sara Jaeger, Rebecca Walker, Kristine Wylie, Mandeep Sekhon, Michael C Becker, Michelle D O'Laughlin, Mark E Schaller, Ginger A Fewell, Kimberly D Delehaunty, Tracie L Miner, William E Nash, Matt Cordes, Hui Du, Hui Sun, Jennifer Edwards, Holland Bradshaw-Cordum, Johar Ali, Stephanie Andrews, Amber Isak, Andrew Vanbrunt, Christine Nguyen, Feiyu Du, Betty Lamar, Laura Courtney, Joelle Kalicki, Philip Ozersky, Lauren Bielicki, Kelsi Scott, Andrea Holmes, Richard Harkins, Anthony Harris, Cynthia Madsen Strong, Shunfang Hou, Chad Tomlinson, Sara Dauphin-Kohlberg, Amy Kozlowicz-Reilly, Shawn Leonard, Theresa Rohlfing, Susan M Rock, Aye-Mon Tin-Wollam, Amanda Abbott, Patrick Minx, Rachel Maupin, Catrina Strowmatt, Phil Latreille, Nancy Miller, Doug Johnson, Jennifer Murray, Jeffrey P Woessner, Michael C Wendl, Shiaw-Pyng Yang, Brian R Schultz, John W Wallis, John Spieth, Tamberlyn A Bieri, Joanne O Nelson, Nicolas Berkowicz, Patricia E Wohldmann, Lisa L Cook, Matthew T Hickenbotham, James Eldred, Donald Williams, Joseph A Bedell, Elaine R Mardis, Sandra W Clifton, Stephanie L Chissoe, Marco A Marra, Christopher Raymond, Eric Haugen, Will Gillett, Yang Zhou, Rose James, Karen Phelps, Shawn Iadanoto, Kerry Bubb, Elizabeth Simms, Ruth Levy, James Clendenning, Rajinder Kaul, W James Kent, Terrence S Furey, Robert A Baertsch, Michael R Brent, Evan Keibler, Paul Flicek, Peer Bork, Mikita Suyama, Jeffrey A Bailey, Matthew E Portnoy, David Torrents, Asif T Chinwalla, Warren R Gish, Sean R Eddy, John D McPherson, Maynard V Olson, Evan E Eichler, Eric D Green, Robert H Waterston, Richard K Wilson

    Nature   424 ( 6945 )   157 - 64   2003.7

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  • DomCut Prediction of inter-domain linker regions in amino acid sequences Reviewed

    Mikita Suyama, Osamu Ohara

    Bioinformatics   19 ( 5 )   673 - 674   2003.3

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    DOI： 10.1093/bioinformatics/btg031

  • DomCut: prediction of inter-domain linker regions in amino acid sequences. International journal

    Mikita Suyama, Osamu Ohara

    Bioinformatics (Oxford, England)   19 ( 5 )   673 - 4   2003.3

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  • The human genome Genes, pseudogenes, and variation on chromosome 7 Reviewed

    R. H. Waterston, L. W. Hillier, L. A. Fulton, R. S. Fulton, T. A. Graves, K. H. Pepin, P. Bork, M. Suyama, D. Torrents, A. T. Chinwalla, E. R. Mardis, J. D. McPherson, R. K. Wilson

    Cold Spring Harbor Symposia on Quantitative Biology   68   13 - 22   2003.1

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    DOI： 10.1101/sqb.2003.68.13

  • Initial sequencing and comparative analysis of the mouse genome Reviewed

    Nature   420 ( 6915 )   520 - 562   2002.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1038/nature01262

  • Initial sequencing and comparative analysis of the mouse genome. International journal

    Nature   420 ( 6915 )   520 - 62   2002.12

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    Language：English   Publishing type：Research paper (scientific journal)  

  • Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster Reviewed

    Evgeny M. Zdobnov, Christian Von Mering, Ivica Letunic, David Torrents, Mikita Suyama, Richard R. Copley, George K. Christophides, Dana Thomasova, Robert A. Holt, G. Mani Subramanian, Hans Michael Mueller, George Dimopoulos, John H. Law, Michael A. Wells, Ewan Birney, Rosane Charlab, Aaron L. Halpern, Elena Kokoza, Cheryl L. Kraft, Zhongwu Lai, Suzanna Lewis, Christos Louis, Carolina Barillas-Mury, Deborah Nusskern, Gerald M. Rubin, Steven L. Salzberg, Granger G. Sutton, Pantelis Topalis, Ron Wides, Patrick Wincker, Mark Yandell, Frank H. Collins, Jose Ribeiro, William M. Gelbart, Fotis C. Kafatos, Peer Bork

    Science   298 ( 5591 )   149 - 159   2002.10

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1126/science.1077061

  • Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. International journal

    Evgeny M Zdobnov, Christian von Mering, Ivica Letunic, David Torrents, Mikita Suyama, Richard R Copley, George K Christophides, Dana Thomasova, Robert A Holt, G Mani Subramanian, Hans-Michael Mueller, George Dimopoulos, John H Law, Michael A Wells, Ewan Birney, Rosane Charlab, Aaron L Halpern, Elena Kokoza, Cheryl L Kraft, Zhongwu Lai, Suzanna Lewis, Christos Louis, Carolina Barillas-Mury, Deborah Nusskern, Gerald M Rubin, Steven L Salzberg, Granger G Sutton, Pantelis Topalis, Ron Wides, Patrick Wincker, Mark Yandell, Frank H Collins, Jose Ribeiro, William M Gelbart, Fotis C Kafatos, Peer Bork

    Science (New York, N.Y.)   298 ( 5591 )   149 - 59   2002.10

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    Language：English   Publishing type：Research paper (scientific journal)  

  • Site-directed removal of N-glycosylation sites in BST-1/CD157 Effects on molecular and functional heterogeneity Reviewed

    S. Yamamoto-Katayama, A. Sato, M. Ariyoshi, M. Suyama, K. Ishihara, T. Hirano, H. Nakamura, K. Morikawa, H. Jingami

    Biochemical Journal   357 ( 2 )   385 - 392   2001.7

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1042/0264-6021:3570385

  • Evolution of prokaryotic gene order Genome rearrangements in closely related species Reviewed

    Mikita Suyama, Peer Bork

    Trends in Genetics   17 ( 1 )   10 - 13   2001.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1016/S0168-9525(00)02159-4

  • TAP (NXF1) belongs to a multigene family of putative RNA export factors with a conserved modular architecture Reviewed

    A. Herold, M. Suyama, J. P. Rodrigues, I. C. Braun, U. Kutay, M. Carmo-Fonseca, P. Bork, E. Izaurralde

    Molecular and cellular biology   20 ( 23 )   8996 - 9008   2000.12

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1128/MCB.20.23.8996-9008.2000

  • Re-annotating the Mycoplasma pneumoniae genome sequence Adding value, function and reading frames Reviewed

    Nucleic acids research   28 ( 17 )   3278 - 3288   2000.9

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    Language：English   Publishing type：Research paper (scientific journal)  

  • HUGE A database for human large proteins identified in the Kazusa cDNA sequencing project Reviewed

    Reiko Kikuno, Takahiro Nagase, Mikita Suyama, Mina Waki, Makoto Hirosawa, Osamu Ohara

    Nucleic acids research   28 ( 1 )   331 - 332   2000.1

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    Language：English   Publishing type：Research paper (scientific journal)  

  • Prediction of structural domains of TAP reveals details of its interaction with p15 and nucleoporins Reviewed

    Mikita Suyama, Tobias Doerks, Isabelle C. Braun, Michael Sattler, Elisa Izaurralde, Peer Bork

    EMBO Reports   1 ( 1 )   53 - 58   2000.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/embo-reports/kvd009

  • HUGE A database for human large proteins identified by Kazusa cDNA sequencing project Reviewed

    Mikita Suyama, Takahiro Nagase, Osamu Ohara

    Nucleic acids research   27 ( 1 )   338 - 339   1999.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/nar/27.1.338

  • Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro Reviewed

    Takahiro Nagase, Ken Ichi Ishikawa, Mikita Suyama, Reiko Kikuno, Makoto Hirosawa, Nobuyuki Miyajima, Ayako Tanaka, Hirokazu Kotani, Nobuo Nomura, Osamu Ohara

    DNA Research   6 ( 1 )   63 - 70   1999.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/6.1.63

  • Purification and some properties of an extracellular oligo-1,6-glucosidase from Bacillus stearothermophilus SA0301 Reviewed International journal

    Tonozuka T, Sato K, Sakaguchi M, Suyama M, Sekine K, Sakano Y

    Journal of Applied Glycoscience   45   1998.6

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    Language：English   Publishing type：Research paper (scientific journal)  

  • A method for comparing circular genomes from gene locations Application to mitochondrial genomes Reviewed

    Katsuhisa Horimoto, Mikita Suyama, Hiroyuki Toh, Kentaro Mori, Jinya Otsuka

    Bioinformatics   14 ( 9 )   789 - 802   1998.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/14.9.789

  • Prediction of the coding sequences of unidentified human genes. XI. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro Reviewed

    Takahiro Nagase, Ken Ichi Ishikawa, Mikita Suyama, Reiko Kikuno, Nobuyuki Miyajima, Ayako Tanaka, Hirokazu Kotani, Nobuo Nomura, Osamu Ohara

    DNA Research   5 ( 5 )   277 - 286   1998.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/5.5.277

  • Prediction of the coding sequences of unidentified human genes. X. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro Reviewed

    Ken Ichi Ishikawa, Takahiro Nagase, Mikita Suyama, Nobuyuki Miyajima, Ayako Tanaka, Hirokazu Kotani, Nobuo Nomura, Osamu Ohara

    DNA Research   5 ( 3 )   169 - 176   1998.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/5.3.169

  • Prediction of the coding sequences of unidentified human genes. XII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro Reviewed

    Takahiro Nagase, Ken Ichi Ishikawa, Mikita Suyama, Reiko Kikuno, Makoto Hirosawa, Nobuyuki Miyajima, Ayako Tanaka, Hirokazu Kotani, Nobuo Nomura, Osamu Ohara

    DNA Research   5 ( 6 )   355 - 364   1998.1

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/dnares/5.6.355

  • Comparison of protein structures using 3D profile alignment Reviewed

    Mikita Suyama, Yo Matsuo, Ken Nishikawa

    Journal of Molecular Evolution   44 ( SUPPL. 1 )   S163 - S173   1997.3

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1007/PL00000065

  • Searching for common sequence patterns among distantly related proteins Reviewed

    Mikita Suyama, Takaaki Nishioka, Jun'ichi Oda

    Protein Engineering, Design and Selection   8 ( 11 )   1075 - 1080   1995.11

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/protein/8.11.1075

  • Searching for amino acid sequence motifs among enzymes The enzyme-reaction database Reviewed

    Mikita Suyama, Atsushi Ogiwara, Takaaki Nishioka, Jun'ichi Oda

    Bioinformatics   9 ( 1 )   9 - 15   1993.2

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    Language：English   Publishing type：Research paper (scientific journal)  

    DOI： 10.1093/bioinformatics/9.1.9

▼display all

Books

  • よくわかるバイオインフォマティクス入門（藤博幸編）　第６章「ゲノム解析」

    須山幹太（ Role： Joint author）

    講談社  2018.12 

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    Responsible for pages：pp.83-96.   Language：Japanese   Book type：Scholarly book

  • 再生医療・細胞治療のための細胞加工物評価技術（監修：佐藤陽治）　「次世代シーケンシングによる細胞のゲノム安定性評価」

    斉藤大助，須山幹太，小原收（ Role： Joint author）

    シーエムシー出版  2016.7 

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    Responsible for pages：pp.86-97.   Language：Japanese   Book type：Scholarly book

Presentations

  • Detection and interpretation of regulatory mutations International conference

    Mikita Suyama

    International Symposium on Frontiers in Bioinformatics  2016.6 

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    Event date： 2016.6

    Language：English   Presentation type：Oral presentation (general)  

    Country：Germany  

  • Exome sequencing Invited International conference

    Mikita Suyama

    Computational Biology: Genomes to Systems (EMBO Practical Course)  2016.6 

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    Event date： 2016.6

    Language：English   Presentation type：Oral presentation (general)  

    Country：Germany  

  • ラットゲノム解析のためのターゲットキャプチャキットの開発とその応用 Invited

    須山 幹太

    第9回ラットリソースリサーチ研究会  2016.1 

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    Event date： 2016.1

    Language：Japanese  

    Venue：京都   Country：Japan  

  • ChromContact: A Web Tool for Analyzing Spatial Contact of Chromosomes from Hi-C data International conference

    T. Sato, M. Suyama

    Annual Meeting of International Human Epigenome Consortium (IHEC) 2015  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Linkage analysis of Heterogeneity in methylation status of adjacent CpG sites International conference

    Daisuke Saito, Mikita Suyama

    Annual Meeting of International Human Epigenome Consortium (IHEC) 2015  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation International conference

    Daisuke Saito, Mikita Suyama

    The 25th Hot Spring Harbor International Symposium  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Understanding genomic features from their structural aspects Invited International conference

    Mikita Suyama

    The 25th Hot Spring Harbor International Symposium  2015.11 

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    Event date： 2015.11

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • クロマチンの構造とがん Invited

    須山 幹太

    第７４回日本癌学会学術総会  2015.10 

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    Event date： 2015.10

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：名古屋   Country：Japan  

  • ラット拡張エクソーム解析の為のプローブデザイン

    吉原 美奈子, 小原 收, 庫本 高志, 須山 幹太

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • RNA-seqデータを利用したヒストン修飾領域同定法

    佐藤 哲也, 大川 恭行, 須山 幹太

    CREST「エピゲノム研究に基づく診断・治療へ向けた新技術の創出」研究領域・第３回領域会議  2014.1 

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    Language：Japanese  

    Venue：福岡   Country：Japan  

  • ピーク検出プログラムのロバスト性を評価する方法

    佐藤 哲也, 須山 幹太

    第8回日本エピジェネティクス研究年会  2014.5 

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    Language：Japanese  

    Venue：東京   Country：Japan  

  • 8-オキソグアニンのゲノムワイドな分布の解析から明らかになったその核内空間配置との関連

    吉原　美奈子, 将麗, 赤塚　慎也, 豊國　伸哉, 須山 幹太

    第37回日本分子生物学会年会  2014.11 

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    Language：Japanese  

    Venue：横浜   Country：Japan  

  • ChIP-seqデータ解析で用いられるピーク検出プログラムのロバスト性評価法

    佐藤 哲也, 須山 幹太

    第37回日本分子生物学会年会  2013.12 

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    Language：Japanese  

    Venue：横浜   Country：Japan  

  • Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. International conference

    M. Yoshihara, L. Jiang, S. Akatsuka, S. Toyokuni, M. Suyama

    The 4D Nucleome 2014  2014.12 

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    Language：English  

    Country：Japan  

  • 環境DNAから多種多様な生物種を同定する新規手法

    佐藤 哲也, 大川 恭行, 須山 幹太

    日本生態学会第62回全国大会  2015.3 

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    Language：Japanese  

    Venue：鹿児島   Country：Japan  

  • Hi-Cデータ検索サーバ「ChromContact」の開発

    佐藤 哲也, 須山 幹太

    第9回日本エピジェネティクス研究会年会  2015.5 

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    Language：Japanese  

    Country：Japan  

  • 隣接CpGサイトの連鎖に注目したメチル化状態不均質性の解析

    斉藤 大助, 須山 幹太

    第9回日本エピジェネティクス研究会年会  2015.5 

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    Language：Japanese  

    Venue：東京   Country：Japan  

  • Hi-Cデータ検索サーバ「ChromContact」の利用

    佐藤　哲也, 須山 幹太

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • ハイブリッド系統マウスのHi-Cデータに基づく相同染色体の核内配置の解析

    伊波 大志, 須山 幹太

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • 個人ゲノムおよびトランスクリプトームデータを用いたアレル特異的転写の解析

    戌亥 海, 須山 幹太

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • ERRFI1遺伝子のエンハンサークラスターに存在する一塩基多型と乾癬の発症リスク

    久保田直人，須山幹太

    第41回日本分子生物学会年会  2018.7 

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    Event date： 2019.11 - 2018.11

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • ショウジョウバエの複眼形成におけるyki mRNAの多段階制御の分子メカニズムと生物学的意義の解明

    梅河内隆成，越田大夢，山田百子，臼井一馬，佐藤哲也，須山幹太，伊藤恵美，大川恭行，山口政光，ヘンリー クラウス，吉田英樹

    第39回日本分子生物学会年会  2019.7 

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    Event date： 2019.7

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • Cluster analysis of chromatin state profiles in differentiating human trophoblast cells. International conference

    Daisuke Saito, Tetsuya Sato, Hidehiro Toh, Hiroaki Okae, Takahiro Arima, Hiroyuki Sasaki, Mikita Suyama

    International Symposium on Epigenome 2019  2019.2 

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    Event date： 2019.2

    Language：English  

    Country：Japan  

  • Understanding gene regulation using chromosome conformation and epigenome data. International conference

    Mikita Suyama

    2019.1 

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    Event date： 2019.1

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • 多次元の指標を用いた腫瘍内不均一性と予後との関連解析

    菊竹智恵，須山幹太

    第41回日本分子生物学会年会  2018.11 

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    Event date： 2018.11

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • 個人ゲノムデータ及びトランスクリプトームデータを用いたエクソン活性化の網羅的探索

    坂口愛美，須山幹太

    第41回日本分子生物学会年会  2018.11 

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    Event date： 2018.11

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • 一細胞トランスクリプトーム解析による胎仔型ライディッヒ前駆細胞の探索

    井上実紀，馬場崇，齋藤大助，大川恭行，須山幹太，諸橋憲一郎

    第41回日本分子生物学会年会  2018.11 

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    Event date： 2018.11

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • ゲノムデータに基づく近交系ラット２５系統の系統関係の解析

    金賢正，吉原美奈子，須山幹太

    第41回日本分子生物学会年会  2018.11 

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    Event date： 2018.11

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • Understanding gene regulation using chromosome conformation and epigenomic data. International conference

    Naoto Kubota, Tetsuya Sato, Mikita Suyama

    2018.10 

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    Event date： 2018.10

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • Pan-cancer analysis of intratumor heterogeneity associated with patient prognosis using multidimensional measures. International conference

    Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama

    2018.10 

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    Event date： 2018.10

    Language：English  

    Country：Japan  

  • 腫瘍内不均一性が予後に及ぼす影響

    菊竹智恵，須山幹太

    第77回日本癌学会学術総会  2018.9 

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    Event date： 2018.9

    Language：Japanese  

    Venue：大阪   Country：Japan  

  • Pan-cancer analysis of intratumor heterogeneity associated with prognosis of patients. International conference

    Chie Kikutake, Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Mikita Suyama

    2018.8 

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    Event date： 2018.8

    Language：English  

    Country：United States  

  • Exploring molecular basis of phenotype-genotype links using chromosome conformation data. International conference

    Mikita Suyama

    2018.5 

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    Event date： 2018.5 - 2018.6

    Language：English   Presentation type：Oral presentation (general)  

    Country：Sweden  

  • ラットゲノム解析ツール Invited

    須山幹太

    2017年度 遺伝研研究会「マウスとラットで拓く新しい比較実験動物学」  2017.12 

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    Event date： 2017.12

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：三島   Country：Japan  

  • Phylogenetic analysis of 25 inbred rat strains

    2017.12 

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    Event date： 2017.12

    Language：English  

    Country：Japan  

  • foxL3制御から見えた，生殖細胞の性決定機構について International conference

    菊池真理子，津田弥与，齋藤大助，重信秀治，須山幹太，西村俊哉，田中実

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • 痙直型脳性麻痺発症に関与するDMRT3遺伝子エンハンサーの同定

    久保田直人，横山俊史，星信彦，須山幹太

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • クロマチンリモデリングの異常によって発症するASDの分子病態

    片山雄太，西山正章，昌子浩孝，大川恭行，川村淳生，佐藤哲也，須山幹太，内匠透，宮川剛，中山敬一

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • 乳がんにおけるHMCN1変異の腫瘍内不均一性の解析

    菊竹智恵，須山幹太

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • 新規エンクソン獲得の網羅的探索

    坂口愛美，須山幹太

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • 外生殖器を用いた組織特異的性差エンハンサーのin vivo評価系の確立

    松下祥子，鈴木堅太郎，佐藤哲也，日野信次朗，梶岡大暉，Alvin Acebedo，中尾光喜，須山幹太，山田源

    ConBio2017 生命科学系学会合同年次大会  2017.12 

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    Event date： 2017.12

    Language：Japanese  

    Venue：神戸   Country：Japan  

  • Identification of DMRT3 gene enhancer involved in the pathogenesis of spastic cerebral palsy International conference

    Naoto Kubota, Mikita Suyama

    The 27th Hot Spring Harbor International Symposium 2017: Frontiers in Stem Cell Research and Reprogramming  2017.10 

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    Event date： 2017.10 - 2017.11

    Language：English  

    Country：Japan  

  • Cluster analysis using chromatin state profiles in trophoblast cell lineage International conference

    Mikita Suyama

    Annual Meeting of International Human Epigenome Consortium  2017.10 

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    Event date： 2017.10

    Language：English  

    Country：Germany  

  • Understanding gene regulation by using high-resolution Hi-C data Invited

    Mikita Suyama

    2017.9 

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    Event date： 2017.9

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • Design and application of a target capture sequencing of exons and conserved non-coding sequences for the rat International conference

    Minako Yoshihara, Osamu Ohara, Takashi Kuramoto, Mikita Suyama

    15th Annual Meeting of the Complex Trait Community in collaboration with the 10th Annual Meeting of Rat Genomics and Models  2017.6 

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    Event date： 2017.6

    Language：English   Presentation type：Oral presentation (general)  

    Country：United States  

  • ChromContactウェブサーバによる高解像度Hi-Cデータの活用 Invited

    須山幹太

    第11回日本エピジェネティクス研究会年会  2017.5 

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    Event date： 2017.5

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：東京   Country：Japan  

  • 拡張エクソーム解析による制御配列変異の検出 Invited

    須山幹太

    国立成育医療研究センター　特別セミナー  2017.3 

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    Event date： 2017.3

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：東京   Country：Japan  

  • Hi-Cデータを活用した遺伝子発現制御の理解 Invited

    須山幹太

    よこはまNMR研究会 第56回ワークショップ「ヌクレオームとビッグデータ」  2017.3 

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    Event date： 2017.3

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：横浜   Country：Japan  

  • Role of Ad4BP/SF-1 in regulating NADPH production in Y-1 cells

    2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Country：Japan  

  • 発生期におけるクロマチンリモデリング異常は自閉症の原因となる

    片山雄太，西山正章，昌子浩孝，大川恭行，川村敦生，佐藤哲也，須山幹太，内匠透，宮川剛，中山敬一

    第39回日本分子生物学会年会  2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • 核内受容体Ad4BP/SF-1によるステロイドホルモン産生の全制御

    馬場崇，大竹博之，井上実紀，佐藤哲也，石原康宏，宮林香奈子，嶋雄一，山崎岳，須山幹太，Choi Man-Ho，大川恭行，諸橋憲一郎

    第39回日本分子生物学会年会  2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • 個人ゲノムおよびトランスクリプトームデータを用いたナンセンス変異依存mRNA分解機構（NMD）の解析

    戌亥海，須山幹太

    第39回日本分子生物学会年会  2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • Hi-Cデータに基づく相同染色体の核内空間配置の解析

    伊波大志，斉藤大助，吉原美奈子，佐藤哲也，須山幹太

    第39回日本分子生物学会年会  2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • 生殖細胞の性決定機構〜FOXL3制御因子の探索〜

    菊地真理子，西村俊哉，斉藤大助，須山幹太，重信秀治，田中実

    第39回日本分子生物学会年会  2016.11 

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    Event date： 2016.11 - 2016.12

    Language：Japanese  

    Venue：横浜   Country：Japan  

  • Using Hi-C data to understand gene regulation Invited

    2016.11 

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    Event date： 2016.11

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • Analysis of nonsense-mediated mRNA decay (NMD) using genomic and transcriptomic data International conference

    Kai Inui, Mikita Suyama

    The Annual Meeting of Am. Soc. Hum. Genet. 2016  2016.10 

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    Event date： 2016.10

    Language：English  

    Country：Canada  

  • ゲノムの構造的あるいは遺伝的なゆらぎと機能

    須山幹太

    実験，理論，データ科学の融合による遺伝分子動態の理解へ向けて  2016.9 

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    Event date： 2016.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：名古屋   Country：Japan  

  • Subcellular localization of yki mRNAs is regulated by stem-loop in the 3'UTR International conference

    Takanari Umegawachi, Hiromu Koshida, Momoko Yamada, Kazuma Usui, Tetsuya Sato, Megumi Ito, Yasuyuki Ohkawa, Mikita Suyama, Masamitsu Yamaguchi, Henry Krause, Hideki Yoshida

    RNA 2016  2016.6 

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    Event date： 2016.6 - 2016.7

    Language：English  

    Country：Japan  

  • Analysis of nonsense-mediated mRNA decay (NMD) using genomic and transcriptomic data International conference

    Kai Inui, Mikita Suyama

    RNA 2016  2016.6 

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    Event date： 2016.6 - 2016.7

    Language：English  

    Country：Japan  

  • 胎仔ライディッヒ細胞の分化と代謝

    井上 実紀, 嶋 雄一, 宮林 香奈子, 佐藤 哲也, 馬場 崇, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第２３回日本ステロイドホルモン学会学術集会  2016.1 

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    Event date： 2016.1

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：倉敷   Country：Japan  

  • Characterization of transcript variants expressed in Alzheimer's disease brain with human transcriptome array and deep RNA sequencing analyses: The Hisayama Study International conference

    Nona Abolhassani, Masaaki Hokama, Daisuke Saitou, Mikita Suyama, Toru Iwaki, Yutaka Kiyohara, Yusaku Nakabeppu

    2nd Zing Neurodegeneration Conference  2015.12 

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    Event date： 2015.12

    Language：English   Presentation type：Oral presentation (general)  

    Country：Mexico  

  • Integrative analysis of reference epigenomes for endometrium International conference

    J. Tomikawa, A. Masuda, N. Katoh, H. Okae, T. Sato, H. Toh, M. Suyama, T. Arima, H. Sasaki, K. Kato, S. Takeda, K. Nakabayashi, K. Hata

    Annual Meeting of International Human Epigenome Consortium (IHEC) 2015  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing International conference

    Hidehiro Toh, Kenjiro Shirane, Fumihito Miura, Naoki Kubo, Kenji Ichiyanagi, Mikita Suyama, Takashi Ito, Hiroyuki Sasaki

    Annual Meeting of International Human Epigenome Consortium (IHEC) 2015  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Integrative analysis obtained from three different approaches demonstrates insulin signaling impairment associated with AEBP1 up-regulation in AD brains; The Hisayama Study International conference

    Nona Abolhassani, Masaaki Hokama, Daisuke Saitou, Masahiro Shijo, Hideomi Hamasaki, Mikita Suyama, Toru Iwaki, Yutaka Kiyohara, Yusaku Nakabeppu

    The 25th Hot Spring Harbor International Symposium  2015.11 

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    Event date： 2015.11

    Language：English  

    Country：Japan  

  • Characterization of transcript variants expressed in Alzheimer's disease brains with human transcriptome array and deep RNA sequencing analyses: The Hisayama Study

    Nona Abolhassani, Masaaki Hokama, Daisuke Saitou, Mikita Suyama, Toru Iwaki, Yutaka Kiyohara, Yusaku Nakabeppu

    The 38th Annual Meeting of the Japan Neuroscience Society  2015.7 

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    Event date： 2015.7

    Language：English   Presentation type：Oral presentation (general)  

    Country：Japan  

  • 遺伝子発現情報を利用したヒストン修飾領域同定法

    佐藤 哲也, 大川 恭行, 須山 幹太

    第７回日本エピジェネティクス研究会年会  2013.5 

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    Event date： 2013.5

    Language：Japanese  

    Venue：奈良県新公会堂   Country：Japan  

  • ショウジョウバエ転写因子DREFを中心とした転写制御ネットワーク：DREFの標的としてのHippo経路関連遺伝子の同定

    藤原俊介, 堀井健志, 平塚賢, 大川 恭行, 佐藤 哲也, 須山 幹太, 吉田英樹, 山口政光

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Venue：福岡   Country：Japan  

  • 機能的な転写因子結合領域の特徴

    佐藤 哲也, 須山 幹太

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Venue：福岡   Country：Japan  

  • 組織特異的転写因子Ad4BP/SF-1による解糖系遺伝子群の転写を介したグルコース代謝制御

    馬場 崇, 大竹 博之, 佐藤 哲也, 宮林 香奈子, 宍戸祐里菜, 嶋 雄一, 木村宏, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese   Presentation type：Symposium, workshop panel (public)  

    Venue：福岡   Country：Japan  

  • 成獣ライディッヒ細胞における新規Ad4BP/SF-1標的遺伝子の同定

    大竹 博之, 馬場 崇, 佐藤 哲也, 嶋 雄一, 宮林 香奈子, 木村宏, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Venue：福岡   Country：Japan  

  • mRNA新規小胞体標的化機構の分子メカニズムの解明

    梅河内隆成, 臼井一馬, 佐藤 哲也, 須山 幹太, 大川 恭行, 山口政光, 吉田英樹

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Venue：福岡   Country：Japan  

  • ショウジョウバエヒストンメチル基転移酵素dG9aは複眼形態形成過程においてEGFR経路の制御に関与する

    嶋路耕平, 小西貴大, 田中伸太朗, 木村宏, 大川 恭行, 佐藤 哲也, 須山 幹太, 吉田英樹, 山口政光

    第35回日本分子生物学会年会  2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Venue：福岡   Country：Japan  

  • Deviation from co-transcriptional splicing in the regions involved in alternative splicing.

    2012.12 

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    Event date： 2012.12

    Language：Japanese  

    Country：Japan  

  • Difference in splicing mechanisms between alternative and constitutive exons

    Computational Biology Research Center Workshop 2012  2012.10 

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    Event date： 2012.10 - 2012.11

    Language：Japanese   Presentation type：Symposium, workshop panel (public)  

    Country：Japan  

  • Mechanistic analysis of transcription by using RNA-seq data. International conference

    Mikita Suyama

    Frontiers in Bioinformatics  2012.10 

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    Event date： 2012.10

    Language：English   Presentation type：Symposium, workshop panel (public)  

    Country：Spain  

  • 比較ゲノム解析・ChIP-seq解析によるモチーフ同定の実際 Invited

    須山 幹太

    JSBi・第３回アグリバイオインフォマティクス研究会「モチーフ解析の最前線  2012.10 

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    Event date： 2012.10

    Language：Japanese   Presentation type：Symposium, workshop panel (public)  

    Venue：東京   Country：Japan  

  • 次世代シーケンサーデータを用いた転写のリードスルーの解析

    岩田 浩明, 佐藤 哲也, 須山 幹太

    日本遺伝学会第84回大会  2012.9 

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    Event date： 2012.9

    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：福岡   Country：Japan  

  • ChIP-Seqデータを用いた核内受容体共役因子の探索

    佐藤哲也，須山幹太

    第34回日本分子生物学会年会  2011.12 

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    Event date： 2011.12

    Country：Japan  

  • RNA-Seq解析による胎仔型および成獣型ライディッヒ細胞特異的発現マーカー遺伝子の検索

    宮林香奈子，嶋雄一，馬場崇，大竹博之，佐藤哲也，大川恭行，須山幹太，諸橋憲一郎

    第34回日本分子生物学会年会  2011.12 

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    Event date： 2011.12

    Venue：パシフィコ横浜   Country：Japan  

  • ChIP-Seq法によるAd4BP/SF-1の標的遺伝子の同定

    馬場崇，大竹博之，宮林香奈子，嶋雄一，佐藤哲也，木村宏，大川恭行，須山幹太，諸橋憲一郎

    第34回日本分子生物学会年会  2011.12 

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    Event date： 2011.12

    Venue：パシフィコ横浜   Country：Japan  

  • Identification of cis-regulatory elements by using genome alignment and high-throughput data. Invited International conference

    Mikita Suyama

    The 4th Global COE International Symposium 2009 joint with the 19th Hot Spring Harbor Symposium "Molecular Evolution and Bioinformatics"  2009.11 

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    Event date： 2009.11

    Presentation type：Oral presentation (general)  

    Country：Japan  

  • 遺伝子発現情報を利用したヒストン修飾領域同定法

    須山 幹太, 佐藤 哲也, 大川 恭行

    第７回日本エピジェネティクス研究会年会  2013.5 

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    Language：Japanese  

    Venue：奈良   Country：Japan  

  • ゲノム情報解析にもとづく性差構築機構の解明

    須山 幹太

    新学術領域研究「性差構築の分子基盤」第５回領域会議  2013.9 

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    Language：Japanese  

    Venue：佐賀   Country：Japan  

  • Ad4BP/SF-1レギュロンによる統括的なステロイドホルモン産生制御

    馬場 崇, 大竹 博之, 宮林 香奈子, 宍戸祐里菜, 嶋 雄一, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第２１回日本ステロイドホルモン学会学術集会  2013.11 

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    Language：Japanese   Presentation type：Oral presentation (general)  

    Country：Japan  

  • 成獣ライディッヒ細胞における新規Ad4BP/SF-1標的遺伝子の同定

    大竹 博之, 馬場 崇, 佐藤 哲也, 嶋 雄一, 宮林 香奈子, 木村宏, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第２１回日本ステロイドホルモン学会学術集会  2013.11 

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    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：大阪   Country：Japan  

  • 好塩基球・好酸球におけるSLPIの制御機構の解明

    松葉慎太郎, 和田俊樹, 武田和也, 佐藤 哲也, 須山 幹太, 高井俊行, 中村晃

    第６３回日本アレルギー学会秋季学術大会  2013.11 

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    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：東京   Country：Japan  

  • 好塩基球・好酸球におけるSLPIの制御機構の解明

    松葉慎太郎, 和田俊樹, 武田和也, 佐藤 哲也, 須山 幹太, 高井俊行, 中村晃

    第６３回日本アレルギー学会秋季学術大会  2013.11 

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    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：東京   Country：Japan  

  • ショウジョウバエ血球細胞の腫瘍化をおこすmxc突然変異の原因遺伝子産物の標的遺伝子群同定と転写制御

    粟根理恵, 佐藤 哲也, 大川 恭行, 須山 幹太, 井上喜博

    第３６回日本分子生物学会年会  2013.12 

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    Language：Japanese  

    Venue：神戸   Country：Japan  

  • RNA-seqデータを利用したヒストン修飾領域同定法

    佐藤 哲也, 大川 恭行, 須山 幹太

    第３６回日本分子生物学会年会  2013.12 

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    Language：Japanese  

    Venue：神戸   Country：Japan  

  • Ad4BP/SF-1レギュロンによる統括的な細胞内代謝制御

    馬場 崇, 大竹 博之, 佐藤 哲也, 宮林 香奈子, 嶋 雄一, 八木 美佳子, 康東天, 須山 幹太

    第３６回日本分子生物学会年会  2013.12 

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    Language：Japanese  

    Venue：神戸   Country：Japan  

  • Cbx2/M33ノックアウトマウス成長期における長管骨形成異常

    福井由宇子, 馬場 崇, 大竹 博之, 佐藤 哲也, 大川 恭行, 須山 幹太, 諸橋 憲一郎, 深見真紀

    第３６回日本分子生物学会年会  2013.12 

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    Language：Japanese  

    Venue：神戸   Country：Japan  

  • 胎仔型ライディッヒ細胞における遺伝子発現プロファイルの経時的変化

    宮林 香奈子, 嶋 雄一, 佐藤 哲也, 馬場 崇, 大竹 博之, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第17回日本生殖内分泌学会学術集会  2013.12 

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    Language：Japanese   Presentation type：Oral presentation (general)  

    Venue：東京   Country：Japan  

  • A pitfall in whole-genome bisulfite sequencing using Illumina HiSeq. International conference

    H. Toh, K. Shirane, F. Miura, N. Kubo, K. Ichiyanagi, M. Suyama, T. Ito, H. Sasaki

    IHEC Annual Meeting  2014.10 

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    Language：English  

    Country：Canada  

  • Role of histone methyltransferase dG9a during Drosophila embryogenesis - genome-wide identification of target genes

    2014.11 

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    Language：Japanese  

    Country：Japan  

  • ショウジョウバエのがん抑制遺伝子であるmxc遺伝子産物の標的遺伝子群同定と転写制御

    粟根 理恵, 尾関 智彦, 佐藤 哲也, 大川 恭行, 須山 幹太, 井上 喜博

    第37回日本分子生物学会年会  2014.11 

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    Language：Japanese  

    Venue：横浜   Country：Japan  

  • A genome-wide screen for mRNAs targeting the ER in SRP-independent manner, and analysis on subcellular localization of yki mRNA

    2014.11 

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    Language：Japanese  

    Country：Japan  

  • セルトリ細胞における性染色体構成に依存した遺伝子発現制御機構の解明

    宍戸 祐里菜, 馬場 崇, 大竹 博之, 佐藤 哲也, 宮林 香奈子, 嶋 雄一, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    第37回日本分子生物学会年会  2014.11 

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    Language：Japanese  

    Venue：横浜   Country：Japan  

  • ICF症候群の新規原因候補遺伝子の同定

    伊藤 雄哉, 新田 洋久, 鵜木 元香, Velasco Guillaume, Francastel Claire, E. Thijssen Peter, M. van der Maarel Silvere, 久保田 健夫, 須山 幹太, 佐々木 裕之

    第9回日本エピジェネティクス研究会年会  2015.5 

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    Language：Japanese  

    Venue：東京   Country：Japan  

  • 新生仔マウスの精原幹細胞の形成と分化における 全ゲノムDNAメチル化およびトランスクリプトーム解析

    久保 直樹, 藤 英博, 白根 健次郎, 白川 峰征, 小林 久人, 佐藤 哲也, 曾根 秀利, 佐藤 康人, 富澤 信一, 鶴崎 美徳, 柴田 弘紀, 才津 浩智, 鈴木 穣, 松本 直通, 須山 幹太, 河野 友宏, 大保 和之, 佐々木 裕之

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • ショウジョウバエヒストンメチル基転移酵素G9aの機能解析

    嶋路 耕平, 小西 貴大, 田中 伸太朗, 吉田 英樹, 加藤 容子, 大川 恭行, 佐藤 哲也, 須山 幹太, 木村 宏, 山口 政光

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • Investigation of molecular mechanism of yki mRNA targeted to the endoplasmic reticulum in SRP-independent pathway

    2015.12 

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    Language：Japanese  

    Country：Japan  

  • 胎仔精巣におけるライディッヒ前駆細胞の単離とその分化誘導系の確立

    井上 実紀, 嶋 雄一, 宮林 香奈子, 佐藤 哲也, 馬場 崇, 大川 恭行, 須山 幹太, 諸橋 憲一郎

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • Functional analysis of Sortilin in plasmacytoid dendritic cells

    2015.12 

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    Language：Japanese  

    Country：Japan  

  • セルトリ細胞における性染色体構成に起因したクロマチン構造変化とその影響評価

    宍戸 祐里菜, 馬場 崇, 佐藤 哲也, 宮林 香奈子, 嶋 雄一, 大川 恭行, 金井 克晃, 須山 幹太, 諸橋 憲一郎

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • イルミナHiSeqにおけるソフトウェアのアップデートが全ゲノムバイサルファイトシークエンシングに及ぼす影響

    藤 英博, 白根 健次郎, 三浦 史仁, 久保 直樹, 一柳 健司, 須山 幹太, 伊藤 隆司, 佐々木 裕之

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • 原発性免疫不全症"ICF症候群"の原因遺伝子ZBTB24とCDCA7の機能解析

    伊藤 雄哉, 新田 洋久, 鵜木 元香, 大石 裕晃, Peter E. Thijssen, Guillaume Velasco, 吉原 美奈子, 須山 幹太, Claire Francastel, Silvere M. Van Der Maarel, 佐々木 裕之

    BMB2015(第38回日本分子生物学会年会第88回日本生化学会大会合同大会)  2015.12 

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    Language：Japanese  

    Country：Japan  

  • 膵疾患の新規バイオマーカーの最新の話題　Cell free DNAを用いた切除不能膵癌患者のバイオマーカー探索

    安森 翔, 藤森 尚, 菊竹 智恵, 寺松 克人, 須山 幹太, 小川 佳宏

    膵臓  2023.7  (一社)日本膵臓学会

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    Language：Japanese  

  • 経時的シングルセルトランスクリプトーム解析を用いた多発性骨髄腫における新規薬剤感受性遺伝子の同定(Identification of novel drug-sensitive genes in multiple myeloma through longitudinal single-cell transcriptome sequencing)

    増田 徹, 土師 正二郎, 中嶋 康博, 津田 麻理子, 木村 大作, 高松 明子, 白土 基明, 菊竹 智恵, 須山 幹太, 大川 恭行, 小川 佳宏

    International Journal of Myeloma  2022.5  (一社)日本骨髄腫学会

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    Language：English  

  • ヒト膜貫通タンパク質を由来とする新規酸性環境標的化ペプチドの探索

    宗川 彰毅, 谷戸 謙太, 新居 輝樹, 岸村 顕広, 菊竹 智恵, 須山 幹太, 森 健, 片山 佳樹

    日本バイオマテリアル学会大会予稿集  2023.10  日本バイオマテリアル学会

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    Language：Japanese  

  • ヒト・プロテオームからの酸性環境標的化ペプチドの探索

    宗川 彰毅, 谷戸 謙太, 新居 輝樹, 岸村 顕広, 菊竹 智恵, 須山 幹太, 森 健, 片山 佳樹

    日本バイオマテリアル学会大会予稿集  2022.11  日本バイオマテリアル学会

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    Language：Japanese  

  • SHRにおける食塩嗜好性メカニズムの探索

    並河 徹, Reza Fahadur, 吉原 美奈子, 須山 幹太, 硲 哲崇

    日本内分泌学会雑誌  2022.3  (一社)日本内分泌学会

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    Language：Japanese  

  • p53機能欠損細胞におけるトリフルリジン誘導性DNA複製ストレスによる細胞毒性効果のメカニズム(Mechanisms of cytotoxicity of trifluridine-induced DNA replication stress in p53 deficient cells)

    飯森 真人, 若狹 武司, 野中 謙太朗, 菊竹 智恵, 須山 幹太, 小武内 尚, 松岡 和明, 沖 英次, 前原 喜彦, 北尾 洋之

    日本癌学会総会記事  2022.9  (一社)日本癌学会

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    Language：English  

  • B細胞発生と活性化　EMC1(ER膜複合体サブユニット1)のCa2+流入とB細胞発生における必須機能(B cell Development and Activation　Essential function for EMC1(ER membrane complex subunit1) in Ca2+ influx and B cell development)

    Kawata Kazuhiko, Kikutake Chie, Suyama Mikita, Baba Yoshihiro

    日本免疫学会総会・学術集会記録  2022.11  (NPO)日本免疫学会

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    Language：English  

  • B細胞におけるケモカイン受容体のCa2+流入と生合成におけるEMC1(ER membrane complex subunit1)の本質的な機能(Essential function of EMC1(ER membrane complex subunit1) in Ca2+ influx and biogenesis of chemokine receptors in B cell)

    Kawata Kazuhiko, Kikutake Chie, Suyama Mikita, Baba Yoshihiro

    日本免疫学会総会・学術集会記録  2023.12  (NPO)日本免疫学会

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    Language：English  

▼display all

MISC

Professional Memberships

  • Japanese Society of Bioinformatics

  • Japanese Cancer Association

Committee Memberships

  • Councilor   Domestic

    2008.4 - 2010.3   

Academic Activities

  • プログラム委員

    第７４回日本癌学会学術総会  （ 名古屋国際会議場 ） 2015.10

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    Type：Competition, symposium, etc. 

  • Organizer International contribution

    EMBO Workshop: Computational Biology: From genomes to systems  （ Okinawa, Japan Japan ） 2015.4

    　More details

    Type：Competition, symposium, etc. 

    Number of participants：30

  • Organizer International contribution

    International Symposium of Frontiers in Bioinformatics  （ Tokyo Institute of Technology Japan ） 2015.4

    　More details

    Type：Competition, symposium, etc. 

    Number of participants：100

  • Organizer International contribution

    International Workshop on High-Throughput Sequence Analysis  （ Okinawa Institute of Science and Technology Japan ） 2013.10

    　More details

    Type：Competition, symposium, etc. 

    Number of participants：50

  • プログラム委員

    日本バイオインフォマティクス学会年会  （ 神戸国際会議場 ） 2011.11 - 2012.11

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    Type：Competition, symposium, etc. 

    Number of participants：300

Research Projects

  • Genetic mechanisms of salt preference in rats and humans

    Grant number：23K21628  2021.4 - 2025.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant type：Scientific research funding

    CiNii Research

  • Elucidation of the mechanism of pancreatic beta-cell failure in diabetes using comparative biology-based approach

    Grant number：21H02390  2021.4 - 2024.3

    Grants-in-Aid for Scientific Research  Grant-in-Aid for Scientific Research (B)

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    Grant type：Scientific research funding

    CiNii Research

  • Hi-Cデータを活用した疾患メカニズムの解釈

    Grant number：18H04717  2018 - 2019

    日本学術振興会・文部科学省  科学研究費助成事業  新学術領域研究

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    Authorship：Principal investigator  Grant type：Scientific research funding

  • 拡張エクソーム解析による疾患モデルラットの原因変異の網羅的探索

    Grant number：17H03619  2017 - 2019

    日本学術振興会  科学研究費助成事業  基盤研究(B)

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    Authorship：Principal investigator  Grant type：Scientific research funding

  • 生殖発生にかかわる細胞のエピゲノム解析基盤研究

    2013.10 - 2019.3

    日本 

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    Authorship：Coinvestigator(s) 

  • 生殖発生にかかわる細胞のエピゲノム解析基盤研究/エピゲノムデータに基づく生殖系遺伝子発現制御機構の解明

    2013 - 2018

    科学研究費助成事業  JST CREST

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    Authorship：Coinvestigator(s)  Grant type：Competitive funding other than Grants-in-Aid for Scientific Research

  • 性差構築の分子基盤

    2010.6 - 2015.3

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    Authorship：Coinvestigator(s) 

  • ゲノム情報解析にもとづく性差構築機構の解明

    2010 - 2014

    日本学術振興会・文部科学省  科学研究費助成事業  新学術領域研究

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    Authorship：Principal investigator  Grant type：Scientific research funding

  • 非コード領域の保存配列モチーフの同定とそこに見られる多型の解析

    2009 - 2011

    日本学術振興会  科学研究費助成事業  基盤研究(C)

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    Authorship：Principal investigator  Grant type：Scientific research funding

  • 非コード領域の配列モチーフ検出システムの構築とそれに基づくゲノムアノテーション

    2008 - 2009

    科学研究費助成事業  特定領域研究

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    Authorship：Principal investigator  Grant type：Scientific research funding

  • 哺乳類のゲノム比較による非コード領域の解析とそのデータの多型解析への応用

    2007

    科学研究費助成事業  若手研究(スタートアップ)

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    Authorship：Principal investigator  Grant type：Scientific research funding

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Class subject

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅳ

    2017.12 - 2018.2   Winter quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅳ

    2017.12 - 2018.2   Winter quarter

  • ﾊﾞｲｵｲﾝﾌｫﾏﾃｨｯｸｽ

    2017.10 - 2018.3   Second semester

  • ﾊﾞｲｵｲﾝﾌｫﾏﾃｨｯｸｽ

    2017.10 - 2018.3   Second semester

  • 生命医科学Ⅱ

    2017.10 - 2017.12   Fall quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅲ

    2017.10 - 2017.12   Fall quarter

  • Medical Life Sciences Ⅱ

    2017.10 - 2017.12   Fall quarter

  • 生命医科学Ⅱ

    2017.10 - 2017.12   Fall quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅲ

    2017.10 - 2017.12   Fall quarter

  • Medical Life Sciences Ⅱ

    2017.10 - 2017.12   Fall quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅱ

    2017.6 - 2017.8   Summer quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅱ

    2017.6 - 2017.8   Summer quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅰ

    2017.4 - 2017.6   Spring quarter

  • 最新ﾄﾋﾟｯｸｽから学ぶ生命科学入門Ⅰ

    2017.4 - 2017.6   Spring quarter

  • ゲノム医学情報学特論

    2013.10 - 2014.3   Second semester

  • 生命科学概論

    2013.10 - 2014.3   Second semester

  • 生体情報学

    2013.10 - 2014.3   Second semester

  • ゲノム医学情報学基礎

    2013.4 - 2013.9   First semester

  • 先端医工学

    2012.10 - 2013.3   Second semester

  • ゲノム医学情報学特論

    2012.10 - 2013.3   Second semester

  • ゲノム医学情報学基礎

    2012.4 - 2012.9   First semester

  • 先端医工学

    2011.10 - 2012.3   Second semester

  • 先端医工学

    2010.10 - 2011.3   Second semester

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FD Participation

  • 2012.4   Role：Participation   Title：全学FD

    Organizer：University-wide

Visiting, concurrent, or part-time lecturers at other universities, institutions, etc.

  • 2013  九州大学・医学部  Classification:Part-time lecturer  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：後期

  • 2013  沖縄科学技術大学院大学  Classification:Intensive course  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：9月30日-10月5日

  • 2012  九州大学・医学部  Classification:Part-time lecturer  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：後期

  • 2011  九州大学・医学部  Classification:Part-time lecturer  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：後期

  • 2011  京都大学・医学研究科  Classification:Part-time lecturer  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：後期

  • 2010  九州大学・医学部  Classification:Part-time lecturer  Domestic/International Classification:Japan 

    Semester, Day Time or Duration：後期

  • 2008  EMBO Course  Classification:Affiliate faculty  Domestic/International Classification:Overseas 

    Semester, Day Time or Duration：8月10-16日

▼display all

Participation in international educational events, etc.

  • 2016.6

    EMBO

    EMBO Practical Course on Computation Biology

    　 More details

    Venue：Heidelberg, Germany

    Number of participants：50

  • 2015.4

    European Molecular Biology Laboratory

    EMBO Workshop: Computational Biology: From genomes to systems

    　 More details

    Venue：Okinawa, Japan

    Number of participants：30

  • 2013.9

    Okinawa Institute of Science and Technology

    Practical Workshop on High-Throughput Sequencing Data Analysis

    　 More details

    Venue：Okinawa, Japan

    Number of participants：50

Travel Abroad

  • 2013.11

    Staying countory name 1：Germany   Staying institution name 1：Kaiserin Friedrich-Haus

  • 2012.10

    Staying countory name 1：Spain   Staying institution name 1：カタロニア工科大学