Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Kinichi Nakashima Last modified date:2020.05.29

Professor / Stem Cell Biology and Medicine / Department of Stem Cell Biology and Medicine / Faculty of Medical Sciences


Papers
1. Yuichi Mishima, Laura Brueckner, Saori Takahashi, Toru Kawakami, Junji Otani, Akira Shinohara, Kohei Takeshita, Ronald Garingalao Garvilles, Mikio Watanabe, Norio Sakai, Hideyuki Takeshima, Charlotte Nachtegael, Atsuya Nishiyama, Makoto Nakanishi, Kyohei Arita, Kinichi Nakashima, Hironobu Hojo, Isao Suetake, Enhanced processivity of Dnmt1 by monoubiquitinated histone H3, Genes to Cells, 10.1111/gtc.12732, 25, 1, 22-32, 2020.01, DNA methylation controls gene expression, and once established, DNA methylation patterns are faithfully copied during DNA replication by the maintenance DNA methyltransferase Dnmt1. In vivo, Dnmt1 interacts with Uhrf1, which recognizes hemimethylated CpGs. Recently, we reported that Uhrf1-catalyzed K18- and K23-ubiquitinated histone H3 binds to the N-terminal region (the replication focus targeting sequence, RFTS) of Dnmt1 to stimulate its methyltransferase activity. However, it is not yet fully understood how ubiquitinated histone H3 stimulates Dnmt1 activity. Here, we show that monoubiquitinated histone H3 stimulates Dnmt1 activity toward DNA with multiple hemimethylated CpGs but not toward DNA with only a single hemimethylated CpG, suggesting an influence of ubiquitination on the processivity of Dnmt1. The Dnmt1 activity stimulated by monoubiquitinated histone H3 was additively enhanced by the Uhrf1 SRA domain, which also binds to RFTS. Thus, Dnmt1 activity is regulated by catalysis (ubiquitination)-dependent and -independent functions of Uhrf1..
2. Hirofumi Noguchi, Jesse Garcia Castillo, Kinichi Nakashima, Samuel J. Pleasure, Suppressor of fused controls perinatal expansion and quiescence of future dentate adult neural stem cells, eLife, 10.7554/eLife.42918, 8, 2019.04, Adult hippocampal neurogenesis requires the quiescent neural stem cell (NSC) pool to persist lifelong. However, establishment and maintenance of quiescent NSC pools during development is not understood. Here, we show that Suppressor of Fused (Sufu) controls establishment of the quiescent NSC pool during mouse dentate gyrus (DG) development by regulating Sonic Hedgehog (Shh) signaling activity. Deletion of Sufu in NSCs early in DG development decreases Shh signaling activity leading to reduced proliferation of NSCs, resulting in a small quiescent NSC pool in adult mice. We found that putative adult NSCs proliferate and increase their numbers in the first postnatal week and subsequently enter a quiescent state towards the end of the first postnatal week. In the absence of Sufu, postnatal expansion of NSCs is compromised, and NSCs prematurely become quiescent. Thus, Sufu is required for Shh signaling activity ensuring expansion and proper transition of NSC pools to quiescent states during DG development..
3. Hirokatsu Saito, Kenshiro Hara, Takashi Tominaga, Kinichi Nakashima, Kentaro Tanemura, Early-life exposure to low levels of permethrin exerts impairments in learning and memory with the effects on neuronal and glial population in adult male mice, Journal of Applied Toxicology, 10.1002/jat.3882, 39, 12, 1651-1662, 2019.12, Permethrin, a pyrethroid chemical, is widely used as a pesticide because of its rapid insecticidal activity. Although permethrin is considered to exert very low toxicity in mammals, the effects of early, low-level, chronic exposure on the adult central nervous system are unclear. In this study, we investigated the effects of low-level, chronic permethrin exposure in early life on the brain functions of adult mice, using environmentally relevant concentrations. We exposed mice to the acceptable daily intake level of permethrin (0.3 ppm) in drinking water during the prenatal and postnatal periods. We then examined the effects on the central nervous system in adult male offspring. In the permethrin group, we detected behavior that displayed incomplete adaptation to a novel environment, as well as an impairment in learning and memory. In addition, immunohistochemical analysis revealed an increase in doublecortin- (an immature neuron marker) positive cells in the hippocampal dentate gyrus in the permethrin exposure group compared with the control group. Additionally, in the permethrin exposure group there was a decrease in astrocyte number in the hilus of the dentate gyrus, and remaining astrocytes were often irregularly shaped. These results suggest that exposure to permethrin at low levels in early life affects the formation of the neural circuit base and behavior after maturation. Therefore, in the central nervous system of male mice, low-level, chronic permethrin exposure during the prenatal and postnatal periods has effects that were not expected based on the known effects of permethrin exposure in mature animals..
4. Taito Matsuda, Takashi Irie, Shutaro Katsurabayashi, Yoshinori Hayashi, Tatsuya Nagai, Nobuhiko Hamazaki, Aliya Mari D. Adefuin, Fumihito Miura, Takashi Ito, Hiroshi Kimura, Katsuhiko Shirahige, Tadayuki Takeda, Katsunori Iwasaki, Takuya Imamura, Kinichi Nakashima, Pioneer Factor NeuroD1 Rearranges Transcriptional and Epigenetic Profiles to Execute Microglia-Neuron Conversion, Neuron, 10.1016/j.neuron.2018.12.010, 101, 3, 472-485.e7, 2019.02, Matsuda et al. report direct neuronal conversion of microglia induced by the expression of a single transcription factor, NeuroD1, which occupies bivalent epigenetic domains for neuronal gene induction. NeuroD1 can also converts microglia into neurons in the adult mouse striatum..
5. Yoshikawa, Y. Ago, T. Kuroda, J. Wakisaka, Y. Tachibana, M. Komori, M. Shibahara, T. Nakashima, H. Nakashima, K. Kitazono, T., Nox4 Promotes Neural Stem/Precursor Cell Proliferation and Neurogenesis in the Hippocampus and Restores Memory Function Following Trimethyltin-Induced Injury, NEUROSCIENCE, 10.1016/j.neuroscience.2018.11.046, 398, 193-205, 2019.02.
6. Keita Tsujimura, Kinichi Nakashima, Rett syndrome and stem cell research, Stem Cell Genetics for Biomedical Research Past, Present, and Future, 10.1007/978-3-319-90695-9_3, 27-41, 2018.06, Rett syndrome (RTT) is a devastating neurodevelopmental disorder resulting from mutations in the X-linked gene encoding methyl-CpG-binding pro- tein 2 (MECP2). MECP2 mutations are also associated with other neurodevelop- mental diseases, including autism and schizophrenia. Therefore, elucidating the mechanism of RTT can contribute to understanding the pathogenesis of a wide range of neurodevelopmental diseases. Despite its importance, however, the RTT pathogenesis remains unclear, and effective therapeutic treatment has not been developed. Offering an opportunity to move toward this goal, however, is the recent advance in the stem cell research field of the development of induced pluripotent stem cell (iPSC) technology. This technology can yield important insights into dis- ease pathophysiology and has the potential to provide disease models for screening new drugs. Here, we discuss applications of recent stem cell technology to the field of research on RTT and describe the stem cell biology of RTT pathogenesis..
7. Naohiro Uezono, Yicheng Zhu, Yusuke Fujimoto, Tetsuro Yasui, Taito Matsuda, Masahide Nakajo, Masahiko Abematsu, Takao Setoguchi, Shuji Mori, Hideo K. Takahashi, Setsuro Komiya, Masahiro Nishibori, Kinichi Nakashima, Prior Treatment with Anti-High Mobility Group Box-1 Antibody Boosts Human Neural Stem Cell Transplantation-Mediated Functional Recovery After Spinal Cord Injury, Stem Cells, 10.1002/stem.2802, 36, 5, 737-750, 2018.05, Together with residual host neurons, transplanted neural stem cell (NSC)-derived neurons play a critical role in reconstructing disrupted neural circuits after spinal cord injury (SCI). Since a large number of tracts are disrupted and the majority of host neurons die around the lesion site as the damage spreads, minimizing this spreading and preserving the lesion site are important for attaining further improvements in reconstruction. High mobility group box-1 (HMGB1) is a damage-associated molecular pattern protein that triggers sterile inflammation after tissue injury. In the ischemic and injured brain, neutralization of HMGB1 with a specific antibody reportedly stabilizes the blood-brain barrier, suppresses inflammatory cytokine expression, and improves functional recovery. Using a SCI model mouse, we here developed a combinatorial treatment for SCI: administering anti-HMGB1 antibody prior to transplantation of NSCs derived from human induced pluripotent stem cells (hiPSC-NSCs) yielded a dramatic improvement in locomotion recovery after SCI. Even anti-HMGB1 antibody treatment alone alleviated blood-spinal cord barrier disruption and edema formation, and increased the number of neurites from spared axons and the survival of host neurons, resulting in functional recovery. However, this recovery was greatly enhanced by the subsequent hiPSC-NSC transplantation, reaching an extent that has never before been reported. We also found that this improved recovery was directly associated with connections established between surviving host neurons and transplant-derived neurons. Taken together, our results highlight combinatorial treatment with anti-HMGB1 antibody and hiPSC-NSC transplantation as a promising novel therapy for SCI. Stem Cells 2018;36:737–750..
8. Hideyuki Nakashima, Keita Tsujimura, Koichiro Irie, Masataka Ishizu, Miao Pan, Tomonori Kameda, Kinichi Nakashima, Canonical TGF-β signaling negatively regulates neuronal morphogenesis through TGIF/Smad complex-mediated CRMP2 suppression, Journal of Neuroscience, 10.1523/JNEUROSCI.2423-17.2018, 38, 20, 4791-4810, 2018.05, Functional neuronal connectivity requires proper neuronal morphogenesis and its dysregulation causes neurodevelopmental diseases. Transforming growth factor-β (TGF-β) family cytokines play pivotal roles in development, but little is known about their contribution to morphological development of neurons. Here we show that the Smad-dependent canonical signaling of TGF-β family cytokines negatively regulates neuronal morphogenesis during brain development. Mechanistically, activated Smads form a complex with transcriptional repressor TG-interacting factor (TGIF), and downregulate the expression of a neuronal polarity regulator, collapsin response mediator protein 2. We also demonstrate that TGF-β family signaling inhibits neurite elongation of human induced pluripotent stem cell-derived neurons. Furthermore, the expression of TGF-β receptor 1, Smad4, or TGIF, which have mutations found in patients with neurodevelopmental disorders, disrupted neuronal morphogenesis in both mouse (male and female) and human (female) neurons. Together, these findings suggest that the regulation of neuronal morphogenesis by an evolutionarily conserved function of TGF-β signaling is involved in the pathogenesis of neurodevelopmental diseases..
9. Atsuhiko Sakai, Taito Matsuda, Hiroyoshi Doi, Yukiko Nagaishi, Kiyoko Kato, Kinichi Nakashima, Ectopic neurogenesis induced by prenatal antiepileptic drug exposure augments seizure susceptibility in adult mice, Proceedings of the National Academy of Sciences of the United States of America, 10.1073/pnas.1716479115, 115, 16, 4270-4275, 2018.04, Epilepsy is a neurological disorder often associated with seizure that affects ∼0.7% of pregnant women. During pregnancy, most epileptic patients are prescribed antiepileptic drugs (AEDs) such as valproic acid (VPA) to control seizure activity. Here, we show that prenatal exposure to VPA in mice increases seizure susceptibility in adult offspring through mislocalization of newborn neurons in the hippocampus. We confirmed that neurons newly generated from neural stem/progenitor cells (NS/PCs) are integrated into the granular cell layer in the adult hippocampus; however, prenatal VPA treatment altered the expression in NS/PCs of genes associated with cell migration, including CXC motif chemokine receptor 4 (Cxcr4), consequently increasing the ectopic localization of newborn neurons in the hilus. We also found that voluntary exercise in a running wheel suppressed this ectopic neurogenesis and countered the enhanced seizure susceptibility caused by prenatal VPA exposure, probably by normalizing the VPA-disrupted expression of multiple genes including Cxcr4 in adult NS/PCs. Replenishing Cxcr4 expression alone in NS/PCs was sufficient to overcome the aberrant migration of newborn neurons and increased seizure susceptibility in VPA-exposed mice. Thus, prenatal exposure to an AED, VPA, has a long-term effect on the behavior of NS/PCs in offspring, but this effect can be counteracted by a simple physical activity. Our findings offer a step to developing strategies for managing detrimental effects in offspring exposed to VPA in utero..
10. Katsunori Semi, Tsukasa Sanosaka, Masakazu Namihira, Kinichi Nakashima, Nuclear factor I/A coordinates the timing of oligodendrocyte differentiation/maturation via olig1 promoter methylation, HAYATI Journal of Biosciences, 10.4308/hjb.25.2.70, 25, 2, 70-78, 2018.04, Transcription factors (TFs) and epigenetic modifications function cooperatively to regulate various biological processes such as cell proliferation, differentiation, maturation, and metabolism. TF binding to regulatory regions of target genes controls their transcriptional activity through alteration of the epigenetic status around the binding regions, leading to transcription network formation regulating cell fates. Although nuclear factor I/A (Nfia) is a well-known TF that induces demethylation of astrocytic genes to confer astrocytic differentiation potential on neural stem/precursor cells (NS/PCs), the epigenetic role of NFIA in oligodendrocytic lineage progression remains unclear. Here, we show that oligodendrocyte differentiation/maturation is delayed in the brains of Nfia-knockout (KO) mice, and that NFIA-regulated DNA demethylation in NS/PCs plays an important role in determining the timing of their differentiation. We further demonstrate that the promoter activity of the oligodendrocyte transcription factor 1 (Olig1) gene, involved in oligodendrocyte differentiation/maturation, is suppressed by DNA methylation, which is in turn regulated by Nfia expression. Our results suggest that NFIA controls the timing of oligodendrocytic differentiation/ maturation via demethylation of cell-type-specific gene promoters..
11. Ayaka Kimura, Taito Matsuda, Atsuhiko Sakai, Naoya Murao, Kinichi Nakashima, HMGB2 expression is associated with transition from a quiescent to an activated state of adult neural stem cells, Developmental Dynamics, 10.1002/dvdy.24559, 247, 1, 229-238, 2018.01, Background: Although quiescent neural stem cells (NSCs) in the adult hippocampus proliferate in response to neurogenic stimuli and subsequently give rise to new neurons continuously throughout life, misregulation of NSCs in pathological conditions, including aging, leads to the impairment of learning and memory. High mobility group B family 1 (HMGB1) and HMGB2, HMG family proteins that function as transcriptional activators through the modulation of chromatin structure, have been assumed to play some role in the regulation of adult NSCs; however, their precise functions and even expression patterns in the adult hippocampus remain elusive. Results: Here we show that expression of HMGB2 but not HMGB1 is restricted to the subset of NSCs and their progenitors. Furthermore, running, a well-known positive neurogenic stimulus, increased the proliferation of HMGB2-expressing cells, whereas aging was accompanied by a marked decrease in these cells. Intriguingly, HMGB2-expressing quiescent NSCs, which were shifted toward the proliferative state, were decreased as aging progressed. Conclusions: HMGB2 expression is strongly associated with transition from the quiescent to the proliferative state of NSCs, supporting the possibility that HMGB2 is involved in the regulation of adult neurogenesis and can be used as a novel marker to identify NSCs primed for activation in the adult hippocampus. Developmental Dynamics 247:229–238, 2018..
12. Masahide Nakajo, Naohiro Uezono, Hideyuki Nakashima, Hidenori Wake, Setsuro Komiya, Masahiro Nishibori, Kinichi Nakashima, Therapeutic time window of anti-high mobility group box-1 antibody administration in mouse model of spinal cord injury, Neuroscience Research, 10.1016/j.neures.2018.03.004, 2018.01, Spinal cord injury (SCI) is a devastating neurologic disorder that often leads to permanent disability, and there is no effective treatment for it. High mobility group box-1 (HMGB1) is a damage-associated molecular protein that triggers sterile inflammation upon injuries. We have previously shown that two administrations of neutralizing monoclonal antibody (mAb) against HMGB1 (immediately after (0 h) and 6 h after) SCI dramatically improves functional recovery after SCI in mice. However, when considering clinical application, 0 h after SCI is not practical. Therefore, in this study, we examined the therapeutic time window of the mAb administration. Injection at 3 h after SCI significantly improved the functional recovery comparably to injection immediately after SCI, while injection at 6 h was less effective, and injection at 9 or 12 h had no therapeutic effect. We also found beneficial effects of injection at 3 h after injury on blood-spinal cord barrier maintenance, inflammatory-related gene expression and preservation of the damaged spinal cord tissue. Taken together, our results suggest that a single administration of anti-HMGB1 mAb within a proper time window could be a novel and potential therapeutic strategy for SCI..
13. Mizuki Honda, Kinichi Nakashima, Sayako Katada, Epigenetic Regulation of Human Neural Stem Cell Differentiation, Results and Problems in Cell Differentiation, 10.1007/978-3-319-93485-3_5, 125-136, 2018.01, Emerging evidence has demonstrated that epigenetic programs influence many aspects of neural stem cell (NSC) behavior, including proliferation and differentiation. It is becoming apparent that epigenetic mechanisms, such as DNA methylation, histone modifications, and noncoding RNA expression, are spatiotemporally regulated and that these intracellular programs, in concert with extracellular signals, ensure appropriate gene activation. Here we summarize recent advances in understanding of the epigenetic regulation of human NSCs directly isolated from the brain or produced from pluripotent stem cells (embryonic and induced pluripotent stem cells, respectively)..
14. Naoya Murao, Shuzo Matsubara, Taito Matsuda, Hirofumi Noguchi, Tetsuji Mutoh, Masahiro Mutoh, Haruhiko Koseki, Masakazu Namihira, Kinichi Nakashima, Np95/Uhrf1 regulates tumor suppressor gene expression of neural stem/precursor cells, contributing to neurogenesis in the adult mouse brain, Neuroscience Research, 10.1016/j.neures.2018.05.007, 2018.01, Adult neurogenesis is a process of generating new neurons from neural stem/precursor cells (NS/PCs) in restricted adult brain regions throughout life. It is now generally known that adult neurogenesis in the hippocampal dentate gyrus (DG) and subventricular zone participates in various higher brain functions, such as learning and memory formation, olfactory discrimination and repair after brain injury. However, the mechanisms underlying adult neurogenesis remain to be fully understood. Here, we show that Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90), which is an essential protein for maintaining DNA methylation during cell division, is involved in multiple processes of adult neurogenesis. Specific ablation of Np95 in adult NS/PCs (aNS/PCs) led to a decrease in their proliferation and an impairment of neuronal differentiation and to suppression of neuronal maturation associated with the impairment of dendritic formation in the hippocampal DG. We also found that deficiency of Np95 in NS/PCs increased the expression of tumor suppressor genes p16 and p53, and confirmed that expression of these genes in NS/PCs recapitulates the phenotype of Np95-deficient NS/PCs. Taken together, our findings suggest that Np95 plays an essential role in proliferation and differentiation of aNS/PCs through the regulation of tumor suppressor gene expression in adult neurogenesis..
15. Yoichiro Kawamura, Sayako Katada, Hirofumi Noguchi, Hiroyuki Yamamoto, Tsukasa Sanosaka, Koji Iihara, Kinichi Nakashima, Synergistic induction of astrocytic differentiation by factors secreted from meninges in the mouse developing brain, FEBS Letters, 10.1002/1873-3468.12881, 591, 22, 3709-3720, 2017.11, Astrocytes, which support diverse neuronal functions, are generated from multipotent neural stem/precursor cells (NS/PCs) during brain development. Although many astrocyte-inducing factors have been identified and studied in vitro, the regions and/or cells that produce these factors in the developing brain remain elusive. Here, we show that meninges-produced factors induce astrocytic differentiation of NS/PCs. Consistent with the timing when astrocytic differentiation of NS/PCs increases, expression of astrocyte-inducing factors is upregulated. Meningeal secretion-mimicking combinatorial treatment of NS/PCs with bone morphogenetic protein 4, retinoic acid and leukemia inhibitory factor synergistically activate the promoter of a typical astrocytic marker, glial fibrillary acidic protein. Taken together, our data suggest that meninges play an important role in astrocytic differentiation of NS/PCs in the developing brain..
16. Tsukasa Sanosaka, Takuya Imamura, Nobuhiko Hamazaki, Muh Chyi Chai, Katsuhide Igarashi, Maky Ideta-Otsuka, Fumihito Miura, Takashi Ito, Nobuyuki Fujii, Kazuho Ikeo, Kinichi Nakashima, DNA Methylome Analysis Identifies Transcription Factor-Based Epigenomic Signatures of Multilineage Competence in Neural Stem/Progenitor Cells, Cell Reports, 10.1016/j.celrep.2017.08.086, 20, 12, 2992-3003, 2017.09, Regulation of the epigenome during in vivo specification of brain stem cells is still poorly understood. Here, we report DNA methylome analyses of directly sampled cortical neural stem and progenitor cells (NS/PCs) at different development stages, as well as those of terminally differentiated cortical neurons, astrocytes, and oligodendrocytes. We found that sequential specification of cortical NS/PCs is regulated by two successive waves of demethylation at early and late development stages, which are responsible for the establishment of neuron- and glia-specific low-methylated regions (LMRs), respectively. The regulatory role of demethylation of the gliogenic genes was substantiated by the enrichment of nuclear factor I (NFI)-binding sites. We provide evidence that de novo DNA methylation of neuron-specific LMRs establishes glia-specific epigenotypes, essentially by silencing neuronal genes. Our data highlight the in vivo implications of DNA methylation dynamics in shaping epigenomic features that confer the differentiation potential of NS/PCs sequentially during development..
17. Mizuki Honda, Kinichi Nakashima, Sayako Katada, PRMT1 regulates astrocytic differentiation of embryonic neural stem/precursor cells, Journal of Neurochemistry, 10.1111/jnc.14123, 142, 6, 901-907, 2017.09, Arginine methylation is a post-translational modification which is catalyzed by protein arginine methyltransferases (PRMTs). Here, we report that PRMT1 is highly expressed in neural stem/precursor cells (NS/PCs) of mouse embryos, and knockdown of PRMT1 in NS/PCs suppresses the generation of astrocytes. The luciferase assay demonstrated that knockdown of PRMT1 inhibits activation of the promoter of a typical astrocytic marker gene, glial fibrillary acidic protein (Gfap), in NS/PCs. The transcription factor signal transducer and activator of transcription 3 (STAT3) is known to generally be critical for astrocytic differentiation of NS/PCs. We found that PRMT1 methylates arginine residue(s) of STAT3 to regulate its activity positively, resulting in the promotion of astrocytic differentiation of NS/PCs. (Figure presented.)..
18. Tetsuro Yasui, Naohiro Uezono, Hideyuki Nakashima, Hirofumi Noguchi, Taito Matsuda, Tomoko Noda-Andoh, Hideyuki Okano, Kinichi Nakashima, Hypoxia Epigenetically Confers Astrocytic Differentiation Potential on Human Pluripotent Cell-Derived Neural Precursor Cells, Stem Cell Reports, 10.1016/j.stemcr.2017.05.001, 8, 6, 1743-1756, 2017.06, Human neural precursor cells (hNPCs) derived from pluripotent stem cells display a high propensity for neuronal differentiation, but they require long-term culturing to differentiate efficiently into astrocytes. The mechanisms underlying this biased fate specification of hNPCs remain elusive. Here, we show that hypoxia confers astrocytic differentiation potential on hNPCs through epigenetic gene regulation, and that this was achieved by cooperation between hypoxia-inducible factor 1α and Notch signaling, accompanied by a reduction of DNA methylation level in the promoter region of a typical astrocyte-specific gene, Glial fibrillary acidic protein. Furthermore, we found that this hypoxic culture condition could be applied to rapid generation of astrocytes from Rett syndrome patient-derived hNPCs, and that these astrocytes impaired neuronal development. Thus, our findings shed further light on the molecular mechanisms regulating hNPC differentiation and provide attractive tools for the development of therapeutic strategies for treating astrocyte-mediated neurological disorders..
19. Rebecca Brulet, Taito Matsuda, Ling Zhang, Carlos Miranda, Mauro Giacca, Brian K. Kaspar, Kinichi Nakashima, Jenny Hsieh, NEUROD1 Instructs Neuronal Conversion in Non-Reactive Astrocytes, Stem Cell Reports, 10.1016/j.stemcr.2017.04.013, 8, 6, 1506-1515, 2017.06, Currently, all methods for converting non-neuronal cells into neurons involve injury to the brain; however, whether neuronal transdifferentiation can occur long after the period of insult remains largely unknown. Here, we use the transcription factor NEUROD1, previously shown to convert reactive glial cells to neurons in the cortex, to determine whether astrocyte-to-neuron transdifferentiation can occur under physiological conditions. We utilized adeno-associated virus 9 (AAV9), which crosses the blood-brain barrier without injury, to deliver NEUROD1 to astrocytes through an intravascular route. Interestingly, we found that a small, but significant number of non-reactive astrocytes converted to neurons in the striatum, but not the cortex. Moreover, astrocytes cultured to minimize their proliferative potential also exhibited limited neuronal transdifferentiation with NEUROD1 expression. Our results show that a single transcription factor can induce astrocyte-to-neuron conversion under physiological conditions, potentially facilitating future clinical approaches long after the acute injury phase..
20. Masahiro Uesaka, Kiyokazu Agata, Takao Oishi, Kinichi Nakashima, Takuya Imamura, Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals, BMC Genomics, 10.1186/s12864-017-3662-1, 18, 1, 2017.04, Background: Recent transcriptome analyses have shown that long non-coding RNAs (ncRNAs) play extensive roles in transcriptional regulation. In particular, we have reported that promoter-associated ncRNAs (pancRNAs) activate the partner gene expression via local epigenetic changes. Results: Here, we identify thousands of genes under pancRNA-mediated transcriptional activation in five mammalian species in common. In the mouse, 1) pancRNA-partnered genes confined their expression pattern to certain tissues compared to pancRNA-lacking genes, 2) expression of pancRNAs was significantly correlated with the enrichment of active chromatin marks, H3K4 trimethylation and H3K27 acetylation, at the promoter regions of the partner genes, 3) H3K4me1 marked the pancRNA-partnered genes regardless of their expression level, and 4) C- or G-skewed motifs were exclusively overrepresented between-200 and-1bp relative to the transcription start sites of the pancRNA-partnered genes. More importantly, the comparative transcriptome analysis among five different mammalian species using a total of 25 counterpart tissues showed that the overall pancRNA expression profile exhibited extremely high species-specificity compared to that of total mRNA, suggesting that interspecies difference in pancRNA repertoires might lead to the diversification of mRNA expression profiles. Conclusions: The present study raises the interesting possibility that the gain and/or loss of gene-activation-associated pancRNA repertoires, caused by formation or disruption of the genomic GC-skewed structure in the course of evolution, finely shape the tissue-specific pattern of gene expression according to a given species..
21. Nobuhiko Hamazaki, Kinichi Nakashima, Katsuhiko Hayashi, Takuya Imamura, Detection of bidirectional promoter-derived lncRNAs from small-scale samples using pre-amplification-free directional RNA-seq method, Methods in Molecular Biology, 10.1007/978-1-4939-6988-3_6, 83-103, 2017.01, Development of high-throughput sequencing technologies has uncovered the immensity of the long noncoding RNA (lncRNA) world. Divergently transcribed lncRNAs from bidirectional gene promoters, called promoter-associated noncoding RNAs (pancRNAs), account for ~20% of the total number of lncRNAs, and this major fraction is involved in many biological processes, such as development and cancer formation. Recently, we have found that the pancRNAs activate their partner genes, as represented by the fact that pancIl17d, a pancRNA that is transcribed from the antisense strand of the promoter region of Interleukin 17d (Il17d) at the onset of zygotic gene activation (ZGA), is essential for mouse preimplantation development through Il17d upregulation. The discovery of the expression of a specific set of pancRNAs during ZGA was achieved by using a method that generates directional RNA-seq libraries from small-scale samples. Although there are several methods available for small-scale samples, most of them require a pre-amplification procedure that frequently generates some amplification biases toward a subset of transcripts. We provide here a highly sensitive and reproducible method based on the preparation of directional RNA-seq libraries from as little as 100 mouse oocytes or embryos without pre-amplification for the quantification of lncRNAs as well as mRNAs..
22. Nobuhiko Hamazaki, Kinichi Nakashima, Takuya Imamura, Manipulation of promoter-associated noncoding RNAs in mouse early embryos for controlling sequence-specific epigenetic status, Methods in Molecular Biology, 10.1007/978-1-4939-6716-2_16, 271-282, 2017.01, In mammals, transcription in the zygote begins after fertilization. This transcriptional wave is called zygotic gene activation (ZGA). During ZGA, epigenetic modifications, such as DNA methylation and histone modifications, are dynamically and drastically reconstructed in a sequence-specific manner. However, how such orchestrated gene upregulation is regulated remains unknown. Recently, using microinjection techniques, we have revealed that a class of long noncoding RNAs, named promoter-associated noncoding RNAs (pancRNAs), mediates specific gene upregulation through promoter DNA demethylation during ZGA. Here, we describe the experimental methods available to control the expression levels of pancRNAs and to evaluate epigenetic status after pancRNA manipulation..
23. Orie Hikabe, Nobuhiko Hamazaki, Go Nagamatsu, Yayoi Obata, Yuji Hirao, Norio Hamada, So Shimamoto, Takuya Imamura, Kinichi Nakashima, Mitinori Saitou, Katsuhiko Hayashi, Reconstitution in vitro of the entire cycle of the mouse female germ line, Nature, 10.1038/nature20104, 539, 7628, 299-303, 2016.11, The female germ line undergoes a unique sequence of differentiation processes that confers totipotency to the egg. The reconstitution of these events in vitro using pluripotent stem cells is a key achievement in reproductive biology and regenerative medicine. Here we report successful reconstitution in vitro of the entire process of oogenesis from mouse pluripotent stem cells. Fully potent mature oocytes were generated in culture from embryonic stem cells and from induced pluripotent stem cells derived from both embryonic fibroblasts and adult tail tip fibroblasts. Moreover, pluripotent stem cell lines were re-derived from the eggs that were generated in vitro, thereby reconstituting the full female germline cycle in a dish. This culture system will provide a platform for elucidating the molecular mechanisms underlying totipotency and the production of oocytes of other mammalian species in culture..
24. Sumiyo Morita, Hirofumi Noguchi, Takuro Horii, Kazuhiko Nakabayashi, Mika Kimura, Kohji Okamura, Atsuhiko Sakai, Hideyuki Nakashima, Kenichiro Hata, Kinichi Nakashima, Izuho Hatada, Targeted DNA demethylation in vivo using dCas9-peptide repeat and scFv-TET1 catalytic domain fusions, Nature Biotechnology, 10.1038/nbt.3658, 34, 10, 1060-1065, 2016.10, Despite the importance of DNA methylation in health and disease, technologies to readily manipulate methylation of specific sequences for functional analysis and therapeutic purposes are lacking. Here we adapt the previously described dCas9-SunTag for efficient, targeted demethylation of specific DNA loci. The original SunTag consists of ten copies of the GCN4 peptide separated by 5-amino-acid linkers. To achieve efficient recruitment of an anti-GCN4 scFv fused to the ten-eleven (TET) 1 hydroxylase, which induces demethylation, we changed the linker length to 22 amino acids. The system attains demethylation efficiencies >50% in seven out of nine loci tested. Four of these seven loci showed demethylation of >90%. We demonstrate targeted demethylation of CpGs in regulatory regions and demethylation-dependent 1.7- to 50-fold upregulation of associated genes both in cell culture (embryonic stem cells, cancer cell lines, primary neural precursor cells) and in vivo in mouse fetuses..
25. Naoki Yamamoto, Kiyokazu Agata, Kinichi Nakashima, Takuya Imamura, Bidirectional promoters link cAMP signaling with irreversible differentiation through promoter-associated non-coding RNA (pancRNA) expression in PC12 cells, Nucleic Acids Research, 10.1093/nar/gkw113, 44, 11, 5105-5122, 2016.06, Bidirectional promoters are the major source of gene activation-associated noncoding RNA (ncRNA). PC12 cells offer an interesting model for understanding the mechanism underlying bidirectional promoter-mediated cell cycle control. Nerve growth factor (NGF)-stimulated PC12 cells elongate neurites, and are in a reversible cell-cycle-arrested state. In contrast, these cells irreversibly differentiate and cannot re-enter the normal cell cycle after NGF plus cAMP treatment. In this study, using directional RNA-seq, we found that bidirectional promoters for protein-coding genes with promoter-associated ncRNA (pancRNA) were enriched for cAMP response element consensus sequences, and were preferred targets for transcriptional regulation by the transcription factors in the cAMP-dependent pathway. A spindle-formation-associated gene, Nusap1 and pancNusap1 were among the most strictly co-transcribed pancRNA-mRNA pairs. This pancRNA-mRNA pair was specifically repressed in irreversibly differentiated PC12 cells. Knockdown (KD) and overexpression experiments showed that pancNusap1 positively regulated the Nusap1 expression in a sequence-specific manner, which was accompanied by histone acetylation at the Nusap1 promoter. Furthermore, pancNusap1 KD recapitulated the effects of cAMP on cell cycle arrest. Thus, we conclude that pancRNA-mediated histone acetylation contributes to the establishment of the cAMP-induced transcription state of the Nusap1 locus and contributes to the irreversible cell cycle exit for terminal differentiation of PC12 cells..
26. Hirofumi Noguchi, Naoya Murao, Ayaka Kimura, Taito Matsuda, Masakazu Namihira, Kinichi Nakashima, DNA methyltransferase 1 is indispensable for development of the hippocampal dentate gyrus, Journal of Neuroscience, 10.1523/JNEUROSCI.0512-16.2016, 36, 22, 6050-6068, 2016.06, Development of the hippocampal dentate gyrus (DG) in the mammalian brain is achieved through multiple processes during late embryonic and postnatal stages, with each developmental step being strictly governed by extracellular cues and intracellular mechanisms. Here, we show that the maintenance DNA methyltransferase 1 (Dnmt1) is critical for development of the DG in the mouse. Deletion of Dnmt1 in neural stem cells (NSCs) at the beginning of DG development led to a smaller size of the granule cell layer in the DG. NSCs lacking Dnmt1 failed to establish proper radial processes or to migrate into the subgranular zone, resulting in aberrant neuronal production in the molecular layer of the DG and a reduction of integrated neurons in the granule cell layer. Interestingly, prenatal deletion of Dnmt1 in NSCs affected not only the developmental progression of the DG but also the properties of NSCs maintained into adulthood: Dnmt1-deficient NSCs displayed impaired neurogenic ability and proliferation. We also found that Dnmt1 deficiency in NSCs decreased the expression of Reelin signaling components in the developing DG and increased that of the cell cycle inhibitors p21 and p57 in the adult DG. Together, these findings led us to propose that Dnmt1 functions as a key regulator to ensure the proper development of the DG, as well as the proper status of NSCs maintained into adulthood, by modulating extracellular signaling and intracellular mechanisms..
27. Koichiro Irie, Keita Tsujimura, Hideyuki Nakashima, Kinichi Nakashima, MicroRNA-214 promotes dendritic development by targeting the schizophrenia-associated gene quaking (Qki), Journal of Biological Chemistry, 10.1074/jbc.M115.705749, 291, 26, 13891-13904, 2016.06, Proper dendritic elaboration of neurons is critical for the formation of functional circuits during brain development. Defects in dendrite morphogenesis are associated with neuropsychiatric disorders, and microRNAs are emerging as regulators of aspects of neuronal maturation such as axonal and dendritic growth, spine formation, and synaptogenesis. Here, we show that miR-214 plays a pivotal role in the regulation of dendritic development. Overexpression of miR-214 increased dendrite size and complexity, whereas blocking of endogenous miR-214-3p, a mature form of miR-214, inhibited dendritic morphogenesis. We also found that miR-214-3p targets quaking (Qki), which is implicated in psychiatric diseases such as schizophrenia, through conserved target sites located in the 3′-untranslated region of Qki mRNA, thereby down-regulating Qki protein levels. Overexpression and knockdown of Qki impaired and enhanced dendritic formation, respectively. Moreover, overexpression of Qki abolished the dendritic growth induced by miR-214 overexpression. Taken together, our findings reveal a crucial role for the miR-214-Qki pathway in the regulation of neuronal dendritic development..
28. Kenji Ito, Tsukasa Sanosaka, Katsuhide Igarashi, Maky Ideta-Otsuka, Akira Aizawa, Yuichi Uosaki, Azumi Noguchi, Hirokazu Arakawa, Kinichi Nakashima, Takumi Takizawa, Identification of genes associated with the astrocyte-specific gene Gfap during astrocyte differentiation, Scientific Reports, 10.1038/srep23903, 6, 2016.04, Chromosomes and genes are non-randomly arranged within the mammalian cell nucleus, and gene clustering is of great significance in transcriptional regulation. However, the relevance of gene clustering and their expression during the differentiation of neural precursor cells (NPCs) into astrocytes remains unclear. We performed a genome-wide enhanced circular chromosomal conformation capture (e4C) to screen for genes associated with the astrocyte-specific gene glial fibrillary acidic protein (Gfap) during astrocyte differentiation. We identified 18 genes that were specifically associated with Gfap and expressed in NPC-derived astrocytes. Our results provide additional evidence for the functional significance of gene clustering in transcriptional regulation during NPC differentiation..
29. Hirofumi Noguchi, Ayaka Kimura, Naoya Murao, Masakazu Namihira, Kinichi Nakashima, Prenatal deletion of DNA methyltransferase 1 in neural stem cells impairs neurogenesis and causes anxiety-like behavior in adulthood, Neurogenesis, 10.1080/23262133.2016.1232679, 3, 1, 2016.01, Despite recent advances in our understanding of epigenetic regulation of central nervous system development, little is known regarding the effects of epigenetic dysregulation on neurogenesis and brain function in adulthood. In the present study, we show that prenatal deletion of DNA methyltransferase 1 (Dnmt1) in neural stem cells results in impaired neurogenesis as well as increases in inflammatory features (e.g., elevated glial fibrillary acidic protein [GFAP] expression in astrocytes and increased numbers of microglia) in the adult mouse brain. Moreover, these mice exhibited anxiety-like behavior during an open-field test. These findings suggest that Dnmt1 plays a critical role in regulating neurogenesis and behavior in the developing brain and into adulthood..
30. Naoya Murao, Hirofumi Noguchi, Kinichi Nakashima, Epigenetic regulation of neural stem cell property from embryo to adult, Neuroepigenetics, 10.1016/j.nepig.2016.01.001, 5, 1-10, 2016.01, Neural stem cells (NSCs) have the ability to self-renew and give rise to neurons and glial cells (astrocytes and oligodendrocytes) in the mammalian central nervous system. This multipotency is acquired by NSCs during development and is maintained throughout life. Proliferation, fate specification, and maturation of NSCs are regulated by both cell intrinsic and extrinsic factors. Epigenetic modification is a representative intrinsic factor, being involved in many biological aspects of central nervous system development and adult neurogenesis through the regulation of NSC dynamics. In this review, we summarize recent progress in the epigenetic regulation of NSC behavior in the embryonic and adult brain, with particular reference to DNA methylation, histone modification, and noncoding RNAs..
31. Berry Juliandi, Kentaro Tanemura, Katsuhide Igarashi, Takashi Tominaga, Yusuke Furukawa, Maky Otsuka, Noriko Moriyama, Daigo Ikegami, Masahiko Abematsu, Tsukasa Sanosaka, Keita Tsujimura, Minoru Narita, Jun Kanno, Kinichi Nakashima, Reduced Adult Hippocampal Neurogenesis and Cognitive Impairments following Prenatal Treatment of the Antiepileptic Drug Valproic Acid, Stem Cell Reports, 10.1016/j.stemcr.2015.10.012, 5, 6, 996-1009, 2015.12, Prenatal exposure to valproic acid (VPA), an established antiepileptic drug, has been reported to impair postnatal cognitive function in children born to VPA-treated epileptic mothers. However, how these defects arise and how they can be overcome remain unknown. Using mice, we found that comparable postnatal cognitive functional impairment is very likely correlated to the untimely enhancement of embryonic neurogenesis, which led to depletion of the neural precursor cell pool and consequently a decreased level of adult neurogenesis in the hippocampus. Moreover, hippocampal neurons in the offspring of VPA-treated mice showed abnormal morphology and activity. Surprisingly, these impairments could be ameliorated by voluntary running. Our study suggests that although prenatal exposure to antiepileptic drugs such as VPA may have detrimental effects that persist until adulthood, these effects may be offset by a simple physical activity such as running..
32. Hirofumi Noguchi, Ayaka Kimura, Naoya Murao, Taito Matsuda, Masakazu Namihira, Kinichi Nakashima, Expression of DNMT1 in neural stem/precursor cells is critical for survival of newly generated neurons in the adult hippocampus, Neuroscience Research, 10.1016/j.neures.2015.01.014, 95, 1-11, 2015.06, Adult neurogenesis persists throughout life in the dentate gyrus (DG) of the hippocampus, and its importance has been highlighted in hippocampus-dependent learning and memory. Adult neurogenesis consists of multiple processes: maintenance and neuronal differentiation of neural stem/precursor cells (NS/PCs), followed by survival and maturation of newborn neurons and their integration into existing neuronal circuitry. However, the mechanisms that govern these processes remain largely unclear. Here we show that DNA methyltransferase 1 (DNMT1), an enzyme responsible for the maintenance of DNA methylation, is highly expressed in proliferative cells in the adult DG and plays an important role in the survival of newly generated neurons. Deletion of Dnmt1 in adult NS/PCs (aNS/PCs) did not affect the proliferation and differentiation of aNS/PCs per se. However, it resulted in a decrease of newly generated mature neurons, probably due to gradual cell death after aNS/PCs differentiated into neurons in the hippocampus. Interestingly, loss of DNMT1 in post-mitotic neurons did not influence their survival. Taken together, these findings suggest that the presence of DNMT1 in aNS/PCs is crucial for the survival of newly generated neurons, but is dispensable once they accomplish neuronal differentiation in the adult hippocampus..
33. Felemban Athary Abdulhaleem M, Xiaohong Song, Rie Kawano, Naohiro Uezono, Ayako Ito, Giasuddin Ahmed, Mahmud Hossain, Kinichi Nakashima, Hideaki Tanaka, Kunimasa Ohta, Akhirin regulates the proliferation and differentiation of neural stem cells in intact and injured mouse spinal cord, Developmental Neurobiology, 10.1002/dneu.22238, 75, 5, 494-504, 2015.05, Although the central nervous system is considered a comparatively static tissue with limited cell turnover, cells with stem cell properties have been isolated from most neural tissues. The spinal cord ependymal cells show neural stem cell potential in vitro and in vivo in injured spinal cord. However, very little is known regarding the ependymal niche in the mouse spinal cord. We previously reported that a secreted factor, chick Akhirin, is expressed in the ciliary marginal zone of the eye, where it works as a heterophilic cell-adhesion molecule. Here, we describe a new crucial function for mouse Akhirin (M-AKH) in regulating the proliferation and differentiation of progenitors in the mouse spinal cord. During embryonic spinal cord development, M-AKH is transiently expressed in the central canal ependymal cells, which possess latent neural stem cell properties. Targeted inactivation of the AKH gene in mice causes a reduction in the size of the spinal cord and decreases BrdU incorporation in the spinal cord. Remarkably, the expression patterns of ependymal niche molecules in AKH knockout (AKH-/-) mice are different from those of AKH+/+, both in vitro and in vivo. Furthermore, we provide evidence that AKH expression in the central canal is rapidly upregulated in the injured spinal cord. Taken together, these results indicate that M-AKH plays a crucial role in mouse spinal cord formation by regulating the ependymal niche in the central canal..
34. Tomoko Andoh-Noda, Wado Akamatsu, Kunio Miyake, Takuya Matsumoto, Ryo Yamaguchi, Tsukasa Sanosaka, Yohei Okada, Tetsuro Kobayashi, Manabu Ohyama, Kinichi Nakashima, Hiroshi Kurosawa, Takeo Kubota, Hideyuki Okano, Differentiation of multipotent neural stem cells derived from Rett syndrome patients is biased toward the astrocytic lineage, Molecular Brain, 10.1186/s13041-015-0121-2, 8, 1, 2015.05, Background: Rett syndrome (RTT) is one of the most prevalent neurodevelopmental disorders in females, caused by de novo mutations in the X-linked methyl CpG-binding protein 2 gene, MECP2. Although abnormal regulation of neuronal genes due to mutant MeCP2 is thought to induce autistic behavior and impaired development in RTT patients, precise cellular mechanisms underlying the aberrant neural progression remain unclear. Results: Two sets of isogenic pairs of either wild-type or mutant MECP2-expressing human induced pluripotent stem cell (hiPSC) lines were generated from a single pair of 10-year-old RTT-monozygotic (MZ) female twins. Mutant MeCP2-expressing hiPSC lines did not express detectable MeCP2 protein during any stage of differentiation. The lack of MeCP2 reflected altered gene expression patterns in differentiated neural cells rather than in undifferentiated hiPSCs, as assessed by microarray analysis. Furthermore, MeCP2 deficiency in the neural cell lineage increased astrocyte-specific differentiation from multipotent neural stem cells. Additionally, chromatin immunoprecipitation (ChIP) and bisulfite sequencing assays indicated that anomalous glial fibrillary acidic protein gene (GFAP) expression in the MeCP2-negative, differentiated neural cells resulted from the absence of MeCP2 binding to the GFAP gene. Conclusions: An isogenic RTT-hiPSC model demonstrated that MeCP2 participates in the differentiation of neural cells. Moreover, MeCP2 deficiency triggers perturbation of astrocytic gene expression, yielding accelerated astrocyte formation from RTT-hiPSC-derived neural stem cells. These findings are likely to shed new light on astrocytic abnormalities in RTT, and suggest that astrocytes, which are required for neuronal homeostasis and function, might be a new target of RTT therapy..
35. Taito Matsuda, Naoya Murao, Yuki Katano, Berry Juliandi, Jun Kohyama, Shizuo Akira, Taro Kawai, Kinichi Nakashima, TLR9 signalling in microglia attenuates seizure-induced aberrant neurogenesis in the adult hippocampus, Nature Communications, 10.1038/ncomms7514, 6, 2015.03, Pathological conditions such as epilepsy cause misregulation of adult neural stem/progenitor populations in the adult hippocampus in mice, and the resulting abnormal neurogenesis leads to impairment in learning and memory. However, how animals cope with abnormal neurogenesis remains unknown. Here we show that microglia in the mouse hippocampus attenuate convulsive seizure-mediated aberrant neurogenesis through the activation of Toll-like receptor 9 (TLR9), an innate immune sensor known to recognize microbial DNA and trigger inflammatory responses. We found that microglia sense self-DNA from degenerating neurons following seizure, and secrete tumour necrosis factor-α, resulting in attenuation of aberrant neurogenesis. Furthermore, TLR9 deficiency exacerbated seizure-induced cognitive decline and recurrent seizure severity. Our findings thus suggest the existence of bidirectional communication between the innate immune and nervous systems for the maintenance of adult brain integrity..
36. Nobuhiko Hamazaki, Masahiro Uesaka, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura, Gene activation-associated long noncoding RNAs function in mouse preimplantation development, Development (Cambridge), 10.1242/dev.116996, 142, 5, 910-920, 2015.01, In mice, zygotic activation occurs for a wide variety of genes, mainly at the 2-cell stage. Long noncoding RNAs (lncRNAs) are increasingly being recognized as modulators of gene expression. In this study, directional RNA-seq of MII oocytes and 2-cell embryos identified more than 1000 divergently transcribed lncRNA/mRNA gene pairs. Expression of these bidirectional promoter-associated noncoding RNAs (pancRNAs) was strongly associated with the upregulation of their cognate genes. Conversely, knockdown of three abundant pancRNAs led to reduced mRNA expression, accompanied by sustained DNA methylation even in the presence of enzymes responsible for DNA demethylation. In particular, microinjection of siRNA against the abundant pancRNA partner of interleukin 17d (Il17d) mRNA at the 1-cell stage caused embryonic lethality, which was rescued by supplying IL17D protein in vitro at the 4-cell stage. Thus, this novel class of lncRNAs can modulate the transcription machinery in cis to activate zygotic genes and is important for preimplantation development..
37. Akihiro Nakamura, Hiroyuki Funaya, Naohiro Uezono, Kinichi Nakashima, Yasumasa Ishida, Tomohiro Suzuki, Shigeharu Wakana, Tomohiro Shibata, Low-cost three-dimensional gait analysis system for mice with an infrared depth sensor, Neuroscience Research, 10.1016/j.neures.2015.06.006, 100, 55-62, 2015.01, Three-dimensional (3D) open-field gait analysis of mice is an essential procedure in genetic and nerve regeneration research. Existing gait analysis systems are generally expensive and may interfere with the natural behaviors of mice because of optical markers and transparent floors. In contrast, the proposed system captures the subjects shape from beneath using a low-cost infrared depth sensor (Microsoft Kinect) and an opaque infrared pass filter. This means that we can track footprints and 3D paw-tip positions without optical markers or a transparent floor, thereby preventing any behavioral changes. Our experimental results suggest with healthy mice that they are more active on opaque floors and spend more time in the center of the open-field, when compared with transparent floors. The proposed system detected footprints with a comparable performance to existing systems, and precisely tracked the 3D paw-tip positions in the depth image coordinates..
38. Keita Tsujimura, Koichiro Irie, Hideyuki Nakashima, Yoshihiro Egashira, Yoichiro Fukao, Masayuki Fujiwara, Masayuki Itoh, Masahiro Uesaka, Takuya Imamura, Yasukazu Nakahata, Yui Yamashita, Takaya Abe, Shigeo Takamori, Kinichi Nakashima, MiR-199a Links MeCP2 with mTOR Signaling and Its Dysregulation Leads to Rett Syndrome Phenotypes, Cell Reports, 10.1016/j.celrep.2015.08.028, 12, 11, 1887-1901, 2015.01, Rett syndrome (RTT) is a neurodevelopmental disorder caused by MECP2 mutations. Although emerging evidence suggests that MeCP2 deficiency is associated with dysregulation of mechanistic target of rapamycin (mTOR), which functions as a hub for various signaling pathways, the mechanism underlying this association and the molecular pathophysiology of RTT remain elusive. We show here that MeCP2 promotes the posttranscriptional processing of particular microRNAs (miRNAs) as a component of the microprocessor Drosha complex. Among the MeCP2-regulated miRNAs, we found that miR-199a positively controls mTOR signaling by targeting inhibitors for mTOR signaling. miR-199a and its targets have opposite effects on mTOR activity, ameliorating and inducing RTT neuronal phenotypes, respectively. Furthermore, genetic deletion of miR-199a-2 led to a reduction of mTOR activity in the brain and recapitulated numerous RTT phenotypes in mice. Together, these findings establish miR-199a as a critical downstream target of MeCP2 in RTT pathogenesis by linking MeCP2 with mTOR signaling..
39. Naoya Murao, Taito Matuda, Hirofumi Noguchi, Haruhiko Koseki, Masakazu Namihira, Kinichi Nakashima, Characterization of Np95 expression in mouse brain from embryo to adult: A novel marker for proliferating neural stem/precursor cells, Neurogenesis, 10.4161/23262133.2014.976026, 1, 1, e976026, 2014.11, Nuclear protein 95 KDa (Np95, also known as UHRF1 or ICBP90) plays an important role in maintaining DNA methylation of newly synthesized DNA strands by recruiting DNA methyltransferase 1 (DNMT1) during cell division. In addition, Np95 participates in chromatin remodeling by interacting with histone modification enzymes such as histone deacetylases. However, its expression pattern and function in the brain have not been analyzed extensively. We here investigated the expression pattern of Np95 in the mouse brain, from developmental to adult stages. In the fetal brain, Np95 is abundantly expressed at the midgestational stage, when a large number of neural stem/precursor cells (NS/PCs) exist. Interestingly, Np95 is expressed specifically in NS/PCs but not in differentiated cells such as neurons or glial cells. Furthermore, we demonstrate that Np95 is preferentially expressed in type 2a cells, which are highly proliferative NS/PCs in the dentate gyrus of the adult hippocampus. Moreover, the number of Np95-expressing cells increases in response to kainic acid administration or to voluntary running, which are known to enhance the proliferation of adult NS/PCs. These results suggest that Np95 participates in the process of proliferation and differentiation of NS/PCs, and that it should be a useful novel marker for proliferating NS/PCs, facilitating the analysis of the complex behavior of NS/PCs in the brain..
40. Masahiko Abematsu, Kinichi Nakashima, Transplantation of neural stem cells with valproate for spinal cord injury, Neuroprotection and Regeneration of the Spinal Cord, 10.1007/978-4-431-54502-6_20, 9784431545026, 247-253, 2014.11, The regenerative capacity of an injured spinal cord is limited, and once paralysis occurs, it is difficult to improve the situation. We have developed a treatment method called the HINT method (HDAC Inhibitor and Neural stem cell Transplantation) that improves hind limb motor functionality in mice with severe spinal cord injuries by using a combination of antiepileptic drugs and neural stem cells. This chapter will introduce you to the new neural damage reconstruction mechanism employed in the HINT method..
41. Weixiang Guo, Keita Tsujimura, Maky Otsuka I, Koichiro Irie, Katsuhide Igarashi, Kinichi Nakashima, Xinyu Zhao, VPA alleviates neurological deficits and restores gene expression in a mouse model of rett syndrome, PLoS One, 10.1371/journal.pone.0100215, 9, 6, 2014.06, Rett syndrome (RTT) is a devastating neurodevelopmental disorder that occurs once in every 10,000-15,000 live female births. Despite intensive research, no effective cure is yet available. Valproic acid (VPA) has been used widely to treat mood disorder, epilepsy, and a growing number of other disorders. In limited clinical studies, VPA has also been used to control seizure in RTT patients with promising albeit somewhat unclear efficacy. In this study we tested the effect of VPA on the neurological symptoms of RTT and discovered that short-term VPA treatment during the symptomatic period could reduce neurological symptoms in RTT mice. We found that VPA restores the expression of a subset of genes in RTT mouse brains, and these genes clustered in neurological disease and developmental disorder networks. Our data suggest that VPA could be used as a drug to alleviate RTT symptoms..
42. Naoki Yamamoto, Masahiro Uesaka, Takuya Imamura, Kinichi Nakashima, Roles of Epigenetics in the Neural Stem Cell and Neuron, Epigenetics in Psychiatry, 10.1016/B978-0-12-417114-5.00004-8, 51-78, 2014.06, For higher-order functions of the mammalian brain such as the regulation of motor behavior, consciousness, emotion, learning, and memory, neurons have to establish complicated and elaborate networks. In addition, the functions of neurons are critically supported by glial cells (astrocytes and oligodendrocytes). All of these neural cell types (i.e., neurons, astrocytes, and oligodendrocytes) are generated from common neural stem cells (NSCs), which also have self-renewal activity. Accumulating evidence suggests that the behavior of NSCs is influenced spatiotemporally by both cell-extrinsic factors, including cytokine signaling, and cell-intrinsic epigenetic changes, which together regulate the proliferation and fate decisions of NSCs to produce glial cells or neurons, including different neuronal subtypes, in a spatiotemporal manner. In the first half of this chapter, we summarize recent advances in elucidating the role of epigenetic control in the differentiation of NSCs. In postmitotic neurons, as well as NSCs, several orchestrated epigenetic mechanisms underlie neuronal functioning critical for memory formation. Recent studies have revealed the presence and physiological significance of changes of the epigenetic modifications within a neuron of an already defined cell fate. A dynamic change of epigenetic status induced by neuronal activity can alter synaptic plasticity, which constitutes part of the mechanisms of learning and memory. In the latter half of the chapter, we describe the role of epigenetic plasticity in non-dividing neurons. We also discuss the robust identity of the neuronal cell fate, as exemplified by the extremely poor ability of neurons to be reprogrammed to pluripotent stem cells..
43. Sang Hoon Yi, Xi Biao He, Yong Hee Rhee, Chang Hwan Park, Takumi Takizawa, Kinichi Nakashima, Sang Hun Lee, Foxa2 acts as a co-activator potentiating expression of the Nurr1-induced DA phenotype via epigenetic regulation, Development (Cambridge), 10.1242/dev.095802, 141, 4, 761-772, 2014.02, Understanding how dopamine (DA) phenotypes are acquired in midbrain DA (mDA) neuron development is important for bioassays and cell replacement therapy for mDA neuron-associated disorders. Here, we demonstrate a feed-forward mechanism of mDA neuron development involving Nurr1 and Foxa2. Nurr1 acts as a transcription factor for DA phenotype gene expression. However, Nurr1-mediated DA gene expression was inactivated by forming a protein complex with CoREST, and then recruiting histone deacetylase 1 (Hdac1), an enzyme catalyzing histone deacetylation, to DA gene promoters. Coexpression of Nurr1 and Foxa2 was established in mDA neuron precursor cells by a positive cross-regulatory loop. In the presence of Foxa2, the Nurr1-CoREST interaction was diminished (by competitive formation of the Nurr1-Foxa2 activator complex), and CoRESTHdac1 proteins were less enriched in DA gene promoters. Consequently, histone 3 acetylation (H3Ac), which is responsible for open chromatin structures, was strikingly increased at DA phenotype gene promoters. These data establish the interplay of Nurr1 and Foxa2 as the crucial determinant for DA phenotype acquisition during mDA neuron development..
44. Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura, Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals, BMC Genomics, 10.1186/1471-2164-15-35, 15, 1, 2014.01, Background: The majority of non-coding RNAs (ncRNAs) involved in mRNA metabolism in mammals have been believed to downregulate the corresponding mRNA expression level in a pre- or post-transcriptional manner by forming short or long ncRNA-mRNA duplex structures. Information on non-duplex-forming long ncRNAs is now also rapidly accumulating. To examine the directional properties of transcription at the whole-genome level, we performed directional RNA-seq analysis of mouse and chimpanzee tissue samples.Results: We found that there is only about 1% of the genome where both the top and bottom strands are utilized for transcription, suggesting that RNA-RNA duplexes are not abundantly formed. Focusing on transcription start sites (TSSs) of protein-coding genes revealed that a significant fraction of them contain switching-points that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription is more prevalent than previously thought. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Genes with tissue-specific promoter-associated ncRNAs (pancRNAs) show a positive correlation between the expression of their pancRNA and mRNA, which is in accord with the proposed role of pancRNA in facultative gene activation, whereas genes with constitutive expression generally lack pancRNAs.Conclusions: We propose that single-stranded ncRNA resulting from head-to-head transcription at GC-rich sequences regulates tissue-specific gene expression..
45. Nunung Yuniarti, Berry Juliandi, Chai MuhChyi, Hirofumi Noguchi, Tsukasa Sanosaka, Kinichi Nakashima, Prenatal exposure to suberoylanilide hydroxamic acid perturbs corticogenesis, Neuroscience Research, 10.1016/j.neures.2013.06.004, 77, 1-2, 42-49, 2013.09, Suberoylanilide hydroxamic acid (SAHA) is one of the epidrugs developed for cancer treatment that works epigenetically by inhibiting histone deacetylases (HDACs). SAHA has been reported to diffuse across the placenta and found in fetal plasma in preclinical study, implying that it can influence fetus if taken by pregnant cancer patients. However, report regarding this aspect and the study of in utero HDAC inhibition by SAHA especially on fate specification of neural stem/progenitor cells within the developing mammalian cortex, is yet unavailable. Here we show that transient exposure of SAHA to mouse embryos during prominent neurogenic period resulted in an enhancement of cortical neurogenesis, which is accompanied by an increased expression of proneuronal transcription factor Neurog1. Neurogenesis was enhanced due to the increase number of proliferating Tbr2+ intermediate progenitor cells following SAHA exposure. In this relation, we observed that SAHA perturbed neonatal cortical lamination because of the increased production of Cux1+ and Satb2+ upper-layer neurons, and decreased that of Ctip2+ deep-layer neurons. Furthermore, an upper-layer neuronal lineage determinant Satb2 was also up-regulated, whereas those of deep-layer ones Fezf2 and Ctip2 were down-regulated by SAHA treatment. Taken together, our study suggests that proper regulation of HDACs is important for precise embryonic corticogenesis..
46. Satoshi Urayama, Katsunori Semi, Tsukasa Sanosaka, Yukina Hori, Masakazu Namihira, Jun Kohyama, Takumi Takizawa, Kinichi Nakashima, Chromatin accessibility at a STAT3 target site is altered prior to astrocyte differentiation, Cell Structure and Function, 10.1247/csf.12034, 38, 1, 55-66, 2013, DNA demethylation of astrocyte-specific gene promoters and STAT3 activation in neural precursor cells (NPCs) are essential for astrogliogenesis in the developing brain. To date, it remains unclear whether DNA methylation is the sole epigenetic determinant responsible for suppressing astrocyte-specific genes. Here, we used mouse embryonic stem cells (TKO ESCs) that lacked all 3 DNA methyltransferase genes, Dnmt1, Dnmt3a, and Dnmt3b, and thereby exhibit complete demethylation of the astrocyte-specific glial fibrillary acidic protein (Gfap) gene promoter. We found that although the Gfap promoter was demethylated, STAT3 failed to bind to its cognate element to induce Gfap transcription, whereas it induced transcription of a different target gene, Socs3. Moreover, although the Gfap promoter region containing the STAT3-binding site (GSBS) is enriched with transcription-repressive histone modifications, such as methylation of H3 at lysine 9 (H3K9me3) and H3K27me3, the reduction of these modifications in TKO ESCs was not sufficient for binding of STAT3 at GSBS. Furthermore, GSBS was digested by micrococcal nuclease in late-gestational NPCs that express GFAP upon LIF stimulation, but not in cells that show no expression of GFAP even in the presence of LIF, indicating that STAT3 can access GSBS in the former cells. We further showed that expression of NF-1A, which is known to potentiate differentiation of mid-gestational NPCs into astrocytes, increased its accessibility. Taken together, our results suggest that chromatin accessibility of GSBS plays a critical role in the regulation of Gfap expression..