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AMED-CREST Data

We have performed epigenomic analysis including whole-genome bisulfite sequencing (WGBS),
chromatin immunoprecipitation (ChIP-seq), and deep sequencing of mRNAs (RNA-seq).
These reference epigenomes have been registered in IHEC reference registry of epigenomes (EpiRR).

Summary of EpiRR

Publications

IHEC-associated publications

All teams

  • Stunnenberg HG; International Human Epigenome Consortium, Hirst M.
    The International Human Epigenome Consortium: A blueprint for scientific collaboration and discovery.
    Cell. (2016) 167, 1145–1149.
  • Suzuki A, Kawano S, Mituyama T, Suyama M, Kanai Y, Shirahige K, Sasaki H, Tokunaga K, Tsuchihara K, Sugano S, Nakai K, Suzuki Y.
    DBTSS/DBKERO for integrated analysis of transcriptional regulation.
    Nucleic Acids Res. (2017) in press.

Team Kanai

  • Umeyama T, Ito T.
    DMS-Seq for In vivo genome-wide mapping of protein-DNA interactions and nucleosome centers.
    Cell Rep. (2017) 21, 289-300.
  • Arai E, Gotoh M, Tian Y, Sakamoto H, Ono M, Matsuda A, Takahashi Y, Miyata S, Totsuka H, Chiku S, Komiyama M, Fujimoto H, Matsumoto K, Yamada T, Yoshida T, Kanai Y.
    Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas.
    Int J Cancer. (2015) 137, 2589–2606.
  • Yokoyama T, Miura F, Araki H, Okamura K, Ito T.
    Changepoint detection in base-resolution methylome data reveals a robust signature of methylated domain landscape.
    BMC Genomics. (2015) 16, 594.
  • Yamanoi K, Arai E, Tian Y, Takahashi Y, Miyata S, Sasaki H, Chiwaki F, Ichikawa H, Sakamoto H, Kushima R, Katai H, Yoshida T, Sakamoto M, Kanai Y.
    Epigenetic clustering of gastric carcinomas based on DNA methylation profiles at the precancerous stage: its correlation with tumor aggressiveness and patient outcome.
    Carcinogenesis. (2015) 36, 509–520.
  • Sakamoto A, Hino S, Nagaoka K, Anan K, Takase R, Matsumori H, Ojima H, Kanai Y, Arita K, Nakao M.
    Lysine demethylase LSD1 coordinates glycolytic and mitochondrial metabolism in hepatocellular carcinoma cells.
    Cancer Res. (2015) 75, 1445–1456.
  • Miura F, Ito T.
    Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging.
    DNA Res. (2015) 22, 13–18.
  • Tian Y, Arai E, Gotoh M, Komiyama M, Fujimoto H, Kanai Y.
    Prognostication of patients with clear cell renal cell carcinomas based on quantification of DNA methylation levels of CpG island methylator phenotype marker genes.
    BMC Cancer. (2014) 14, 772.
  • Arai E, Sakamoto H, Ichikawa H, Totsuka H, Chiku S, Gotoh M, Mori T, Nakatani T, Ohnami S, Nakagawa T, Fujimoto H, Wang L, Aburatani H, Yoshida T, Kanai Y.
    Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome.
    Int J Cancer. (2014) 135, 1330–1342.
  • Miura F, Enomoto Y, Dairiki R, Ito T.
    Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
    Nucleic Acids Res. (2012) 40, e136.
  • Arai E, Chiku S, Mori T, Gotoh M, Nakagawa T, Fujimoto H, Kanai Y.
    Single-CpG-resolution methylome analysis identifies clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas.
    Carcinogenesis. (2012) 33, 1487–1493.

Team Shirahige

  • Nakato R, Shirahige K.
    Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation.
    Brief Bioinform. (2017) 18, 279–290.
  • Saito Y, Mituyama T.
    Detection of differentially methylated regions from bisulfite-seq data by hidden Markov models incorporating genome-wide methylation level distributions.
    BMC Genomics. (2015) 16, S3.
  • Saito Y, Tsuji J, Mituyama T.
    Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions.
    Nucleic Acids Res. (2014) 42, e45.
  • Nakato R, Itoh T, Shirahige K.
    DROMPA: easy-to-handle peak calling and visualization software for the computational analysis and validation of ChIP-seq data.
    Genes Cells. (2013) 18, 589–601.

Team Sasaki

  • Toh H, Shirane K, Miura F, Kubo N, Ichiyanagi K, Hayashi K, Saitou M, Suyama M, Ito T, Sasaki H.
    Software updates in the Illumina HiSeq platform affect whole-genome bisulfite sequencing.
    BMC Genomics. (2017) 18, 31.
  • Hamada H, Okae H, Toh H, Chiba H, Hiura H, Shirane K, Sato T, Suyama M, Yaegashi N, Sasaki H, Arima T.
    Allele-specific methylome and transcriptome analysis reveals widespread imprinting in the human placenta.
    Am J Hum Genet. (2016) 99, 1045–1058.
  • Okae H, Arima T.
    DNA methylation dynamics during early human development.
    J Mamm Ova Res. (2016) 33, 101–107.
  • Masuda A, Katoh N, Nakabayashi K, Kato K, Sonoda K, Kitade M, Takeda S, Hata K, Tomikawa J.
    An improved method for isolation of epithelial and stromal cells from the human endometrium.
    J Reprod Dev. (2016) 62, 213–218.
  • Kawai T, Yamada T, Abe K, Okamura K, Kamura H, Akaishi R, Minakami H, Nakabayashi K, Hata K.
    Increased epigenetic alterations at the promoters of transcriptional regulators following inadequate maternal gestational weight gain.
    Sci Rep. (2015) 5, 14224.
  • Sato T, Suyama M.
    ChromContact: A web tool for analyzing spatial contact of chromosomes from Hi-C data.
    BMC Genomics. (2015) 16, 1060.
  • Saito D, Suyama M.
    Linkage disequilibrium analysis of allelic heterogeneity in DNA methylation.
    Epigenetics. (2015) 10, 1093–1098.
  • Okae H, Chiba H, Hiura H, Hamada H, Sato A, Utsunomiya T, Kikuchi H, Yoshida H, Tanaka A, Suyama M, Arima T.
    Genome-wide analysis of DNA methylation dynamics during early human development.
    PLoS Genet. (2014) 10, e1004868.

Other selected publications

Team Kanai

  • Sanosaka T, Imamura T, Hamazaki N, Chai M, Igarashi K, Ideta-Otsuka M, Miura F, Ito T, Fujii N, Ikeo K, Nakashima K.
    DNA methylome analysis Identifies transcription factor-based epigenomic signatures of multilineage competence in neural stem/progenitor cells.
    Cell Rep. (2017) 20, 2992-3003.
  • Ohara K, Arai E, Takahashi Y, Ito N, Shibuya A, Tsuta K, Kushima R, Tsuda H, Ojima H, Fujimoto H, Watanabe SI, Katai H, Kinoshita T, Shibata T, Kohno T, Kanai Y.
    Genes involved in development and differentiation are commonly methylated in cancers derived from multiple organs: a single-institutional methylome analysis using 1007 tissue specimens.
    Carcinogenesis. (2017) 38, 241-251.
  • Kuramoto J, Arai E, Tian Y, Funahashi N, Hiramoto M, Nammo T, Nozaki Y, Takahashi Y, Ito N, Shibuya A, Ojima H, Sukeda A, Seki Y, Kasama K, Yasuda K, Kanai Y.
    Genome-wide DNA methylation analysis during non-alcoholic steatohepatitis-related multistage hepatocarcinogenesis: comparison with hepatitis virus-related carcinogenesis.
    Carcinogenesis. (2017) 38, 261-270.
  • Alexandrov LB, Ju YS Haase K, Loo PV Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR.
    Mutational signatures associated with tobacco smoking in human cancer.
    Science. (2016) 354, 618–622.
  • Kataoka K, Shiraishi Y, Takeda Y, Sakata S, Matsumoto M, Nagano S, Maeda T, Nagata Y, Kitanaka A, Mizuno S, Tanaka H, Chiba K, Ito S, Watatani Y, Kakiuchi N, Suzuki H, Yoshizato T, Yoshida K, Sanada M, Itonaga H, Imaizumi Y, Totoki Y, Munakata W, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Masuda K, Minato N, Kashiwase K, Izutsu K, Takaori-Kondo A, Miyazaki Y, Takahashi S, Shibata T, Kawamoto H, Akatsuka Y, Shimoda K, Takeuchi K, Seya T, Miyano S, Ogawa S.
    Aberrant PD-L1 expression through 3'-UTR disruption in multiple cancers.
    Nature. (2016) 534, 402–406.
  • Koike T, Wakai T, Jincho Y, Sakashita A, Kobayashi H, Mizutani E, Wakayama S, Miura F, Ito T, Kono T.
    DNA methylation errors in cloned mouse sperm by germ line barrier evasion.
    Biol Reprod. (2016) 94, 128.
  • Fujimoto A, Furuta M, Totoki Y, Tsunoda T, Kato M, Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi SI, Wardell CP, Hayami S, Nakamura T, Aikata H, Arihiro K, Boroevich KA, Abe T, Nakano K, Maejima K, Sasaki-Oku A, Ohsawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Ohashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusaka T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamaue H, Chayama K, Miyano S, Aburatani H, Shibata T, Nakagawa H.
    Whole-genome mutational landscape and characterization of noncoding and structural mutations in liver cancer.
    Nat Genet. (2016) 48, 500–509.
  • Robles AI, Arai E, Mathé EA, Okayama H, Schetter AJ, Brown D, Petersen D, Bowman ED, Noro R, Welsh JA, Edelman DC, Stevenson HS, Wang Y, Tsuchiya N, Kohno T, Skaug V, Mollerup S, Haugen A, Meltzer PS, Yokota J, Kanai Y, Harris CC.
    An integrated prognostic classifier for Stage I lung adenocarcinoma based on mRNA, microRNA, and DNA methylation biomarkers.
    J Thorac Oncol. (2015) 10, 1037–1048.
  • Creixell P, Reimand J, Haider S, Wu G, Shibata T, Vazquez M, Mustonen V, Gonzalez-Perez A, Pearson J, Sander C, Raphael1 BJ, Marks1 DS, Ouellette BF, Valencia A, Bader GD, Boutros PC, Stuart JM, Linding R, Lopez-Bigas N, Stein LD.
    Pathway and network analysis of cancer genomes.
    Nat Methods. (2015) 12, 615–621.
  • Colicchio JM, Miura F, Kelly JK, Ito T, Hileman LC.
    DNA methylation and gene expression in Mimulus guttatus.
    BMC Genomics. (2015) 16, 507.
  • Suzuki A, Matsushima K, Makinoshima H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y.
    Single-cell analysis of lung adenocarcinoma cell lines reveals diverse expression patterns of individual cells invoked by a molecular target drug treatment.
    Genome Biol. (2015) 16, 66.
  • Suzuki A, Wakaguri H, Yamashita R, Kawano S, Tsuchihara K, Sugano S, Suzuki Y, Nakai K.
    DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.
    Nucleic Acids Res. (2015) 43, D87–91.
  • Totoki Y, Tatsuno K, Covington KR, Ueda H, Creighton CJ, Kato M, Tsuji S, Donehower LA, Slagle BL, Nakamura H, Yamamoto S, Shinbrot E, Hama N, Lehmkuhl M, Hosoda F, Arai Y, Walker K, Dahdouli M, Gotoh K, Nagae G, Gingras MC, Muzny DM, Ojima H, Shimada K, Midorikawa Y, Goss JA, Cotton R, Hayashi A, Shibahara J, Ishikawa S, Guiteau J, Tanaka M, Urushidate T, Ohashi S, Okada N, Doddapaneni H, Wang M, Zhu Y, Dinh H, Okusaka T, Kokudo N, Kosuge T, Takayama T, Fukayama M, Gibbs RA, Wheeler DA, Aburatani H, Shibata T.
    Trans-ancestry mutational landscape of hepatocellular carcinoma genomes.
    Nat Genet. (2014) 46, 1267–1273.
  • Suzuki A, Makinoshima H, Wakaguri H, Esumi H, Sugano S, Kohno T, Tsuchihara K, Suzuki Y.
    Aberrant transcriptional regulations in cancers: genome, transcriptome and epigenome analysis of lung adenocarcinoma cell lines.
    Nucleic Acids Res. (2014) 42, 13557–13572.
  • Sato T, Arai E, Kohno T, Takahashi Y, Miyata S, Tsuta K, Watanabe S, Soejima K, Betsuyaku T, Kanai Y.
    Epigenetic clustering of lung adenocarcinomas based on DNA methylation profiles in adjacent lung tissue: Its correlation with smoking history and chronic obstructive pulmonary disease.
    Int J Cancer. (2014) 135, 319–334.
  • Sato T, Arai E, Kohno T, Tsuta K, Watanabe S, Soejima K, Betsuyaku T, Kanai Y.
    DNA methylation profiles at precancerous stages associated with recurrence of lung adenocarcinoma.
    PLoS One. (2013) 8, e59444.
  • Fukuda K, Ichiyanagi K, Yamada Y, Go Y, Udono T, Wada S, Maeda T, Soejima H, Saitou N, Ito T, Sasaki H.
    Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes.
    J Hum Genet. (2013) 58, 446–454.
  • Kobayashi H, Sakurai T, Miura F, Imai M, Mochiduki K, Yanagisawa E, Sakashita A, Wakai T, Suzuki Y, Ito T, Matsui Y, Kono T.
    High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice.
    Genome Res. (2013) 23, 616–627.
  • Shirane K, Toh H, Kobayashi H, Miura F, Chiba H, Ito T, Kono T, Sasaki H.
    Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases.
    PLoS Genet. (2013) 9, e1003439.
  • Fujimoto A, Totoki Y, Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hoshono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakao K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi S, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamae H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T, Nakagawa H.
    Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators.
    Nat Genet. (2012) 44, 760–764.
  • Gotoh M, Arai E, Wakai-Ushijima S, Hiraoka N, Kosuge T, Hosoda F, Shibata T, Kondo T, Yokoi S, Imoto I, Inazawa J, Kanai Y.
    Diagnosis and prognostication of ductal adenocarcinomas of the pancreas based on genome-wide DNA methylation profiling by bacterial artificial chromosome array-based methylated CpG island amplification.
    J Biomed Biotechnol. (2011) 2011, 780836.
  • Watanabe T, Tomizawa S, Mitsuya K, Totoki Y, Yamamoto Y, Kuramochi-Miyagawa S, Iida N, Hoki Y, Murphy PJ, Toyoda A, Gotoh K, Hiura H, Arima T, Fujiyama A, Sado T, Shibata T, Nakano T, Lin H, Ichiyanagi K, Soloway PD, Sasaki H.
    Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.
    Science. (2011) 332, 848–852.
  • Totoki Y, Tatsuno K, Yamamoto S, Arai Y, Hosoda F, Ishikawa S, Tsustumi S, Sonoda K, Totsuka H, Shirakihara T, Sakamoto H, Wang L, Ojima H, Shimada K, Kosuge T, Okusaka T, Kato K, Kusuda J, Yoshida T, Aburatani H, Shibata T.
    High-resolution characterization of a hepatocellular carcinoma genome.
    Nat Genet. (2011) 43, 464–469.

Team Shirahige

  • Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS, Dominguez D, Rhodes D, Humphrey TC, Shirahige K, Esashi F.
    MRG15-mediated tethering of PALB2 to unperturbed chromatin protects active genes from genotoxic stress.
    Proc Natl Acad Sci USA. (2017) 114, 7671-7676.
  • Miyakawa T, Tanaka T, Ago Y, Hashimoto H, Shirahige K, Yamashita T.
    Decreased cohesin in the brain leads to defective synapse development and anxiety-related behavior.
    J Exp Med. (2017) 21, 289-300.
  • Saito Y, Nagae G, Motoi N, Miyauchi E, Ninomiya H, Uehara H, Mun M, Okumura S, Ohyanagi F, Nishio M, Satoh Y, Aburatani H, Ishikawa Y.
    Prognostic significance of CpG island methylator phenotype in surgically resected small cell lung carcinoma.
    Cancer Sci. (2016) 107, 320–325.
  • 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.
    Histone H4 lysine 20 acetylation is associated with gene repression in human cells.
    Sci Rep. (2016) 6, 24318.
  • Koya J, Kataoka K, Sato T, Bando M, Kato Y, Tsuruta-Kishino T, Kobayashi H, Narukawa K, Miyoshi H, Shirahige K, Kurokawa M.
    DNMT3A R882 mutants interact with polycomb proteins to block haematopoietic stem and leukaemic cell differentiation.
    Nat Commun. (2016) 7, 10924.
  • Uchi R, Takahashi Y, Niida A, Shimamura T, Hirata H, Sugimachi K, Sawada G, Iwaya T, Kurashige J, Shinden Y, Iguchi T, Eguchi H, Chiba K, Shiraishi Y, Nagae G, Yoshida K, Nagata Y, Haeno H, Yamamoto H, Ishii H, Doki Y, Iinuma H, Sasaki S, Nagayama S, Yamada K, Yachida S, Kato M, Shibata T, Oki E, Saeki H, Shirabe K, Oda Y, Maehara Y, Komune S, Mori M, Suzuki Y, Yamamoto K, Aburatani H, Ogawa S, Miyano S, Mimori K.
    Integrated multiregional analysis proposing a new model of colorectal cancer evolution.
    PLoS Genet. (2016) 12, e1005778.
  • Hayashi-Takanaka Y, Maehara K, Harada A, Umehara T, Yokoyama S, Obuse C, Ohkawa Y, Nozaki N, Kimura H.
    Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies.
    Chromosome Res. (2015) 23, 753–766.
  • Dias JD, Rito T, Torlai Triglia E, Kukalev A, Ferrai C, Chotalia M, Brookes E, Kimura H, Pombo A.
    Methylation of RNA polymerase II non-consensus Lysine residues marks early transcription in mammalian cells.
    eLife. (2015) 4, e11215.
  • Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga J, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S.
    Integrated molecular analysis of adult T cell leukemia/lymphoma.
    Nat Genet. (2015) 47, 1304–1315.
  • Maehara K, Harada A, Sato Y, Matsumoto M, Nakayama KI, Kimura H, Ohkawa Y.
    Tissue-specific expression of histone H3 variants diversified after species separation.
    Epigenetics Chromatin. (2015) 8, 35.
  • Huang D, Nagata Y, Grossmann V, Radivoyevitch T, Okuno Y, Nagae G, Hosono N, Schnittger S, Sanada M, Przychodzen B, Kon A, Polprasert C, Shen W, Clemente MJ, Phillips JG, Alpermann T, Yoshida K, Nadarajah N, Sekeres MA, Oakley K, Nguyen N, Shiraishi Y, Shiozawa Y, Chiba K, Tanaka H, Koeffler HP, Klein HU, Dugas M, Aburatani H, Miyano S, Haferlach C, Kern W, Haferlach T, Du Y, Ogawa S, Makishima H.
    BRCC3 mutations in myeloid neoplasms.
    Haematologica. (2015) 100, 1051–1057.
  • Chen ST, Okada M, Nakato R, Izumi K, Bando M, Shirahige K.
    The deubiquitinating enzyme USP7 regulates androgen receptor activity by modulating its binding to chromatin.
    J Biol Chem. (2015) 290, 21713–21723.
  • Masuda K, Akiyama K, Arakawa M, Nishi E, Kitazawa N, Higuchi T, Katou Y, Shirahige K, Izumi K.
    Exome sequencing identification of EP300 mutation in a proband with coloboma and imperforate anus: possible expansion of the phenotypic spectrum of Rubinstein-Taybi syndrome.
    Mol Syndromol. (2015) 6, 99–103.
  • Sutani T, Sakata T, Nakato R, Masuda K, Ishibashi M, Yamashita D, Suzuki Y, Hirano T, Bando M, Shirahige K.
    Condensin targets and reduces unwound DNA structures associated with transcription in mitotic chromosome condensation.
    Nat Commun. (2015) 6, 7815.
  • Seki M, Nishimura R, Yoshida K, Shimamura T, Shiraishi Y, Sato Y, Kato M, Chiba K, Tanaka H, Hoshino N, Nagae G, Shiozawa Y, Okuno Y, Hosoi H, Tanaka Y, Okita H, Miyachi M, Souzaki R, Taguchi T, Koh K, Hanada R, Kato K, Nomura Y, Akiyama M, Oka A, Igarashi T, Miyano S, Aburatani H, Hayashi Y, Ogawa S, Takita J.
    Integrated genetic and epigenetic analysis defines novel molecular subgroups in rhabdomyosarcoma.
    Nat Commun. (2015) 6, 7557.
  • Truong TP, Sakata-Yanagimoto M, Yamada M, Nagae G, Enami T, Nakamoto-Matsubara R, Aburatani H, Chiba S.
    Age-dependent decrease of DNA hydroxymethylation in human T cells.
    J Clin Exp Hematop. (2015) 55, 1–6.
  • Stasevich TJ, Hayashi-Takanaka Y, Sato Y, Maehara K, Ohkawa Y, Sakata-Sogawa K, Tokunaga M, Nagase T, Nozaki N, McNally JG, Kimura H.
    Regulation of RNA polymerase II activation by histone acetylation in single living cells.
    Nature. (2014) 516, 272–275.
  • Takada H, Saito Y, Mituyama T, Wei Z, Yoshihara E, Jacinto S, Downes M, Evans RM, Kida YS.
    Methylome, transcriptome, and PPAR(γ) cistrome analyses reveal two epigenetic transitions in fat cells.
    Epigenetics. (2014) 9, 1195–1206.
  • Zierhut C, Jenness C, Kimura H, Funabiki H.
    Nucleosomal regulation of chromatin composition and nuclear assembly revealed by histone depletion.
    Nature Struct Mol Biol. (2014) 21, 617–625.
  • Maejima T, Inoue T, Kanki Y, Kohro T, Li G, Ohta Y, Kimura H, Kobayashi K, Taguchi A, Tsutsumi S, Iwanari H, Yamamoto S, Aruga H, Dong S, Stevens JF, Poh HM, Yamamoto K, Kawamura T, Mimura I, Suehiro J, Sugiyama A, Kaneki K, Shibata H, Yoshinaka Y, Doi T, Asanuma A, Tanabe T, Tanaka T, Minami T, Hamakubo T, Sakai J, Nozaki N, Aburatani H, Nangaku M, Ruan X, Tanabe H, Ruan T, Ihara S, Endo A, Kodama T, Wada Y.
    Direct evidence for pitavastatin induced chromatin structure change in the KLF4 gene in endothelial cells.
    PLoS One. (2014) 9, e96005.
  • Inoue T, Kohro T, Tanaka T, Kanki Y, Li G, Poh HM, Mimura I, Kobayashi M, Taguchi A, Maejima T, Suehiro J, Sugiyama A, Kaneki K, Aruga H, Dong S, Stevens JF, Yamamoto S, Tsutsumi S, Fujita T, Ruan X, Aburatani H, Nangaku M, Ruan Y, Kodama T, Wada Y.
    Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements.
    Genome Biol. (2014) 15, R63.
  • Suzuki T, Muto N, Bando M, Itoh Y, Masaki A, Ri M, Ota Y, Nakagawa H, Iida S, Shirahige K, Miyata N.
    Design, synthesis, and biological activity of NCC149 derivatives as histone deacetylase 8-selective inhibitors.
    ChemMedChem. (2014) 9, 657–664.
  • Shinagawa T, Takagi T, Tsukamoto D, Tomaru C, Huynh LM, Sivaraman P, Kumarevel T, Inoue K, Nakato R, Katou Y, Sado T, Takahashi S, Ogura A, Shirahige K, Ishii S.
    Histone variants enriched in oocytes enhance reprogramming to induced pluripotent stem cells.
    Cell Stem Cell. (2014) 14, 217–227.
  • Aramaki S, Hayashi K, Kurimoto K, Ohta H, Yabuta Y, Iwanari H, Mochizuki Y, Hamakubo T, Kato Y, Shirahige K, Saitou M.
    A mesodermal factor, T, specifies mouse germ cell fate by directly activating germline determinants.
    Dev Cell. (2013) 27, 516–529.
  • Chandra T, Kirschner K, Thuret JY, Pope BD, Ryba T, Newman S, Ahmed K, Samarajiwa SA, Salama R, Carroll T, Stark R, Janky R, Narita M, Xue L, Chicas A, Nũnez S, Janknecht R, Hayashi-Takanaka Y, Wilson MD, Marshall A, Odom DT, Babu MM, Bazett-Jones DP, Tavaré S, Edwards PA, Lowe SW, Kimura H, Gilbert DM, Narita M.
    Independence of repressive histone marks and chromatin compaction during senescent heterochromatic layer formation.
    Mol Cell. (2012) 47, 203–214.
  • Nozawa RS, Nagao K, Igami KT, Shibata S, Shirai N, Nozaki N, Sado T, Kimura H, Obuse C.
    Human inactive X chromosome is compacted through a PRC2-independent SMCHD1-HBiX1 pathway.
    Nat Struct Mol Biol. (2013) 20, 566–573.
  • Yamaji M, Ueda J, Hayashi K, Ohta H, Yabuta Y, Kurimoto K, Nakato R, Yamada Y, Shirahige K, Saitou M.
    PRDM14 ensures naive pluripotency through dual regulation of signaling and epigenetic pathways in mouse embryonic stem cells.
    Cell Stem Cell. (2013) 12, 368–382.
  • Suzuki T, Ota Y, Ri M, Bando M, Gotoh A, Itoh Y, Tsumoto H, Tatum PR, Mizukami T, Nakagawa H, Iida S, Ueda R, Shirahige K, Miyata N.
    Rapid discovery of highly potent and selective inhibitors of histone deacetylase 8 using click chemistry to generate candidate libraries.
    J Med Chem. (2012) 55, 9562–9575.
  • Deardorff MA, Bando M, Nakato R, Watrin E, Itoh T, Minamino M, Saitoh K, Komata M, Katou Y, Clark D, Cole KE, De Baere E, Decroos C, Di Donato N, Ernst S, Francey LJ, Gyftodimou Y, Hirashima K, Hullings M, Ishikawa Y, Jaulin C, Kaur M, Kiyono T, Lombardi PM, Magnaghi-Jaulin L, Mortier GR, Nozaki N, Petersen MB, Seimiya H, Siu VM, Suzuki Y, Takagaki K, Wilde JJ, Willems PJ, Prigent C, Gillessen-Kaesbach G, Christianson DW, Kaiser FJ, Jackson LG, Hirota T, Krantz ID, Shirahige K.
    HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle.
    Nature. (2012) 489, 313–317.

Team Sasaki

  • Maenohara S, Unoki M, Toh H, Ohishi H, Sharif J, Koseki H, Sasaki H.
    Role of UHRF1 in de novo DNA methylation in oocytes and maintenance methylation in preimplantation embryos.
    PLoS Genet. (2017) 13, e1007042.
  • Sugimura S, Kobayashi N, Okae H, Yamanouchi T, Matsuda H, Kojima T, Yajima A, Hashiyada Y, Kaneda M, Sato K, Imai K, Tanemura K, Arima T, Gilchrist RB.
    Transcriptomic signature of the follicular somatic compartment surrounding an oocyte with high developmental competence.
    Sci Rep. (2017) 7, 6815.
  • Yoshihara M, Sato T, Saito D, Ohara O, Kuramoto T, Suyama M.
    A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo.
    BMC Genet. (2017) 18, 29.
  • Shirane K, Kurimoto K, Yabuta Y, Yamaji M, Satoh J, Ito S, Watanabe A, Hayashi K, Saitou M, Sasaki H.
    Global landscape and regulatory principles of DNA methylation reprogramming for germ cell specification by mouse pluripotent stem cells.
    Dev Cell. (2016) 39, 87–103.
  • Kobayashi N, Okae H, Hiura H, Chiba H, Shirakata Y, Hara K, Tanemura K, Arima T.
    Genome-scale assessment of age-related DNA methylation changes in mouse spermatozoa.
    PLoS One. (2016) 23, 11.
  • Kubo N, Toh H, Shirane K, Shirakawa T, Kobayashi H, Sato T, Sone H, Sato Y, Tomizawa S, Tsurusaki Y, Shibata H, Saitsu H, Suzuki Y, Matumoto N, Suyama M, Kono T, Ohbo K, Sasaki H.
    DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis.
    BMC Genomics. (2015) 16, 624.
  • Kitamura A, Miyauchi N, Hamada H, Hiura H, Chiba H, Okae H, Sato A, John RM, Arima T.
    Epigenetic alterations in sperm associated with male infertility.
    Congenit Anom (Kyoto). (2015) 55, 133–144.
  • Migita O, Maehara K, Kamura H, Miyakoshi K, Tanaka M, Morokuma S, Fukushima K, Shimamoto T, Saito S, Sago H, Nishihama K, Abe K, Nakabayashi K, Umezawa A, Okamura K, Hata K.
    Compilation of copy number variants identified in phenotypically normal and parous Japanese women.
    J Hum Genet. (2014) 59, 326–331.