* … corresponding author
† … These authors contributed equally to this work.
[Myogenesis] … Skeletal Muscle differentiation/regeneration
[Transcriptomics] … Chromatin/Epigenomics/NGS
[Method] … Methodological papers
Bold title … Selected Papers

2024

• [Transcriptomics]Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility.
  Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y.
  Nat Genet. 2024 Feb 15. doi: 10.1038/s41588-024-01658-1. [Pubmed]
• [Transcriptomics]Genome-wide mapping and cryo-EM structural analyses of the overlapping tri-nucleosome composed of hexasome-hexasome-octasome moieties.
  Nishimura M#, Fujii T#, Tanaka H, Maehara K, Morishima K, Shimizu M, Kobayashi Y, Nozawa K, Takizawa Y, Sugiyama M, Ohkawa Y*, Kurumizaka H*.
  Commun Biol. 2024 Jan 8;7(1):61. doi: 10.1038/s42003-023-05694-1. [Pubmed]

2023

• [Transcriptomics]Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8.
  Hirai S, Kujirai T, Akatsu M, Ogasawara M, Ehara H, Sekine SI, Ohkawa Y, Takizawa Y, Kurumizaka H.
  J Biochem. 2023 Nov 30;174(6):549-559. doi: 10.1093/jb/mvad069. [Pubmed]
• [Transcriptomics]Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure.
  Oka M, Otani M, Miyamoto Y, Oshima R, Adachi J, Tomonaga T, Asally M, Nagaoka Y, Tanaka K, Toyoda A, Ichikawa K, Morishita S, Isono K, Koseki H, Nakato R*, Ohkawa Y*, Yoneda Y*.
  Cell Rep. 2023 Aug 29;42(8):112884. doi: 10.1016/j.celrep.2023.112884. Epub 2023 Jul 29. [Pubmed]
• [Transcriptomics]FOXK1 promotes nonalcoholic fatty liver disease by mediating mTORC1-dependent inhibition of hepatic fatty acid oxidation.
  Fujinuma S, Nakatsumi H, Shimizu H, Sugiyama S, Harada A, Goya T, Tanaka M, Kohjima M, Takahashi M, Izumi Y, Yagi M, Kang D, Kaneko M, Shigeta M, Bamba T, Ohkawa Y, Nakayama KI.
  Cell Rep. 2023 May 30;42(5):112530. doi: 10.1016/j.celrep.2023.112530. Epub 2023 May 18. [Pubmed]
• [Transcriptomics]Design and implementation of a hybrid cloud system for large-scale human genomic research.
  Nagasaki M, Sekiya Y, Asakura A, Teraoka R, Otokozawa R, Hashimoto H, Kawaguchi T, Fukazawa K, Inadomi Y, Murata KT, Ohkawa Y, Yamaguchi I, Mizuhara T, Tokunaga K, Sekiya Y, Hanawa T, Yamada R, Matsuda F.
  Hum Genome Var. 2023 Feb 8;10(1):6. doi: 10.1038/s41439-023-00231-2. [Pubmed]
• [Myogenesis]Senescence atlas reveals an aged-like inflamed niche that blunts muscle regeneration.
  Moiseeva V, Cisneros A, Sica V, Deryagin O, Lai Y, Jung S, Andrés E, An J, Segalés J, Ortet L, Lukesova V, Volpe G, Benguria A, Dopazo A, Benitah SA, Urano Y, Del Sol A, Esteban MA, Ohkawa Y, Serrano AL, Perdiguero E, Muñoz-Cánoves P.
  Nature. 2023 Jan;613(7942):169-178. doi: 10.1038/s41586-022-05535-x. Epub 2022 Dec 21. [Pubmed]

2022

• [Transcriptomics]STREAMING-tag system reveals spatiotemporal relationships between transcriptional regulatory factors and transcriptional activity.
  Ohishi H, Shimada S, Uchino S, Li J, Sato Y, Shintani M, Owada H, Ohkawa Y, Pertsinidis A, Yamamoto T, Kimura H, Ochiai H.
  Nat Commun. 2022 Dec 20;13(1):7672. doi: 10.1038/s41467-022-35286-2. [Pubmed]
• [Transcriptomics]Prostaglandin E2 receptor Ptger4b regulates female-specific peptidergic neurons and female sexual receptivity in medaka.
  Fleming T, Kikuchi Y, Nakajo M, Tachizawa M, Inazumi T, Tsuchiya S, Sugimoto Y, Saito D, Suyama M, Ohkawa Y, Baba T, Morohashi KI, Okubo K.
  Commun Biol. 2022 Nov 10;5(1):1215. doi: 10.1038/s42003-022-04195-x. [Pubmed]
• [Transcriptomics]Tmsb10 triggers fetal Leydig differentiation by suppressing the RAS/ERK pathway.
  Inoue M, Baba T, Takahashi F, Terao M, Yanai S, Shima Y, Saito D, Sugihara K, Miura T, Takada S, Suyama M, Ohkawa Y, Morohashi KI.
  Commun Biol. 2022 Sep 15;5(1):974. doi: 10.1038/s42003-022-03941-5. [Pubmed]
• [Transcriptomics]Drosophila transcription factor NF-Y suppresses transcription of the lipase 4 gene, a key gene for lipid storage.
  Yoshioka Y, Anzai K, Kowada R, Hiratsuka K, Hirayabu T, Yasuda M, Ohkawa Y, Sato T, Suyama M, Yoshida H, Yamaguchi M.
  Exp Cell Res. 2022 Nov 1;420(1):113307. doi: 10.1016/j.yexcr.2022.113307. Epub 2022 Aug 24. [Pubmed]
• [Transcriptomics]Identification of a drug-response gene in multiple myeloma through longitudinal single-cell transcriptome sequencing.
  Masuda T, Haji S, Nakashima Y, Tsuda M, Kimura D, Takamatsu A, Iwahashi N, Umakoshi H, Shiratsuchi M, Kikutake C, Suyama M, Ohkawa Y, Ogawa Y.
  iScience. 2022 Jul 19;25(8):104781. doi: 10.1016/j.isci.2022.104781. eCollection 2022 Aug 19. [Pubmed]
• [Transcriptomics]Photo-isolation chemistry for high-resolution and deep spatial transcriptome with mouse tissue sections.
  Honda M, Kimura R, Harada A, Maehara K, Tanaka K, Ohkawa Y*, Oki S*.
  STAR Protoc. 2022 Apr 22;3(2):101346. doi: 10.1016/j.xpro.2022.101346. eCollection 2022 Jun 17. [Pubmed]
• [Transcriptomics]Tenogenic Induction From Induced Pluripotent Stem Cells Unveils the Trajectory Towards Tenocyte Differentiation.
  Yoshimoto Y, Uezumi A, Ikemoto-Uezumi M, Tanaka K, Yu X, Kurosawa T, Yambe S, Maehara K, Ohkawa Y, Sotomaru Y, Shukunami C.
  Front Cell Dev Biol. 2022 Mar 9;10:780038. doi: 10.3389/fcell.2022.780038. eCollection 2022. [Pubmed]
• [Transcriptomics]A spinal microglia population involved in remitting and relapsing neuropathic pain.
  Kohno K, Shirasaka R, Yoshihara K, Mikuriya S, Tanaka K, Takanami K, Inoue K, Sakamoto H, Ohkawa Y, Masuda T, Tsuda M.
  Science. 2022 Apr;376(6588):86-90. doi: 10.1126/science.abf6805. Epub 2022 Mar 31. [Pubmed]
• [Transcriptomics]Uterus-specific transcriptional regulation underlies eggshell pigment production in Japanese quail.
  Ishishita S, Kitahara S, Takahashi M, Iwasaki S, Tatsumoto S, Hara I, Kaneko Y, Kinoshita K, Yamaguchi K, Harada A, Ohmori Y, Ohkawa Y, Go Y, Shigenobu S, Matsuda Y, Suzuki T.
  PLoS One. 2022 Mar 10;17(3):e0265008. doi: 10.1371/journal.pone.0265008. eCollection 2022. [Pubmed]
• [Myogenesis]Uhrf1 governs the proliferation and differentiation of muscle satellite cells.
  Sakai H, Sawada Y, Tokunaga N, Tanaka K, Nakagawa S, Sakakibara I, Ono Y, Fukada SI, Ohkawa Y, Kikugawa T, Saika T, Imai Y.
  iScience. 2022 Feb 14;25(3):103928. doi: 10.1016/j.isci.2022.103928. eCollection 2022 Mar 18. [Pubmed]

2021

• [Transcriptomics]Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections.
  Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, Ohkawa Y*. Mol Syst Biol. 2021 Nov;17(11):e10323. doi: 10.15252/msb.202110323.  [PubMed]
  
• [Transcriptomics]Neural stem/precursor cells dynamically change their epigenetic landscape to differentially respond to BMP signaling for fate switching during brain development.
  Katada S, Takouda J, Nakagawa T, Honda M, Igarashi K, Imamura T, Ohkawa Y, Sato S, Kurumizaka H, Nakashima K.
  Genes Dev. 2021 Nov 1;35(21-22):1431-1444.  doi:10.1101/gad.348797.121. [Pubmed]
• [Transcriptomics]Recent advances in single-cell epigenomics. Harada A, Kimura H, Ohkawa Y*.
  Curr Opin Struct Biol. 2021 Jul 21;71:116-122. doi: 10.1016/j.sbi.2021.06.010. Review. [PubMed]
• [Transcriptomics][Method]High-depth spatial transcriptome analysis by photo-isolation chemistry.
  Honda M, Oki S, Kimura R, Harada A, Maehara K, Tanaka K, Meno C, Ohkawa Y*.
  Nat Commun. 2021 Jul 20;12(1):4416. doi: 10.1038/s41467-021-24691-8. [PubMed]
• [Transcriptomics]An extensive and dynamic trans-omic network illustrating prominent regulatory mechanisms in response to insulin in the liver.
  Matsuzaki F, Uda S, Yamauchi Y, Matsumoto M, Soga T, Maehara K, Ohkawa Y, Nakayama KI, Kuroda S, Kubota H.
  Cell Rep. 2021 Aug 24;36(8):109569. doi: 10.1016/j.celrep.2021.109569. [PubMed]
• [Transcriptomics]Integrated Analysis of Transcriptome and Histone Modifications in Granulosa Cells During Ovulation in Female Mice.
  Shirafuta Y, Tamura I, Ohkawa Y, Maekawa R, Doi-Tanaka Y, Takagi H, Mihara Y, Shinagawa M, Taketani T, Sato S, Tamura H, Sugino N.
  Endocrinology. 2021 Sep 1;162(9):bqab128. doi: 10.1210/endocr/bqab128. [PubMed]
• [Transcriptomics]Totipotency of mouse zygotes extends to single blastomeres of embryos at the four-cell stage.
  Maemura M, Taketsuru H, Nakajima Y, Shao R, Kakihara A, Nogami J, Ohkawa Y, Tsukada YI. Sci Rep. 2021 May 27;11(1):11167. doi: 10.1038/s41598-021-90653-1. [PubMed]
• [Transcriptomics]Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle.
  Yoshioka K, Nagahisa H, Miura F, Araki H, Kamei Y, Kitajima Y, Seko D, Nogami J, Tsuchiya Y, Okazaki N, Yonekura A, Ohba S, Sumita Y, Chiba K, Ito K, Asahina I, Ogawa Y, Ito T, Ohkawa Y, Ono Y. Sci Adv. 2021 Jun 9;7(24):eabd7924. doi: 10.1126/sciadv.abd7924. [PubMed]
• [Transcriptomics]Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts.
  Miyawaki-Kuwakado A, Wu Q, Harada A, Tomimatsu K, Fujii T, Maehara K, Ohkawa Y*. Genes Cells. 2021 May 13. doi: 10.1111/gtc.12870. [PubMed]
• [Transcriptomics]Chromatin structure-dependent histone incorporation revealed by a genome-wide deposition assay.
  Tachiwana H, Dacher M, Maehara K, Harada A, Seto Y, Katayama R, Ohkawa Y, Kimura H, Kurumizaka H, Saitoh N. Elife. 2021 May 10;10:e66290. doi: 10.7554/eLife.66290. [PubMed]
• [Transcriptomics]Targeted inhibition of EPAS1-driven IL-31 production by a small-molecule compound.
  Kamikaseda Y, Uruno T, Kunimura K, Harada A, Saiki K, Oisaki K, Sakata D, Nakahara T, Kido-Nakahara M, Kanai M, Nakamura S, Ohkawa Y, Furue M, Fukui Y. J Allergy Clin Immunol. 2021 Apr 2:S0091-6749(21)00551-0. doi: 10.1016/j.jaci.2021.03.029. [PubMed]
• [Transcriptomics]H4K20me1 and H3K27me3 are concurrently loaded onto the inactive X chromosome but dispensable for inducing gene silencing.
  Tjalsma SJD, Hori M, Sato Y, Bousard A, Ohi A, Raposo AC, Roensch J, Le Saux A, Nogami J, Maehara K, Kujirai T, Handa T, Bagés-Arnal S, Ohkawa Y, Kurumizaka H, da Rocha ST, Żylicz JJ, Kimura H, Heard E. EMBO Rep. 2021 Mar 3;22(3):e51989. doi: 10.15252/embr.202051989.[PubMed]
• [Myogenesis][Transcriptomics]Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle.
  Wu Q, Fujii T, Harada A, Tomimatsu K, Miyawaki-Kuwakado A, Fujita M, Maehara K, Ohkawa Y*. J Biochem. 2021 Jan 21:mvab001. doi: 10.1093/jb/mvab001.[PubMed]
• [Transcriptomics]Gene expression and functional abnormalities in XX/Sry Leydig cells.
  Yanai S, Baba T, Inui K, Miyabayashi K, Han S, Inoue M, Takahashi F, Kanai Y, Ohkawa Y, Choi MH, Morohashi KI. Sci Rep. 2021 Jan 12;11(1):719. doi: 10.1038/s41598-020-80741-z.[PubMed]
• [Transcriptomics]Transcription factor C/EBPβ induces genome-wide H3K27ac and upregulates gene expression during decidualization of human endometrial stromal cells.
  Tamura I, Maekawa R, Jozaki K, Ohkawa Y, Takagi H, Doi-Tanaka Y, Shirafuta Y, Mihara Y, Taketani T, Sato S, Tamura H, Sugino N. Mol Cell Endocrinol. 2021 Jan 15;520:111085. doi: 10.1016/j.mce.2020.111085.[PubMed]

2020

• [Transcriptomics]Subnuclear gene positioning through lamina association affects copper tolerance.
  Sakamoto Y, Sato M, Sato Y, Harada A, Suzuki T, Goto C, Tamura K, Toyooka K, Kimura H, Ohkawa Y, Hara-Nishimura I, Takagi S, Matsunaga S.
  Nat Commun. 2020 Nov 20;11(1):5914. doi: 10.1038/s41467-020-19621-z.[PubMed]
• [Transcriptomics]Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input.
  Handa T#, Harada A#, Maehara K#, Sato S, Nakao M, Goto N, Kurumizaka H, Ohkawa Y*, Kimura H*
  Nat Protoc. 2020 Oct;15(10):3334-3360. doi: 10.1038/s41596-020-0375-8.[PubMed]
• [Transcriptomics]Direct reprogramming of human umbilical vein- and peripheral blood-derived endothelial cells into hepatic progenitor cells.
  Inada H, Udono M, Matsuda-Ito K, Horisawa K, Ohkawa Y, Miura S, Goya T, Yamamoto J, Nagasaki M, Ueno K, Saitou D, Suyama M, Maehara Y, Kumamaru W, Ogawa Y, Sekiya S, Suzuki A
  Nat Commun. 2020 Oct 21;11(1):5292. doi: 10.1038/s41467-020-19041-z.[PubMed]
• [Transcriptomics]The Dynamics of Transcriptional Activation by Hepatic Reprogramming Factors.
  Horisawa K, Udono M, Ueno K, Ohkawa Y, Nagasaki M, Sekiya S, Suzuki A.
  Mol Cell. 2020 Jul 27:S1097-2765(20)30502-5. doi: 10.1016/j.molcel.2020.07.012. [PubMed]
• [Transcriptomics]Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.
  Ochiai H, Hayashi T, Umeda M, Yoshimura M, Harada A, Shimizu Y, Nakano K, Saitoh N, Liu Z, Yamamoto T, Okamura T, Ohkawa Y, Kimura H, Nikaido I.
  Sci Adv. 2020 Jun 17;6(25):eaaz6699. doi: 10.1126/sciadv.aaz6699. [PubMed]
• [Transcriptomics]Genomic Profiling by ALaP-Seq Reveals Transcriptional Regulation by PML Bodies through DNMT3A Exclusion.
  Kurihara M, Kato K, Sanbo C, Shigenobu S, Ohkawa Y, Fuchigami T, Miyanari Y.
  Mol Cell. 2020 May 7;78(3):493-505.e8. doi: 10.1016/j.molcel.2020.04.004. [PubMed]
• [Transcriptomics]TKIs induce alternative spliced BCR-ABLIns35bp variant via inhibition of RNA polymerase Ⅱ on genomic BCR-ABL.
  Yuda J, Odawara J, Minami M, Muta T, Kohno K, Tanimoto K, Eto T, Shima T, Kikushige Y, Kato K, Takenaka K, Iwasaki H, Minami Y, Ohkawa Y, Akashi K, Miyamoto T.
  Cancer Sci. 2020 Apr 21. doi: 10.1111/cas.14424. [PubMed]
• [Transcriptomics]The role of galanin in the differentiation of mucosal mast cells in mice.
  Yamaguchi T, Ikeda Y, Tashiro K, Ohkawa Y, Kawabata K.
  Eur J Immunol. 2020 Jan;50(1):110-118. doi: 10.1002/eji.201848061. [PubMed]

2019

• [Transcriptomics]Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells.
  Oka M, Mura S, Otani M, Miyamoto Y, Nogami J, Maehara K, Harada A, Tachibana T, Yoneda Y, Ohkawa Y.
  Elife. 2019 Nov 22;8. pii: e46667. doi: 10.7554/eLife.46667.[PubMed]
• [Transcriptomics]Cell competition corrects noisy Wnt morphogen gradients to achieve robust patterning in the zebrafish embryo.
  Akieda Y, Ogamino S, Furuie H, Ishitani S, Akiyoshi R, Nogami J, Masuda T, Shimizu N, Ohkawa Y, Ishitani T.
  Nat Commun. 2019 Oct 17;10(1):4710. doi: 10.1038/s41467-019-12609-4. [PubMed]
• [Myogenesis][Transcriptomics] Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle.
  Fukuda S, Kaneshige A, Kaji T, Noguchi YT, Takemoto Y, Zhang L, Tsujikawa K, Kokubo H, Uezumi A, Maehara K, Harada A, Ohkawa Y, Fukada SI.
  Elife. 2019 Sep 23;8. pii: e48284. doi: 10.7554/eLife.48284. [PubMed]
• [Transcriptomics] The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis.
  Abdalla MOA, Yamamoto T, Maehara K, Nogami J, Ohkawa Y, Miura H, Poonperm R, Hiratani I, Nakayama H, Nakao M, Saitoh N.
  Nat Commun. 2019 Aug 22;10(1):3778. doi: 10.1038/s41467-019-11378-4. [PubMed]
• [Transcriptomics] Biochemical analysis of nucleosome targeting by Tn5 transposase.
  Sato S, Arimura Y, Kujirai T, Harada A, Maehara K, Nogami J, Ohkawa Y, Kurumizaka H.
  Open Biol. 2019 Aug 30;9(8):190116. doi: 10.1098/rsob.190116. [PubMed]
• [Transcriptomics] Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes.
  Konno D, Kishida C, Maehara K, Ohkawa Y, Kiyonari H, Okada S, Matsuzaki F.
  Development. 2019 Aug 1. pii: dev.174243. doi: 10.1242/dev.174243. [PubMed]
• [Myogenesis][Transcriptomics] Calcineurin broadly regulates the initiation of skeletal muscle-specific gene expression by binding target promoters and facilitating the interaction of the SWI/SNF chromatin remodeling enzyme.
  Witwicka H, Nogami J, Syed SA, Maehara K, Padilla-Benavides T, Ohkawa Y, Imbalzano AN.
  Mol Cell Biol. 2019 Jul 15.;pii: MCB.00063-19. doi: 10.1128/MCB.00063-19. [PubMed]
• [Transcriptomics] Regulation of ectopic heterochromatin-mediated epigenetic diversification by the JmjC family protein Epe1.
  Sorida M, Hirauchi T, Ishizaki H, Kaito W, Shimada A, Mori C, Chikashige Y, Hiraoka Y, Suzuki Y, Ohkawa Y, Kato H, Takahata S, Murakami Y.
  PLoS Genet. 2019 Jun 17;15(6):e1008129. doi: 10.1371/journal.pgen.1008129. [PubMed]
• [Transcriptomics] CLEC3A, MMP7, and LCN2 as novel markers for predicting recurrence in resected G1 and G2 pancreatic neuroendocrine tumors.
  Miki M, Oono T, Fujimori N, Takaoka T, Kawabe K, Miyasaka Y, Ohtsuka T, Saito D, Nakamura M, Ohkawa Y, Oda Y, Suyama M, Ito T, Ogawa Y.
  Cancer Med. 2019 May 25. doi: 10.1002/cam4.2232. [PubMed]
• [Transcriptomics] Anti-tumour effects of antimicrobial peptides, components of the innate immune system, against haematopoietic tumours in Drosophila mxc mutants.
  Araki M, Kurihara M, Kinoshita S, Awane R, Sato T, Ohkawa Y, Inoue YH.
  Dis Model Mech. 2019 Jun 18;12(6). pii: dmm037721. doi: 10.1242/dmm.037721. [PubMed]
• [Transcriptomics] Modeling latent flows on single-cell data using the Hodge decomposition.
  Maehara K, *Ohkawa Y
  bioRxiv. March 28, 2019. doi: https://doi.org/10.1101/592089 [biorxiv]
• [Transcriptomics] Macrophage centripetal migration drives spontaneous healing process after spinal cord injury.
  Kobayakawa K, Ohkawa Y, Yoshizaki S, Tamaru T, Saito T, Kijima K, Yokota K, Hara M, Kubota K, Matsumoto Y, Harimaya K, Ozato K, Masuda T, Tsuda M, Tamura T, Inoue K, Edgerton VR, Iwamoto Y, Nakashima Y, Okada S.
  Sci Adv. May 15;5(5):eaav5086. doi: 10.1126/sciadv.aav5086. [PubMed]
• [Transcriptomics] A chromatin integration labeling method enables epigenomic profiling with lower input.
  †Harada A, †Maehara K, †Handa T, Arimura Y, Nogami J, Hayashi-Takanaka Y, Shirahige K, Kurumizaka H, *Kimura H, and *Ohkawa Y.
  Nat Cell Biol. Feb;21(2):287-296. doi: 10.1038/s41556-018-0248-3. [PubMed]
• [Transcriptomics] Transcriptome profiling of refractory atopic keratoconjunctivitis by RNA sequencing.
  Matsuda A, Asada Y, Suita N, Iwamoto S, Hirakata T, Yokoi N, Ohkawa Y, Okada Y, Yokomizo T, Ebihara N.
  J Allergy Clin Immunol. 2019 Apr;143(4):1610-1614.e6. doi: 10.1016/j.jaci.2018.11.007. [PubMed]
• [Transcriptomics] miR-124 dosage regulates prefrontal cortex function by dopaminergic modulation.
  Kozuka T, Omori Y, Watanabe S, Tarusawa E, Yamamoto H, Chaya T, Furuhashi M, Morita M, Sato T, Hirose S, Ohkawa Y, Yoshimura Y, Hikida T, Furukawa T.
  Sci Rep. 2019 Mar 5;9(1):3445. doi: 10.1038/s41598-019-38910-2. Feb;21(2):287-296. doi: 10.1038/s41556-018-0248-3. [PubMed]
• [Transcriptomics] Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones.
  Katoh-Fukui Y, Baba T, Sato T, Otake H, Nagakui-Noguchi Y, Shindo M, Suyama M, Ohkawa Y, Tsumura H, Morohashi KI, Fukami M.
  Bone. 2019 Mar;120:219-231. doi: 10.1016/j.bone.2018.10.021. [PubMed]
• [Transcriptomics] Locomotor Training Increases Synaptic Structure With High NGL-2 Expression After Spinal Cord Hemisection.
  Kobayakawa K, DePetro KA, Zhong H, Pham B, Hara M, Harada A, Nogami J, Ohkawa Y, Edgerton VR.
  Neurorehabil Neural Repair. 2019 Mar;33(3):225-231. doi: 10.1177/1545968319829456. [PubMed]
• [Transcriptomics] Cell-autonomous and redundant roles of Hey1 and HeyL in muscle stem cells: HeyL requires Hes1 to bind diverse DNA sites.
  Noguchi YT, Nakamura M, Hino N, Nogami J, Tsuji S, Sato T, Zhang L, Tsujikawa K, Tanaka T, Izawa K, Okada Y, Doi T, Kokubo H, Harada A, Uezumi A, Gessler M, Ohkawa Y, Fukada SI.
  Development. 2019 Feb 20;146(4). pii: dev163618. doi: 10.1242/dev.163618. [PubMed]
• [Transcriptomics] Pathological changes of distal motor neurons after complete spinal cord injury.
  Yokota K, Kubota K, Kobayakawa K, Saito T, Hara M, Kijima K, Maeda T, Katoh H, Ohkawa Y, Nakashima Y, Okada S.
  Mol Brain. 2019 Jan 9;12(1):4. doi: 10.1186/s13041-018-0422-3. [PubMed]

2018

• [Myogenesis][Transcriptomics]Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration.
  †Harada A, †Maehara K, Ono Y, Taguchi H, Yoshioka K, Kitajima Y, Xie Y, Sato Y, Iwasaki T, Nogami J, Okada S, Komatsu T, Semba Y, Takemoto T, Kimura H, Kurumizaka H, *Ohkawa Y.
  Nat Commun. 2018 Apr [PubMed]
• [Transcriptomics] Fetal Leydig cells dedifferentiate and serve as adult Leydig stem cells.
  Shima Y, Miyabayashi K, Sato T, Suyama M, Ohkawa Y, Doi M, Okamura H, Suzuki K.
  Development. 2018 Dec [PubMed]
• [Transcriptomics] [Transcriptomics] Cancer-associated mutations of histones H2B, H3.1 and H2A.Z.1 affect the structure and stability of the nucleosome.
  Arimura Y, Ikura M, Fujita R, Noda M, Kobayashi W, Horikoshi N, Sun J, Shi L, Kusakabe M, Harata M, Ohkawa Y, Tashiro S, Kimura H, Ikura T, Kurumizaka H.
  Nucleic Acids Res. 2018 Nov [PubMed]
• Prolonged inhibition of hepatocellular carcinoma cell proliferation by combinatorial expression of defined transcription factors.
  Takashima Y, Horisawa K, Udono M, Ohkawa Y, Suzuki A.
  Cancer Sci. 2018 Nov [PubMed]
• [Transcriptomics] Mouse polycomb group gene Cbx2 promotes osteoblastic but suppresses adipogenic differentiation in postnatal long bones.
  Katoh-Fukui Y, Baba T, Sato T, Otake H, Nagakui-Noguchi Y, Shindo M, Suyama M, Ohkawa Y, Tsumura H, Morohashi KI, Fukami M.
  Bone. 2018 Oct [PubMed]
• [Transcriptomics]MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast.
  Luo D, Kato D, Nogami J, Ohkawa Y, Kurumizaka H, Kono H.
  Nucleic Acids Res. 2018 Jun [PubMed]
• [Transcriptomics]Genome-wide analysis of the spatiotemporal regulation of firing and dormant replication origins in human cells.
  Sugimoto N, Maehara K, Yoshida K, Ohkawa Y, Fujita M.
  Nucleic Acids Res. 2018 Jun [PubMed]
• [Transcriptomics]Ad4BP/SF-1 regulates cholesterol synthesis to boost the production of steroids.
  Baba T, Otake H, Inoue M, Sato T, Ishihara Y, Moon JY, Tsuchiya M, Miyabayashi K, Ogawa H, Shima Y, Wang L, Sato R, Yamazaki T, Suyama M, Nomura M, Choi MH, Ohkawa Y, Morohashi KI.
  Commun Biol. 2018 Mar [PubMed]
• [Transcriptomics]The Autism-Related Protein CHD8 Cooperates with C/EBPβ to Regulate Adipogenesis.
  Kita Y, Katayama Y, Shiraishi T, Oka T, Sato T, Suyama M, Ohkawa Y, Miyata K, Oike Y, Shirane M, Nishiyama M, Nakayama KI.
  Cell Rep. 2018 May [PubMed]
• [Transcriptomics]Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence.
  Takizawa Y, Tanaka H, Machida S, Koyama M, Maehara K, Ohkawa Y, Wade PA, Wolf M, Kurumizaka H.
  Open Biol. 2018 Mar [PubMed]
• [Transcriptomics]Direct Reprogramming of Spiral Ganglion Non-neuronal Cells into Neurons: Toward Ameliorating Sensorineural Hearing Loss by Gene Therapy.
  Noda T, Meas SJ, Nogami J, Amemiya Y, Uchi R, Ohkawa Y, Nishimura K, Dabdoub A.
  Front Cell Dev Biol. 2018 Feb [PubMed]
• [Transcriptomics] Identification of miR-305, a microRNA that promotes aging, and its target mRNAs in Drosophila.
  Ueda M, Sato T, Ohkawa Y, Inoue YH.
  Genes Cells. 2018 Feb;23(2):80-93. [PubMed]
• [Method]Sensitive detection of fluorescence in western blotting by merging images.
  Kondo Y, Higa S, Iwasaki T, Matsumoto T, Maehara K, Harada A, Baba Y, Fujita M, *Ohkawa Y.
  PLoS One. 2018 Jan 19;13(1):e0191532. [PubMed]

2017

• [Myogenesis] [Review]Temporal regulation of chromatin during myoblast differentiation.
  Harada A, Ohkawa Y*, Imbalzano AN*.
  Semin Cell Dev Biol. 2017 Dec;72:77-86. Review. [PubMed]
• [Transcriptomics] Ser7 of RNAPII-CTD facilitates heterochromatin formation by linking ncRNA to RNAi.
  Kajitani T, Kato H, Chikashige Y, Tsutsumi C, Hiraoka Y, Kimura H, Ohkawa Y,Obuse C, Hermand D, Murakami Y.
  Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11208-E11217. [PubMed]
• [Transcriptomics] Histone methyltransferase G9a is a key regulator of the starvation-induced behaviors in Drosophila melanogaster.
  Shimaji K, Tanaka R, Maeda T, Ozaki M, Yoshida H, Ohkawa Y, Sato T, Suyama M, Yamaguchi M.
  Sci Rep. 2017 Nov 7;7(1):14763. [PubMed]
• [Method] Biochemical and immunological characterization of a novel monoclonal antibody against mouse leukotriene B4 receptor 1.
  Sasaki F, Koga T, Saeki K, Okuno T, Kazuno S, Fujimura T, Ohkawa Y, Yokomizo T.
  PLoS One. 2017 Sep 18;12(9):e0185133. [PubMed]
• [Myogenesis]The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation.
  Kudou K, Komatsu T, Nogami J, Maehara K, Harada A, Saeki H, Oki E, Maehara Y, *Ohkawa Y.
  Open Biol. 2017 Sep;7(9). [PubMed]
• [Transcriptomics] The novel heme-dependent inducible protein, SRRD regulates heme biosynthesis and circadian rhythms.
  Adachi Y, Umeda M, Kawazoe A, Sato T, Ohkawa Y, Kitajima S, Izawa S, Sagami I, Taketani S.
  Arch Biochem Biophys. 2017 Oct 1;631:19-29. [PubMed]
• [Transcriptomics] Persistent detection of alternatively spliced BCR-ABL variant results in a failure to achieve deep molecular response.
  Yuda J, Miyamoto T, Odawara J, Ohkawa Y, Semba Y, Hayashi M, Miyamura K, Tanimoto M, Yamamoto K, Taniwaki M, Akashi K.
  Cancer Sci. 2017 Aug 12. [PubMed]
• [Transcriptomics] Evolution of the sperm methylome of primates is associated with retrotransposon insertions and genome instability.
  Fukuda K, Inoguchi Y, Ichiyanagi K, Ichiyanagi T, Go Y, Nagano M, Yanagawa Y, Takaesu N, Ohkawa Y, Imai H, Sasaki H.
  Hum Mol Genet. 2017 Jun 20. [PubMed]
• [Transcriptomics] Interaction of reactive astrocytes with type I collagen induces astrocytic scar formation through the integrin-N-cadherin pathway after spinal cord injury.
  Hara M, Kobayakawa K, Ohkawa Y, Kumamaru H, Yokota K, Saito T, Kijima K, Yoshizaki S, Harimaya K, Nakashima Y, Okada S.
  Nat Med. 2017 Jul;23(7):818-828. [PubMed]
• [Transcriptomics]Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells.
  Semba Y, Harada A, Maehara K, Oki S, Meno C, Ueda J, Yamagata K, Suzuki A, Onimaru M, Nogami J, Okada S, Akashi K, *Ohkawa Y
  Nucleic Acids Res. 2017 May 26. [PubMed]
• [Transcriptomics] Crystal structure of the overlapping dinucleosome composed of hexasome and octasome.
  Kato D, Osakabe A, Arimura Y, Mizukami Y, Horikoshi N, Saikusa K, Akashi S, Nishimura Y, Park SY, Nogami J, Maehara K, Ohkawa Y, Matsumoto A, Kono H, Inoue R, Sugiyama M, Kurumizaka H*.
  Science 2017 Apr 14. [PubMed]
• [Transcriptomics]Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8
  Taguchi H, Xie Y, Horikoshi N, Maehara K, Harada A, Nogami J, Sato K, Arimura Y, Osakabe A, Kujirai T, Iwasaki T, Semba Y, Tachibana T, Kimura H, Ohkawa Y*, and Kurumizaka H*
  Biochemistry 2017 Apr 10. [PubMed]
• [Transcriptomics]Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis.
  Ueda J*†, Harada A†, Urahama T, Machida S, Maehara K, Hada M, Makino Y, Nogami J, Horikoshi N, Osakabe A, Taguchi H, Tanaka H, Tachiwana H, Yao T, Yamada M, Iwamoto T, Isotani A, Ikawa M, Tachibana T,Okada Y, Kimura H, Ohkawa Y, Kurumizaka H, Yamagata K.
  Cell Rep. 2017 Jan 17;18(3):593-600. [PubMed]
• [Transcriptomics] Periostin Promotes Scar Formation through the Interaction between Pericytes and InfiltratingMonocytes/Macrophages after Spinal Cord Injury.
  Yokota K, Kobayakawa K, Saito T, Hara M, Kijima K, Ohkawa Y, Harada A, Okazaki K, Ishihara K, Yoshida S, Kudo A, Iwamoto Y, Okada S.
  Am J Pathol. 2017 Jan 9. pii: S0002-9440(16)30531-4. [PubMed]
• [Transcriptomics] Control of tissue size and development by a regulatory element in the yorkie 3’UTR.
  Umegawachi T, Yoshida H, Koshida H, Yamada M, Ohkawa Y, Sato T, Suyama M, Krause HM, Yamaguchi M.
  Am J Cancer Res. 2017 Mar 1;7(3):673-687. [PubMed]
• [Transcriptomics] Thymine DNA glycosylase modulates DNA damage response and gene expression by base excision repair-dependent and independent mechanisms.
  Nakamura T, Murakami K, Tada H, Uehara Y, Nogami J, Maehara K, Ohkawa Y, Saitoh H, Nishitani H, Ono T, Nishi R, Yokoi M, Sakai W, Sugasawa K.
  Genes Cells. 2017 Apr;22(4):392-405. [PubMed]
• [Transcriptomics] Role of Ad4-binding protein/steroidogenic factor 1 in regulating NADPH production in adrenocortical Y-1 cells.
  Li B, Baba T, Miyabayashi K, Sato T, Shima Y, Ichinose T, Miura D, Ohkawa Y, Suyama M, Morohashi KI.
  Endocr J. 2017 Mar 31;64(3):315-324. [PubMed]
• [Transcriptomics] Differential lactate and cholesterol synthetic activities in XY and XX Sertoli cells.
  Shishido Y, Baba T, Sato T, Shima Y, Miyabayashi K, Inoue M, Akiyama H, Kimura H, Kanai Y, Ishihara Y, Haraguchi S, Miyazaki A, Rozman D, Yamazaki T, Choi MH, Ohkawa Y, Suyama M, Morohashi KI.
  Sci Rep. 2017 Feb 2;7:41912. [PubMed]

2016

• [Transcriptomics] Alterations in Fetal Leydig Cell Gene Expression during Fetal and Adult Development.
  Miyabayashi K, Shima Y, Inoue M, Sato T, Baba T, Ohkawa Y, Suyama M, Morohashi KI.
  Sex Dev. 2016 Dec 14.[PubMed]
• [Transcriptomics] GWAS of clinically defined gout and subtypes identifies multiple susceptibility loci that include uratetransporter genes.
  Nakayama A, Nakaoka H, Yamamoto K, Sakiyama M, Shaukat A, Toyoda Y,Okada Y, Kamatani Y, Nakamura T, Takada T , Inoue K, Yasujima T, Yuasa H, Shirahama Y, Nakashima H, Shimizu S, Higashino T, Kawamura Y, Ogata H, Kawaguchi M, Ohkawa Y, Danjoh I, Tokumasu A, Ooyama K, Ito T, Kondo T, Wakai K, Stiburkova B, Pavelka K, Stamp LK, Dalbeth N; Eurogout Consortium, Sakurai Y, Suzuki H, Hosoyamada M, Fujimori S, Yokoo T, Hosoya T, Inoue I, Takahashi A, Kubo M, Ooyama H, Shimizu T, Ichida K, Shinomiya N, Merriman TR, Matsuo H.
  Ann Rheum Dis. 2016 Nov 29. pii: annrheumdis-2016-209632.[PubMed]
• [Method] A One-Step Immunostaining Method to Visualize Rodent Muscle Fiber Type within a Single Specimen.
  Sawano S, Komiya Y, Ichitsubo R, Ohkawa Y, Nakamura M, Tatsumi R, Ikeuchi Y, Mizunoya W.
  PLoS One. 2016 Nov 4;11(11):e0166080.[PubMed]
• [Method] Identification of Immunoglobulin Gene Sequences from a Small Read Number of mRNA-Seq Using Hybridomas.
  Kuniyoshi Y†, Maehara K†, Iwasaki T, Hayashi M, Semba Y, Fujita M, Sato Y, Kimura H, Harada A, *Ohkawa Y.
  PLoS One. 2016 Oct 27;11(10):e0165473.[PubMed]
• [Transcriptomics] CHD8 haploinsufficiency results inautistic-like phenotypes in mice.
  Katayama Y, Nishiyama M, Shoji H, Ohkawa Y, Kawamura A, Sato T, Suyama M, Takumi T, Miyakawa T, Nakayama KI.
  Nature. 2016 Sep 7.[PubMed]
• [Transcriptomics] MRG15 is required for pre-mRNA splicing and spermatogenesis.
  Iwamori N, Tominaga K, Sato T, Riehle K, Iwamori T, Ohkawa Y, Coarfa C, Ono E, Matzuk MM.
  Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):E5408-15.[PubMed]
• [Transcriptomics] LATS2 Positively Regulates Polycomb Repressive Complex 2.
  Torigata K, Daisuke O, Mukai S, Hatanaka A, Ohka F, Motooka D, Nakamura S,Ohkawa Y, Yabuta N, Kondo Y, Nojima H.
  PLoS One. 2016 Jul 19;11(7):e0158562.[PubMed]
• [Transcriptomics] TLR signals posttranscriptionally regulate the cytokine trafficking mediator sortilin.
  Yabe-Wada T*, Matsuba S, Takeda K, Sato T, Suyama M, Ohkawa Y, Takai T, Shi H, Philpott CC, Nakamura A.
  Sci Rep. 2016 May 25;6:26566.[PubMed]
• [Transcriptomics] The feasibility of in vivo imaging of infiltrating blood cells for predicting the functional prognosis after spinal cord injury.
  Yokota K, Saito T, Kobayakawa K, Kubota K, Hara M, Murata M, Ohkawa Y, Iwamoto Y, Okada S.
  Sci Rep. 2016 May 9;6:25673.[PubMed]
• [Transcriptomics] Histone H4 lysine 20 acetylation is associated with gene repression in human cells.
  Kaimori JY†, Maehara K†, Hayashi-Takanaka Y, Harada A, Fukuda M, Yamamoto S, Ichimaru N, Umehara T, Yokoyama S, Matsuda R, Ikura T, Nagao K, Obuse C, Nozaki N, Takahara S, Takao T, Ohkawa Y, Kimura H, Isaka Y.
  Sci Rep. 2016 Apr 11;6:24318.[PubMed]
• [Transcriptomics] Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing.
  Kobayashi W, Takaku M, Machida S, Tachiwana H, Maehara K, Ohkawa Y, Kurumizaka H.
  Sci Rep. 2016 Apr 7;6:24228.[PubMed]
• [Transcriptomics] Structure and function of human histone H3.Y nucleosome.
  Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H.
  Nucleic Acids Res. 2016 Mar 25.[PubMed]
• [Transcriptomics]Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2.
  Hayashi M, Maehara K, Harada A, Semba Y, Kudo K, Takahashi H, Oki S, Meno C, Ichiyanagi K, Akashi K, *Ohkawa Y.
  J Cell Biochem 2016 Mar;117(3):780-92.[PubMed]
• [Transcriptomics] Identification of low-abundance proteins in serum via the isolation of HSP72 complexes.
  Tanaka M, *Shiota M, Nakao T, Uemura R, Nishi S, Ohkawa Y, Matsumoto M, Yamaguchi M, Osada-Oka M, Inagaki A, Takahashi K, Nakayama KI, Gi M, Izumi Y, Miura K, Iwao H.
  J Proteomics. 2016 Mar 16;136:214-21. pii: S1874-3919(16)30010-0.[PubMed]
• [Transcriptomics] Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis.
  Urahama T, Harada A, Maehara K, Horikoshi N, Sato K, Sato Y, Shiraishi K, Sugino N, Osakabe A, Tachiwana H, Kagawa W, Kimura H, Ohkawa Y, Kurumizaka H.
  Epigenetics＆Chromatin. 2016 Jan 15;9:2.[PubMed]
• [Transcriptomics] Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes.
  Oka M*, Mura S, Yamada K, Sangel P, Hirata S, Maehara K, Kawakami K, Tachibana T, Ohkawa Y, Kimura H, Yoneda Y.
  Elife. 2016 Jan 7;5. pii: e09540.[PubMed]
• [Transcriptomics] Isolation and characterization of fetal Leydig progenitor cells of male mice.
  Inoue M, Shima Y, Miyabayashi K, Tokunaga K, Sato T, Baba T, Ohkawa Y, Akiyama H, Suyama M, Morohashi KI.
  Endocrinology. 2016 Mar;157(3):1222-33.[PubMed]
• [Transcriptomics]Exploration of nucleosome positioning patterns in transcription factor function.
  Maehara K, *Ohkawa Y.
  Sci Rep. 2016 Jan 21;6:19620.[PubMed]

2015

• [Transcriptomics] Histone chaperone CAF-1 mediates repressive histone modifications to protect preimplantation mouse embryos from endogenous retrotransposons.
  Hatanaka Y, Inoue K, Oikawa M, Kamimura S, Ogonuki N, Kodama EN, Ohkawa Y, Tsukada Y, Ogura A.
  Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14641-6.[PubMed]
• [Transcriptomics] Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA.
  Osakabe A, Adachi F, Arimura Y, Maehara K, Ohkawa Y, Kurumizaka H.
  Open Biol. 2015 Oct 7;5(10).[PubMed]
• [Myogenesis]Tissue-specific expression of histone H3 variants diversified after species separation.
  Maehara K, Harada A, Sato Y, Matsumoto M,Nakayama K, Kimura H, *Ohkawa Y.
  Epigenetics＆Chromatin 2015 Sep 17;8:35.[PubMed]
• [Transcriptomics] Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies.
  Hayashi-Takanaka Y, Maehara K, Harada A, Umehara T, Yokoyama S, Obuse C, Ohkawa Y, Nozaki N, Kimura H.
  Chromosome Res. 2015 Dec;23(4):753-66.[PubMed]
• [Transcriptomics] Genomewide identification of target genes of histone methyltransferase dG9a during Drosophila embryogenesis.
  Shimaji K, Konishi T, Tanaka S, Yoshida H, Kato Y, Ohkawa Y, Sato T, Suyama M, Kimura H,Yamaguchi M.
  Genes Cells. 2015 Nov;20(11):902-14.[PubMed]
• [Transcriptomics] Engrafted Neural Stem/Progenitor Cells Promote Functional Recovery through Synapse Reorganization with Spared Host Neurons after Spinal Cord Injury.
  Yokota K, Kobayakawa K, Kubota K, Miyawaki A, Okano H, Ohkawa Y, Iwamoto Y, Okada S.
  Sci Rep. 2015 Aug 11;5(2):264-77.[PubMed]
• [Transcriptomics] foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka.
  Nishimura T, Sato T, Yamamoto Y, Watakabe I, Ohkawa Y, Suyama M, Kobayashi S, Tanaka M.
  Science. 2015 Jul 17;349(6245):328-31.[PubMed]
• [Myogenesis] Opposing calcium-dependent signalling pathways control skeletal muscle differentiation by regulating a chromatin remodelling enzyme.
  Nasipakb B, Padilla-Benavides T, Green K, Leszyk J, Mao W, Konda S, Sif S, Shaffer S, Ohkawa Y, Imbalzano AN.
  Nat Commun. 2015 Jun 17;6:7441.[PubMed]
• [Method]agplus: a rapid and flexible tool for aggregation plots.
  Maehara K, *Ohkawa Y.
  Bioinformatics 2015 Sep 15;31(18):3046-7.[PubMed]
• [Transcriptomics] Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture.
  Sugimoto N, Maehara K, Yoshida K, Yasukouchi S, Osano S, Watanabe S, Aizawa M, Yugawa T, Kiyono T, Kurumizaka H, Ohkawa Y, Fujita M.
  Nucleic Acids Res. 2015 Jul 13;43(12):5898-911.[PubMed]
• [Transcriptomics] PSMC5, a 19S Proteasomal ATPase, Regulates Cocaine Action in the Nucleus Accumbens.
  Ohnishi YH, Ohnishi YN, Nakamura T, Ohno M, Kennedy PJ, Ohkawa Y, Nishi A, Neve R, Tsuzuki T, Nestler EJ.
  PLoS One. 2015 May 11;10(5):e0126710.[PubMed]
• [Transcriptomics] A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation.
  Tomita S, Abdalla MO, Fujiwara S, Matsumori H, Maehara K, Ohkawa Y, Iwase H, Saitoh N, Nakao M.
  Nat Commun. 2015 Apr 29;6:6966.[PubMed]
• [Transcriptomics] SWI/SNF chromatin-remodeling complexes function in noncoding RNA-dependent assembly of nuclear bodies.
  Kawaguchi T, Tanigawa A, Naganuma T, Ohkawa Y, Souquere S, Pierron G, Hirose T.
  Proc Natl Acad Sci U S A. 2015 Apr 7;112(14):4304-9.[PubMed]
• [Myogenesis]Spatial re-organization of myogenic regulatory sequences temporally controls gene expression.
  
  Harada A, Mallappa C, Okada S, Butler JT, Baker SP, Lawrence JB, *Ohkawa Y, *Imbalzano AN.
  Nucleic Acids Res. 2015 Feb 27;43(4):2008-21.[PubMed]
• [Transcriptomics] MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex.
  Takahashi H, Takigawa I, Watanabe M, Anwar D, Shibata M, Tomomori-Sato C, Sato S, Ranjan A, Seidel CW, Tsukiyama T, Mizushima W, Hayashi M, Ohkawa Y, Conaway JW, Conaway RC, Hatakeyama S.
  Nat Commun. 2015 Jan 9;6:5941.[PubMed]
• [Myogenesis]Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle.
  Harada A, Maehara K, Sato Y, Konno D, Tachibana T, Kimura H, *Ohkawa Y.
  Nucleic Acids Res. 2015 Jan 43(2):775-86.[PubMed]
• [Transcriptomics] A genome-wide analysis identifies a notch-RBP-Jκ-IL-7Rα axis that controls IL-17-producing γδ T cell homeostasis in mice.
  Nakamura M, Shibata K, Hatano S, Sato T, Ohkawa Y, Yamada H, Ikuta K, Yoshikai Y.
  J Immunol. 2015 Jan 1;194(1):243-51.[PubMed]

2014

• [Transcriptomics] Interleukin-10-producing plasmablasts exert regulatory function in autoimmune inflammation.
  Matsumoto M, Baba A, Yokota T, Nishikawa H, Ohkawa Y, Kayama H, Kallies A, Nutt SL, Sakaguchi S, Takeda K, Kurosaki T, Baba Y.
  Immunity. 2014 Dec 18;41(6):1040-51.[PubMed]
• [Transcriptomics] SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data.
  *Oki S, Maehara K, Ohkawa Y, Meno C.
  Genes Cells. 2014 Oct 17 ;19(12):919-26.[PubMed]
• [Transcriptomics] Acute hyperglycemia impairs functional improvement after spinal cord injury in mice and humans.
  Kobayakawa K, Kumamaru H, Saiwai H, Kubota K, Ohkawa Y, Kishimoto J, Yokota K, Ideta R, Shiba K, Tozaki-Saitoh H, Inoue K, Iwamoto Y, Okada S.
  Sci Transl Med. 2014 Oct 1;6(256):256ra137.[PubMed]
• [Transcriptomics] Regulation of RNA polymerase II activation by histone acetylation in single living cells.
  *Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K,Tokunaga M, Nagase T, Nozaki N, James G. McNally JG, Kimura H
  Nature. 2014 Sep 11;516(7530):272-5.[PubMed]
• [Method] Establishment of neutralizing rat monoclonal antibodies for fibroblast growth factor-2.
  Tanaka M, Yamaguchi M, *Shiota M, Kawamoto Y, Takahashi K, Inagaki A, Osada-Oka M, Harada A, Wanibuchi H, Izumi Y, Miura K, Iwao H, *Ohkawa Y.
  Monoclon Antib Immunodiagn Immunother. 2014 Aug;33(4):261-9.[PubMed]
• [Transcriptomics] Genome-wide analysis of histone modifications in human endometrial stromal cells.
  Tamura I, Ohkawa Y, Sato T, Suyama M, Jozaki K, Okada M, Lee L, Maekawa R, Asada H, Sato S, Yamagata Y, Tamura H, Sugino N.
  Mol Endocrinol. 2014 Jul 28(10):1656-69.[PubMed]
• [Transcriptomics] Identification of Myelin Transcription Factor 1 (MyT1) as a Subunit of the Neural Cell Type-specific Lysine-specific Demethylase 1 (LSD1) Complex.
  *Yokoyama A, Igarashi K, Sato T, Takagi K, Otsuka I M, Shishido Y, Baba T, Ito R, Kanno J, Ohkawa Y, Morohashi KI, Sugawara A.
  J Biol Chem. 2014 Jun 27;289(26):18152-18162.[PubMed]
• [Transcriptomics] Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, MethylRO.
  Ueda J, Maehara K, Mashiko D, Ichinose T, Yao T, Hori M, Sato Y, Kimura K, Ohkawa Y, Yamagata K.
  Stem Cell Reports. 2014 Jun 3;2(6):910-24.[PubMed]
• [Transcriptomics] Glycolytic genes are targets of the nuclear receptor Ad4BP/SF-1.
  Baba T, Otake H, Sato T, Miyabayashi K, Shishido Y, Wang CY, Shima Y, Kimura H, Yagi M, Ishihara Y, Hino S, Ogawa H, Nakao M, Yamazaki T, Kang D, Ohkawa Y, Suyama M, Chung BC, Morohashi K.
  Nat Commun. 2014 Apr 14;5:3634.[PubMed]
• [Transcriptomics] Hsc70 contributes to cancer cell survival by preventing Rab1A degradation under stress conditions.
  Tanaka M, Mun S, Harada A, Ohkawa Y, Inagaki A, Sano S, Takahashi K, Izumi Y, Osada-Oka M, Wanibuchi H, Yamagata M, Yukimura T, Miura K, Shiota M, Iwao H.
  PLoS One. 2014 May 6;9(5):e96785.[PubMed]
• [Method]Generation of a monoclonal antibody for INI1/hSNF5/BAF47.
  Harada A, Hayashi M, Kuniyoshi Y, Semba Y, Sugahara S, Tachibana T, *Ohkawa Y, Fujita M.
  Monoclon Antib Immunodiagn Immunother. 2014 Feb;33(1):49-51.[PubMed]
• [Method]Production of a monoclonal antibody for C/EBPβ: the subnuclear localization of C/EBPβ in mouse L929 cells.
  Harada A, Okazaki E, Okada S, Tachibana T, *Ohkawa Y.
  Monoclon Antib Immunodiagn Immunother. 2014 Feb;33(1):34-7.[PubMed]
• [Transcriptomics] The PPARγ locus makes long-range chromatin interactions with selected tissue-specific gene loci during adipocyte differentiation in a protein kinase A dependent manner.
  LeBlanc SE, Wu Q, Barutcu AR, Xiao H, Ohkawa Y, Imbalzano AN.
  PLoS One. 2014 Jan 20;9(1):e86140.[PubMed]

2013

• [Transcriptomics]A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples.
  Maehara K, Odawara J, Harada A, Yoshimi T, Nagao K, Obuse C, Akashi K, Tachibana T, Sakata T, *Ohkawa Y.
  Nucleic Acids Res. 2013 Jan 7;41(1):54-62.[PubMed]
• [Transcriptomics] Human TREX component Thoc5 affects alternative polyadenylation site choice by recruiting mammalian cleavage factor I.
  *Katahira J, Okuzaki D, Inoue H, Yoneda Y, Maehara K, Ohkawa Y.
  Nucleic Acids Res. 2013 Aug 1;41(14):7060-7072.[PubMed]
• [Transcriptomics] Ly6C+ Ly6G- Myeloid-derived suppressor cells play a critical role in the resolution of acute inflammation and the subsequent tissue repair process after spinal cord injury.
  Saiwai H, Kumamaru H, Ohkawa Y, Kubota K, Kobayakawa K, Yamada H, Yokomizo T, Iwamoto Y, Okada S.
  J Neurochem. 2013 Apr;125(1):74-88.[PubMed]
• [Transcriptomics] Therapeutic activities of engrafted neural stem/precursor cells are not dormant in the chronically injured spinal cord.
  Kumamaru H, Saiwai H, Kubota K, Kobayakawa K, Yokota K, Ohkawa Y, Shiba K, Iwamoto Y, Okada S.
  Stem Cells. 2013 Aug;31(8):1535-47.[PubMed]
• [Transcriptomics] Wnt signaling regulates left-right axis formation in the node of mouse embryos.
  Kitajima K, Oki S, Ohkawa Y, Sumi T, Meno C.
  Dev Biol. 2013 Aug 15;380(2):222-32.[PubMed]
• [Transcriptomics] A panel of specific monoclonal antibodies directed against various phosphorylated histones H3.
  Yoshimi T, Ohkawa Y, Azuma M, Tachibana T.
  Monoclon Antib Immunodiagn Immunother. 2013 Apr;32(2):119-24.[PubMed]
• [Transcriptomics] β-Catenin signaling regulates Foxa2 expression during endometrial hyperplasia formation.
  Villacorte M, Suzuki K, Hirasawa A, Ohkawa Y, Suyama M, Maruyama T, Aoki D, Ogino Y, Miyagawa S, Terabayashi T, Tomooka Y, Nakagata N, Yamada G.
  Oncogene. 2013 Jul 18;32(29):3477-82.[PubMed]

2012

• [Myogenesis]Chd2 interacts with H3.3 to determine myogenic cell fate.
  Harada A, Okada S, Konno D, Odawara J, Yoshimi T, Yoshimura S, Kumamaru H, Saiwai H, Tsubota T, Kurumizaka H, Akashi K, Tachibana T, Imbalzano AN, *Ohkawa Y.
  EMBO J. 2012 Jun 29;31(13):2994-3007.[PubMed]
• [Transcriptomics] Essential roles of gangliosides in the formation and maintenance of membrane microdomains in brain tissues.
  Ohmi Y, Ohkawa Y, Yamauchi Y, Tajima O, Furukawa K, Furukawa K.
  Neurochem Res. 2012 Jun;37(6):1185-91.[PubMed]
• [Transcriptomics] Direct isolation and RNA-seq reveal environment-dependent properties of engrafted neural stem/progenitor cells.
  Kumamaru H, Ohkawa Y, Saiwai H, Yamada H, Kubota K, Kobayakawa K, Akashi K, Okano H, Iwamoto Y, Okada S.
  Nat Commun. 2012;3:1140.[PubMed]
• [Transcriptomics] Surf4 modulates STIM1-dependent calcium entry.
  Fujii Y, Shiota M, Ohkawa Y, Baba A, Wanibuchi H, Kinashi T, Kurosaki T, Baba Y.
  Biochem Biophys Res Commun. 2012 Jun 15;422(4):615-20.[PubMed]
• [Transcriptomics] Myeloperoxidase exacerbates secondary injury by generating highly reactive oxygen species and mediating neutrophil recruitment in experimental spinal cord injury.
  Kubota K, Saiwai H, Kumamaru H, Maeda T, Ohkawa Y, Aratani Y, Nagano T, Iwamoto Y, Okada S.
  Spine. 2012 Jul 15;37(16):1363-9.[PubMed]
• [Myogenesis] An improved restriction enzyme accessibility assay for analyzing changes in chromatin structure in samples of limited cell number.
  Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN.
  Methods Mol Biol. 2012;798:531-42.[PubMed]
• [Myogenesis] Isolation of nuclei from skeletal muscle satellite cells and myofibers for use in chromatin immunoprecipitation assays.
  Ohkawa Y, Mallappa C, Vallaster CS, Imbalzano AN.
  Methods Mol Biol. 2012;798:517-30.[PubMed]
• [Transcriptomics] Age-related differences in cellular and molecular profiles of inflammatory responses after spinal cord injury.
  Kumamaru H, Saiwai H, Ohkawa Y, Yamada H, Iwamoto Y, Okada S.
  J Cell Physiol. 2012 Apr;227(4):1335-46.[PubMed]

2011

• [Transcriptomics] Chromatin accessibility and transcription factor binding at the PPARγ2 promoter during adipogenesis is protein kinase A-dependent.
  Xiao H, Leblanc SE, Wu Q, Konda S, Salma N, Marfella CG, Ohkawa Y, *Imbalzano AN.
  J Cell Physiol. 2011 Jan;226(1):86-93.[PubMed]
• [Transcriptomics] The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach.
  Odawara J, Harada A, Yoshimi T, Maehara K, Tachibana T, Okada S, Akashi K, *Ohkawa Y.
  BMC Genomics. 2011 Oct 20;12:516.[PubMed]
• [Method] Generation of a rat monoclonal antibody specific for hsp72.
  Tanaka M, Shiota M, Okada S, Harada A, Odawara J, Mun S, Iwao H, *Ohkawa Y.
  Hybridoma. 2011 Aug;30(4):397-400.[PubMed]
• [Method] Flow cytometric sorting of neuronal and glial nuclei from central nervous system tissue.
  *Okada S, Saiwai H, Kumamaru H, Kubota K, Harada A, Yamaguchi M, Iwamoto Y, *Ohkawa Y.
  J Cell Physiol. 2011 Feb;226(2):552-8.[PubMed]

2010

• Ossification of the posterior longitudinal ligament of the lumbar spine: a case series.
  Okada S, Maeda T, Saiwai H, Ohkawa Y, Shiba K, Iwamoto Y.
  Neurosurgery. 2010 Nov;67(5):1311-8; discussion 1318.[PubMed]
• [Method] Generation of a rat monoclonal antibody specific for heat shock cognate protein 70.
  Shiota M, Saiwai H, Mun S, Harada A, Okada S, Odawara J, Tanaka M, Iwao H, *Ohkawa Y.
  Hybridoma 2010 Oct;29(5):453-6.[PubMed]
• [Method] Monoclonal antibody specific for Dhx9/NDHII/RHA.
  Kotani M, Harada A, Odawara J, Azuma M, Okada S, Nishiyama Y, Nakamura M, Tachibana T, *Ohkawa Y.
  Hybridoma 2010 Jun;29(3):259-61.[PubMed]
• [Method] Rat monoclonal antibody specific for MyoD.
  Harada A, Ohkawa Y, Ao S, Odawara J, Okada S, Azuma M, Nishiyama Y, Nakamura M, Tachibana T.
  Hybridoma 2010 Jun;29(3):255-8.[PubMed]
• [Method] Rat monoclonal antibody specific for the chromatin remodeling factor, CHD1.
  Yoshimura S, Harada A, Odawara J, Azuma M, Okada S, Nakamura M, Ohkawa Y, Tachibana T.
  Hybridoma 2010 Jun;29(3):237-40.[PubMed]
• The LTB4-BLT1 axis mediates neutrophil infiltration and secondary injury in experimental spinal cord injury.
  Saiwai H, Ohkawa Y, Yamada H, Kumamaru H, Harada A, Okano H, Yokomizo T, Iwamoto Y, Okada S.
  Am J Pathol. 2010 May;176(5):2352-66.[PubMed]
• [Method]Generation of a rat monoclonal antibody specific for CHD2.
  Harada A, Yoshimura S, Odawara J, Azuma M, Okada S, Nakamura M, Tachibana T, *Ohkawa Y.
  Hybridoma 2010 Apr;29(2):173-7.[PubMed]
• [Method] Harada A, Okada S, Odawara J, Kumamaru H, Saiwai H, Aoki M, Nakamura M, Nishiyama Y, *Ohkawa Y.
  Production of a rat monoclonal antibody specific for Myf5.
  Hybridoma 2010 Feb;29(1):59-62.[PubMed]
• [Myogenesis] Myogenic microRNA expression requires ATP-dependent chromatin remodeling enzyme function.
  Mallappa C, Nasipak BT, Etheridge L, Androphy EJ, Jones SN, Sagerström CG, Ohkawa Y, Imbalzano AN.
  Mol Cell Biol. 2010 Jul;30(13):3176-86.[PubMed]
• [Method] A rat monoclonal antibody against the chromatin remodeling factor CHD5.
  S, Yoshimi T, Ohkawa Y, Azuma M, Tachibana T.
  Hybridoma 2010 Feb;29(1):63-6.[PubMed]

2009

• [Method] Production of a rat monoclonal antibody against Brg1.
  Ohkawa Y, Harada A, Nakamura M, Yoshimura S, Tachibana T.
  Hybridoma 2009 Dec;28(6):463-6.[PubMed]
• [Method] Generation of a rat monoclonal antibody specific for Brm.
  Okada S, Harada A, Saiwai H, Nakamura M, *Ohkawa Y.
  Hybridoma 2009 Dec;28(6):455-8.[PubMed]
• [Method] Generation of a rat monoclonal antibody specific for Pax7.
  Harada A, Okada S, Saiwai H, Aoki M, Nakamura M, *Ohkawa Y.
  Hybridoma 2009 Dec;28(6):451-3.[PubMed]
• Does ossification of the posterior longitudinal ligament affect the neurological outcome after traumatic cervical cord injury?
  Okada S, Maeda T, Ohkawa Y, Harimaya K, Saiwai H, Kumamaru H, Matsumoto Y, Doi T, Ueta T, Shiba K, Iwamoto Y.
  Spine. 2009 May 15;34(11):1148-52.[PubMed]

〜2008

• [Myogenesis] Myogenin and the SWI/SNF ATPase Brg1 maintain myogenic gene expression at different stages of skeletal myogenesis.
  Ohkawa Y, Yoshimura S, Higashi C, Marfella CG, Dacwag CS, Tachibana T, Imbalzano AN.
  J Biol Chem. 2007 Mar 2;282(9):6564-70.[PubMed]
• [Myogenesis] The protein arginine methyltransferase Prmt5 is required for myogenesis because it facilitates ATP-dependent chromatin remodeling.
  Dacwag CS, Ohkawa Y, Pal S, Sif S, Imbalzano AN.
  Mol Cell Biol. 2007 Jan;27(1):384-94.[PubMed]
• Mutation of the SNF2 family member Chd2 affects mouse development and survival.
  Marfella CG1, Ohkawa Y, Coles AH, Garlick DS, Jones SN, Imbalzano AN.
  J Cell Physiol. 2006 Oct;209(1):162-71.[PubMed]
• The microphthalmia-associated transcription factor requires SWI/SNF enzymes to activate melanocyte-specific genes.
  de la Serna IL, Ohkawa Y, Higashi C, Dutta C, Osias J, Kommajosyula N, Tachibana T, Imbalzano AN.
  J Biol Chem. 2006 Jul 21;281(29):20233-41.[PubMed]
• [Myogenesis] Chromatin remodelling in mammalian differentiation: lessons from ATP-dependent remodellers.
  de la Serna IL, Ohkawa Y, Imbalzano AN.
  Nat Rev Genet. 2006 Jun;7(6):461-73.[PubMed]
• [Myogenesis] Skeletal muscle specification by myogenin and Mef2D via the SWI/SNF ATPase Brg1.
  Ohkawa Y, Marfella CG, Imbalzano AN.
  EMBO J. 2006 Feb 8;25(3):490-501.[PubMed]
• [Myogenesis] MyoD targets chromatin remodeling complexes to the myogenin locus prior to forming a stable DNA-bound complex.
  de la Serna IL, Ohkawa Y, Berkes CA, Bergstrom DA, Dacwag CS, Tapscott SJ, Imbalzano AN.
  Mol Cell Biol. 2005 May;25(10):3997-4009.[PubMed]
• SWI/SNF chromatin remodeling complex is obligatory for BMP2-induced, Runx2-dependent skeletal gene expression that controls osteoblast differentiation.
  Young DW, Pratap J, Javed A, Weiner B, Ohkawa Y, van Wijnen A, Montecino M, Stein GS, Stein JL, Imbalzano AN, Lian JB.
  J Cell Biochem. 2005 Mar 1;94(4):720-30.[PubMed]
• Epiregulin as a major autocrine/paracrine factor released from ERK- and p38MAPK-activated vascular smooth muscle cells.
  Takahashi M, Hayashi K, Yoshida K, Ohkawa Y, Komurasaki T, Kitabatake A, Ogawa A, Nishida W, Yano M, Monden M, Sobue K.
  Circulation. 2003 Nov 18;108(20):2524-9.[PubMed]
• Vascular remodeling induced by naturally occurring unsaturated lysophosphatidic acid in vivo.
  Yoshida K, Nishida W, Hayashi K, Ohkawa Y, Ogawa A, Aoki J, Arai H, Sobue K.
  Circulation. 2003 Oct 7;108(14):1746-52.[PubMed]
• Calcineurin-mediated pathway involved in the differentiated phenotype of smooth muscle cells.
  Ohkawa Y, Hayashi K, Sobue K.
  Biochem Biophys Res Commun. 2003 Jan 31;301(1):78-83.[PubMed]
• A triad of serum response factor and the GATA and NK families governs the transcription of smooth and cardiac muscle genes.
  Nishida W, Nakamura M, Mori S, Takahashi M, Ohkawa Y, Tadokoro S, Yoshida K, Hiwada K, Hayashi K, Sobue K.
  J Biol Chem. 2002 Mar 1;277(9):7308-17.[PubMed]