| 1. |
Sushil Bhandari, KwangHeum Hong, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Yong-Il Kim, In-Koo Nam, Charles G Sagerstrom, Mako Nakamura, Seong-Kyu Choe, nudt7 gene depletion causes transcriptomic change in early development of zebrafish., Journal of biochemistry, 10.1093/jb/mvac086, 2022.10, The Nudt family has been identified as enzymes performing Coenzyme A to 3'5'-ADP + 4'-phospho pantetheine catalysis. The members of this family have been shown to be particularly involved in lipid metabolism, while their involvement in gene regulation through regulating transcription or mRNA metabolism has also been suggested. Here, we focused on peroxisomal NUDT7, possessing enzymatic activity similar to that of its paralog, peroxisomal NUDT19, which is involved in mRNA degradation. No reports have been published about the Nudt family in zebrafish. Our transcriptomic data showed that the Nudt family members are highly expressed around zygotic gene activation (ZGA) in developing zebrafish embryos. Therefore, we confirmed the computational prediction that the products of the nudt7 gene in zebrafish were localized in the peroxisome and highly expressed in early embryogenesis. The depletion of nudt7 genes by the CRISPR/Cas9 system did not affect development; however, it decreased the rate of transcription in ZGA. In addition, H3K27ac ChIP-seq analysis demonstrated that this decrease in transcription was correlated with the genome-wide decrease of H3K27ac level. This study suggests that peroxisomal Nudt7 functions in regulating transcription in ZGA via formation of the H3K27ac domain in active chromatin.. |
| 2. |
Seiya Hirai, Kosuke Tomimatsu, Atsuko Miyawaki-Kuwakado, Yoshimasa Takizawa, Tetsuro Komatsu, Taro Tachibana, Yutaro Fukushima, Yasuko Takeda, Lumi Negishi, Tomoya Kujirai, Masako Koyama, Yasuyuki Ohkawa, Hitoshi Kurumizaka, Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant., Nucleic acids research, 10.1093/nar/gkab1137, 2021.12, Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain in mice. However, its function has remained enigmatic. We found that H3mm18 is incorporated into chromatin in cells with low efficiency, as compared to H3.3. We determined the structures of the nucleosome core particle (NCP) containing H3mm18 by cryo-electron microscopy, which revealed that the entry/exit DNA regions are drastically disordered in the H3mm18 NCP. Consistently, the H3mm18 NCP is substantially unstable in vitro. The forced expression of H3mm18 in mouse myoblast C2C12 cells markedly suppressed muscle differentiation. A transcriptome analysis revealed that the forced expression of H3mm18 affected the expression of multiple genes, and suppressed a group of genes involved in muscle development. These results suggest a novel gene expression regulation system in which the chromatin landscape is altered by the formation of unusual nucleosomes with a histone variant, H3mm18, and provide important insight into understanding transcription regulation by chromatin.. |
| 3. |
Yeon Suk Jung, Shin-ei Matsumoto, Makiko Yamashita, Kosuke Tomimatsu, Kiichiro Teruya, Yoshinori Katakura, Sanetaka Shirahata, Propionibacterium acnes acts as an adjuvant in in vitro immunization of human peripheral blood mononuclear cells, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.70159, 71, 8, 1963-1969, 2007.08, We have established an in vitro immunization protocol whereby human peripheral blood mononuclear cells (PBMCs) are initially treated with L-leucyl-L-leucine methyl ester (LLME) and subsequently sensitized with antigen in the presence of interleukin (IL)-2, IL-4, and adjuvant. This protocol resulted in the production of antigen -specific antibodies. PBMCs are potentiated to react with exogenous antigens upon treatment with LLME. We are using this system to investigate the immunomodulatory activity of additives. In the present study, we aimed to evaluate the immunomodulatory activity of Propionibacterium acnes (P. acnes), which is known to exhibit various immunomodulatory effects in murine models, using this in vitro immunization protocol. P. acnes was found to augment the production of antigen-specific antibodies by PBMC, possibly through increased production of inflammatory cytokines and/or increased T-B cell interaction. P. acnes hence appears to act as an adjuvant in the antibody response in in vitro immunization.. |
| 4. |
Takashi Tamura, Kosuke Tomimatsu, Yoshinori Katakura, Makiko Yamashita, Shin-ei Matsumoto, Yoshihiro Aiba, Yeon Suk Jung, Yoshiichi Abe, Tsukasa Fujiki, Kiichiro Teruya, Sanetaka Shirahata, Anti-peptide antibody production elicited by in vitro immunization of human peripheral blood mononuclear cells, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.60460, 71, 12, 2871-2875, 2007.12, Human monoclonal antibodies have great potential for use in the treatment of various diseases. We have established an in vitro immunization protocol for inducing antigen-specific antibody production from human peripheral blood mononuclear cells (PBMCs). In the in vitro immunization protocol, PBMCs are pretreated with L-leucyl-L-leucine methyl ester (LLME) to remove suppressive cells, and are sensitized and cultured with a soluble antigen in the presence of IL-2, IL-4 and muramyl dipeptide for 8d, and then an antigen-specific antibody is produced. In this study, we examined the novel possibility of an in vitro immunization protocol, specifically, whether LLME-treated PBMCs can be sensitized with a peptide antigen to produce an anti-peptide antibody. The results indicate that antigen-specific immune responses were elicited by a peptide antigen derived from rice allergen, a cholera toxin B subunit, and TNF-alpha as a sensitizing antigen in in vitro immunization. These results suggest that the in vitro immunization protocol is applicable in the generation of an anti-peptide antibody against various antigens, including food allergens, foreign antigens, and self-antigens.. |
| 5. |
Yeon Suk Jung, Shin-Ei Matsumoto, Yoshinori Katakura, Makiko Yamashita, Kosuke Tomimatsu, Shigeru Kabayama, Kiichiro Teruya, Sanetaka Shirahata, Generation of human monoclonal antibodies against Propionibacterium acnes by applying the phage display method to human peripheral blood mononuclear cells immunized in vitro, CYTOTECHNOLOGY, 10.1007/s10616-008-9138-z, 57, 2, 169-175, 2008.06, Propionibacterium acnes is a gram-positive, non-spore-forming, rod-shaped bacterium that is often detected in normal human skin flora. P. acnes has been associated with many diseases. In this study, we attempted to generate anti-P. acnes human monoclonal antibodies. A phage antibody library was first generated from human peripheral blood mononuclear cells immunized in vitro with P. acnes using the phage display method, and P. acnes-specific phage antibodies were obtained using solid phase panning. Antigen-specific variable region genes were then amplified and recombined into vectors expressing human IgG antibodies. The results indicated that the recombinant human IgG antibodies exhibited P. acnes-specific binding. This study demonstrates that the combined use of an in vitro immunization protocol and the phage display method enables the generation of human monoclonal antibodies against pathogenic bacteria and toxic antigens.. |
| 6. |
Shin-ei Matsumoto, Makiko Yamashita, Yoshinori Katakura, Yoshihiro Aiba, Kosuke Tomimatsu, Shigeru Kabayama, Kiichiro Teruya, Sanetaka Shirahata, A rapid and efficient strategy to generate antigen-specific human monoclonal antibody by in vitro immunization and the phage display method, JOURNAL OF IMMUNOLOGICAL METHODS, 10.1016/j.jim.2007.12.005, 332, 1-2, 2-9, 2008.03, An in vitro immunization (IVI) protocol was developed for inducing antigen-specific immune responses in human peripheral blood mononuclear cells (PBMCs). After antigen sensitization of PBMCs by IVI, B cells producing antigen-specific antibody can be propagated within a week. Here, we attempted to establish a rapid, efficient strategy to obtain antigen-specific antibody by the phage display method using in vitro immunized PBMCs. Heavy and light chain variable region genes were easily amplified from these PBMCs immunized with mite extract (ME). After generating a combinatorial phage library (1.6 x 10(5) members), 4 antigen-specific clones were selected by 5 panning rounds using biotinylated antigen and streptavidin magnetic beads. Next, we combined variable region genes of these selected clones with human IgG constant region genes and produced human IgG-type antibody. Direct and competitive enzyme-linked immunosorbent assays demonstrated that the mAb 1C11 clone bound specifically to ME. We thus established a rapid, efficient method to obtain antigen-specific human antibody genes and produce human monoclonal IgG antibody using the phage antibody library generated from in vitro immunized PBMCs. (C) 2007 Elsevier B.V. All rights reserved.. |
| 7. |
Kosuke Tomimatsu, Shin-ei Matsumoto, Makiko Yamashita, Kiichiro Teruya, Yoshinori Katakura, Shigeru Kabayama, Sanetaka Shirahata, Production of Human Monoclonal Antibodies against Fc epsilon RI alpha by a Method Combining in Vitro Immunization with Phage Display, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.80640, 73, 7, 1465-1469, 2009.07, An in vitro immunization protocol using human peripheral blood mononuclear cells (PBMC) was developed to generate human antigen-specific antibodies. Monoclonal antibodies have great potential, and in particular, efficient acquirement of monoclonal antibodies against membrane proteins provides advantages. In this study, we tried to generate a human monoclonal antibody against the high affinity IgE receptor, Fc epsilon RI alpha, using a method combining in vitro immunization and phage display. Heavy and light chain variable region genes were obtained from PBMC immunized in vitro with Fc epsilon RI alpha-expressed KU812F cells. Subsequently a combined phage antibody library 6 x 10(3) in the size was generated. Antigen-specific phage antibody clones were selected by panning with recombinant Fc epsilon RI alpha and recombined to produce human IgG format antibodies using CHO cells. The antibodies exhibited specific binding against Fc epsilon RI alpha. These results suggest that one can obtain membrane protein-specific human monoclonal antibodies from a relatively small phage antibody library using in vitro immunized PBMCs.. |
| 8. |
Hanxu Yan, Huaize Tian, Tomoya Kinjo, Takeki Hamasaki, Kosuke Tomimatsu, Noboru Nakamichi, Kiichiro Teruya, Shigeru Kabayama, Sanetaka Shirahata, Extension of the Lifespan of Caenorhabditis elegans by the Use of Electrolyzed Reduced Water, BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY, 10.1271/bbb.100250, 74, 10, 2011-2015, 2010.10, Electrolyzed reduced water (ERW) has attracted much attention because of its therapeutic effects. In the present study, a new culture medium, which we designated Water medium, was developed to elucidate the effects of ERW on the lifespan of Caenorhabditis elegans. Wild-type C. elegans had a significantly shorter lifespan in Water medium than in conventional S medium. However, worms cultured in ERW-Water medium exhibited a significantly extended lifespan (from 11% to 41%) compared with worms cultured in ultrapure water-Water medium. There was no difference between the lifespans of worms cultured in ERW-S medium and ultrapure water-S medium. Nematodes cultured in ultrapure water-Water medium showed significantly higher levels of reactive oxygen species than those cultured in ultrapure water-S medium. Moreover, ERW-Water medium significantly reduced the ROS accumulation induced in the worms by paraquat, suggesting that ERW-Water medium extends the longevity of nematodes at least partly by scavenging ROS.. |
| 9. |
Mahito Sadaie, Rafik Salama, Thomas Carroll, Kosuke Tomimatsu, Tamir Chandra, Andrew R.J. Young, Masako Narita, Pedro A. Pérez-Mancera, Dorothy C. Bennett, Heung Chong, Hiroshi Kimura, Masashi Narita, Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence, Genes and Development, 10.1101/gad.217281.113, 27, 16, 1800-1808, 2013.08, Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression. © 2013, Published by Cold Spring Harbor Laboratory Press.. |
| 10. |
Kosuke Tomimatsu, Shin-Ei Matsumoto, Hayato Tanaka, Makiko Yamashita, Hidekazu Nakanishi, Kiichiro Teruya, Saiko Kazuno, Tomoya Kinjo, Takeki Hamasaki, Ken-Ichi Kusumoto, Shigeru Kabayama, Yoshinori Katakura, Sanetaka Shirahata, A rapid screening and production method using a novel mammalian cell display to isolate human monoclonal antibodies, Biochemical and Biophysical Research Communications, 10.1016/j.bbrc.2013.10.007, 441, 1, 59-64, 2013.11, Antibody display methods are increasingly being used to produce human monoclonal antibodies for disease therapy. Rapid screening and isolation of specific human antibody genes are valuable for producing human monoclonal antibodies showing high specificity and affinity. In this report, we describe a novel mammalian cell display method in which whole human IgG is displayed on the cell surface of CHO cells. Cells expressing antigen-specific human monoclonal IgGs with high affinity on the cell surface after normal folding and posttranscriptional modification were screened using a cell sorter. The membrane-type IgG-expressing CHO cells were then converted to IgG-secreting cells by transfection with a plasmid coding Cre recombinase. This mammalian cell display method was applied to in vitro affinity maturation of monoclonal C9 IgG specific to the human high-affinity IgE receptor (FcεRIα). The CDR3 of the C9 heavy chain variable region gene was randomly mutated and inserted into pcDNA5FRT/IgG. A C9 IgG (CDRH3r)-expressing CHO cell display library consisting of 1.1 × 106 independent clones was constructed. IgG-displaying cells showing high reactivity to FcεRIα antigen were screened by the cell sorter, resulting in the establishment of a CHO cell line producing with higher reactivity than the parent C9 IgG. © 2013 Elsevier Inc. All rights reserved.. |
| 11. |
Kosuke Tomimatsu, Masashi Narita, Translating the effects of mTOR on secretory senescence, NATURE CELL BIOLOGY, 10.1038/ncb3244, 17, 10, 1230-1232, 2015.10. |
| 12. |
Kristina Kirschner, Shamith A. Samarajiwa, Jonathan M. Cairns, Suraj Menon, Pedro A. Perez-Mancera, Kosuke Tomimatsu, Camino Bermejo-Rodriguez, Yoko Ito, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimura, Tetsuya Ohbayashi, Simon Tavare, Masashi Narita, Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53, PLOS GENETICS, 10.1371/journal.pgen.1005053, 11, 3, e1005053, 2015.03, The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.. |
| 13. |
Matthew Hoare, Yoko Ito, Tae-Won Kang, Michael P. Weekes, Nicholas J. Matheson, Daniel A. Patten, Shishir Shetty, Aled J. Parry, Suraj Menon, Rafik Salama, Robin Antrobus, Kosuke Tomimatsu, William Howat, Paul J. Lehner, Lars Zender, Masashi Narita, NOTCH1 mediates a switch between two distinct secretomes during senescence, NATURE CELL BIOLOGY, 10.1038/ncb3397, 18, 9, 979-992, 2016.09, Senescence, a persistent form of cell-cycle arrest, is often associated with a diverse secretome, which provides complex functionality for senescent cells within the tissue microenvironment. We show that oncogene-induced senescence is accompanied by a dynamic fluctuation of NOTCH1 activity, which drives a TGF-beta-rich secretome, while suppressing the senescence-associated pro-inflammatory secretome through inhibition of C/EBP beta. NOTCH1 and NOTCH1-driven TGF-beta contribute to 'lateral induction of senescence' through a juxtacrine NOTCH-JAG1 pathway. In addition, NOTCH1 inhibition during senescence facilitates upregulation of pro-inflammatory cytokines, promoting lymphocyte recruitment and senescence surveillance in vivo. As enforced activation of NOTCH1 signalling confers a near mutually exclusive secretory profile compared with typical senescence, our data collectively indicate that the dynamic alteration of NOTCH1 activity during senescence dictates a functional balance between these two distinct secretomes: one representing TGF-beta and the other pro-inflammatory cytokines, highlighting that NOTCH1 is a temporospatial controller of secretome composition.. |
| 14. |
Kosuke Tomimatsu, Kenji Kokura, Tadashi Nishida, Yuki Yoshimura, Yasuhiro Kazuki, Masashi Narita, Mitsuo Oshimura, Tetsuya Ohbayashi, Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome, FEBS OPEN BIO, 10.1002/2211-5463.12169, 7, 3, 306-317, 2017.03, The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site-specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross-reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering.. |
| 15. |
Kazumitsu Maehara, Kosuke Tomimatsu, Akihito Harada, Kaori Tanaka, Shoko Sato, Seiji Okada, Tetsuya Handa, Hitoshi Kurumizaka, Hiroshi Kimura, Yasuyuki Ohkawa, Modeling population size independent tissue epigenomes by ChIL-seq with single-thin sections, Molecular Systems Biology, 10.1101/2020.12.18.423434, 2020.12, AbstractRecent advances in omics studies have enabled analysis at the single-cell level; however, methods for analyzing the whole cell of large organs and tissues remain challenging. Here, we developed a method named tsChIL to understand the diverse cellular dynamics at the tissue level using high-depth epigenomic data. tsChIL allowed the analysis of a single tissue section and could reproducibly acquire epigenomic profiles from several types of tissues, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation of cells in regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analysis by tsChIL can elucidate in vivo cell-type dynamics of tissues.. |
| 16. |
Kosuke Tomimatsu, Dóra Bihary, Ioana Olan, Aled J. Parry, Stefan Schoenfelder, Adelyne S. L. Chan, Guy St. C. Slater, Yoko Ito, Peter J. Rugg-Gunn, Kristina Kirschner, Camino Bermejo-Rodriguez, Tomomi Seko, Hiroyuki Kugoh, Ken Shiraishi, Koji Sayama, Hiroshi Kimura, Peter Fraser, Masako Narita, Shamith A. Samarajiwa, Masashi Narita, Locus-specific induction of gene expression from heterochromatin loci during cellular senescence, Nature Aging, 10.1038/s43587-021-00147-y, 2021.12, <title>Abstract</title> Cellular senescence is a fate-determined state, accompanied by reorganization of heterochromatin. While lineage-appropriate genes can be temporarily repressed through facultative heterochromatin, stable silencing of lineage-inappropriate genes often involves the constitutive heterochromatic mark, histone H3K9me3. The fate of these heterochromatic genes during the chromatin reorganization accompanying senescence is unclear. Here we show a small number of lineage-inappropriate genes are derepressed in senescent cells from H3K9me3 regions that gain open chromatin marks. DNA FISH experiments reveal that these gene loci, which are tightly condensed at the nuclear periphery in proliferative cells, are physically decompacted during senescence. Among these gene loci, <italic>NLRP3</italic> is predominantly expressed in immune cells, such as macrophages, where it resides within an open topologically associated domain (TAD). In contrast, <italic>NLRP3</italic> is derepressed in senescent fibroblasts, potentially due to the local disruption of the H3K9me3-rich TAD that contains it. The role of NLRP3 has been implicated in the amplification of inflammatory cytokine signalling in senescence and aging, underscoring the functional relevance of gene induction from ‘permissive’ H3K9me3 regions in senescent cells.. |
| 17. |
Atsuko Miyawaki-Kuwakado, Qianmei Wu, Akihito Harada, Kosuke Tomimatsu, Takeru Fujii, Kazumitsu Maehara, Yasuyuki Ohkawa, Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts., Genes to cells : devoted to molecular & cellular mechanisms, 10.1111/gtc.12870, 2021.05, Single-cell RNA-sequencing analysis is one of the most effective tools for understanding specific cellular states. The use of single cells or pooled cells in RNA-seq analysis requires the isolation of cells from a tissue or culture. Although trypsin or more recently cold-active protease (CAP) has been used for cell dissociation, the extent to which the gene expression changes are suppressed has not been clarified. To this end, we conducted detailed profiling of the enzyme-dependent gene expression changes in mouse skeletal muscle progenitor cells, focusing on the enzyme treatment time, amount, and temperature. We found that the genes whose expression was changed by the enzyme treatment could be classified in a time-dependent manner, and that there were genes whose expression was changed independently of the enzyme treatment time, amount, and temperature. This study will be useful as reference data for genes that should be excluded or considered for RNA-seq analysis using enzyme isolation methods.. |
| 18. |
Qianmei Wu, Takeru Fujii, Akihito Harada, Kosuke Tomimatsu, Atsuko Miyawaki-Kuwakado, Masatoshi Fujita, Kazumitsu Maehara, Yasuyuki Ohkawa, Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle., Journal of biochemistry, 10.1093/jb/mvab001, 2021.01, MyoD, a myogenic differentiation protein, has been studied for its critical role in skeletal muscle differentiation. MyoD-expressing myoblasts have a potency to be differentiated with proliferation of ectopic cells. However, little is known about the effect on chromatin structure of MyoD binding in proliferative myoblasts. In this study, we evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing. Genome-wide analysis of histone modifications was performed in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle. We found that MyoD-bound genome regions had elevated levels of active histone modifications, such as H3K4me1/2/3, and H3K27ac, compared with MyoD-unbound genome regions during the cell cycle. We also demonstrated that the elevated H3K4me2/3 modification level was maintained during the cell cycle, whereas the H3K27ac and H3K4me1 modification levels decreased to the same level as MyoD-unbound genome regions during the later phases. Immunoblot analysis revealed that MyoD abundance was high in the G1 phase then decreased in the S and G2/M phases. Our results suggest that MyoD binding formed selective epigenetic memories with H3K4me2/3 during the cell cycle in addition to myogenic gene induction via active chromatin formation coupled with transcription.. |
| 19. |
Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura, Epigenetic effects induced by the ectopic expression of Pax7 in 3T3-L1., Journal of biochemistry, 10.1093/jb/mvab030, 2021.03, Although skeletal muscle cells and adipocytes are derived from the same mesoderm, they do not transdifferentiate in vivo and are strictly distinct at the level of gene expression. To elucidate some of the regulatory mechanisms underlying this strict distinction, Pax7, a myogenic factor, was ectopically expressed in 3T3-L1 adipose progenitor cells to perturb their adipocyte differentiation potential. Transcriptome analysis showed that ectopic expression of Pax7 repressed the expression of some adipocyte genes and induced expression of some skeletal muscle cell genes. We next profiled the epigenomic state altered by Pax7 expression using H3K27ac, an activating histone mark, and H3K27me3, a repressive histone mark, as indicators. Our results show that ectopic expression of Pax7 did not result in the formation of H3K27ac at loci of skeletal muscle-related genes, but instead resulted in the formation of H3K27me3 at adipocyte-related gene loci. These findings suggest that the primary function of ectopic Pax7 expression is the formation of H3K27me3, and muscle gene expression results from secondary regulation.. |
| 20. |
Mahito Sadaie, Rafik Salama, Thomas Carroll, Kosuke Tomimatsu, Tamir Chandra, Andrew R.J. Young, Masako Narita, Pedro A. Pérez-Mancera, Dorothy C. Bennett, Heung Chong, Hiroshi Kimura, Masashi Narita, Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence , Genes and Development, 2013.08. |
| 21. |
Kosuke Tomimatsu, Shin-Ei Matsumoto, Hayato Tanaka, Makiko Yamashita, Hidekazu Nakanishi, Kiichiro Teruya, Saiko Kazuno, Tomoya Kinjo, Takeki Hamasaki, Ken-Ichi Kusumoto, Shigeru Kabayama, Yoshinori Katakura, Sanetaka Shirahata, A rapid screening and production method using a novel mammalian cell display to isolate human monoclonal antibodies , Biochemical and Biophysical Research Communications, 2013.11. |
| 22. |
Kosuke Tomimatsu, Sanetaka Shirahata, Antigen-specific in vitro immunization: A source for human monoclonal antibodies , Methods in Molecular Biology, 2014.08. |
| 23. |
Kristina Kirschner, Shamith A. Samarajiwa, Jonathan M. Cairns, Suraj Menon, Pedro A. Perez-Mancera, Kosuke Tomimatsu, Camino Bermejo-Rodriguez, Yoko Ito, Tamir Chandra, Masako Narita, Scott K. Lyons, Andy G. Lynch, Hiroshi Kimura, Tetsuya Ohbayashi, Simon Tavare, Masashi Narita, Phenotype Specific Analyses Reveal Distinct Regulatory Mechanism for Chronically Activated p53 , Plos Genetics, 2015.03. |
| 24. |
Kosuke Tomimatsu, Masashi Narita, Translating the effects of mTOR on secretory senescence , Nature Cell Biology, 2015.10. |
| 25. |
Matthew Hoare, Yoko Ito, Tae-Won Kang, Michael P. Weekes, Nicholas J. Matheson, Daniel A. Patten, Shishir Shetty, Aled J. Parry, Suraj Menon, Rafik Salama, Robin Antrobus, Kosuke Tomimatsu, William Howat, Paul J. Lehner, Lars Zender, Masashi Narita, NOTCH1 mediates a switch between two distinct secretomes during senescence , Nature Cell Biology, 2016.09. |
| 26. |
Kosuke Tomimatsu, Kenji Kokura, Tadashi Nishida, Yuki Yoshimura, Yasuhiro Kazuki, Masashi Narita, Mitsuo Oshimura, Tetsuya Ohbayashi, Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome , FEBS Open Bio, 2017.03. |
| 27. |
Parry AJ, Hoare M, Bihary D, Hansel-Hertcsh R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russell A, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M, NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. , Nature Communications, 2018.11. |
| 28. |
Masayuki Nagasawa, Kosuke Tomimatsu, Koji Terada, Kenta Kondo, Kazuko Miyazaki, Masaki Miyazaki, Daisuke Motooka, Daisuke Okuzaki, Tetsuya Yoshida, Susumu Kageyama, Hiroshi Kawamoto, Akihiro Kawauchi, Yasutoshi Agata, Long non-coding RNA MANCR is a target of BET bromodomain protein BRD4 and plays a critical role in cellular migration and invasion abilities of prostate cancer, Biochemical and Biophysical Research Communications, 2020.03. |
