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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


Team Arima

  • Jeyarajah MJ, Bhattad GJ, Kelly RD, Yang P, Okae H, Arima T, Renaud SJ.
    The multifaceted role of GCM1 during trophoblast differentiation in the human placenta.
    Proc Natl Acad Sci USA. (2022) in press.
  • Kobayashi N, Okae H, Hiura H, Kubota N, Kobayashi HE, Shibata S, Oike A, Hori T, Kikutake C, Hamada H, Kaji H, Suyama M, Bortolin-Cavaillé M, Cavaillé J, Arima T.
    The microRNA cluster C19MC confers differentiation potential into trophoblast lineages upon human pluripotent stem cells.
    Nat Commun. (2022) 13, 3071.
  • Hada M, Miura H, Tanigawa A, Matoba S, Inoue K, Ogonuki N, Hirose M, Watanabe N, Nakato R, Fujiki K, Hasegawa A, Sakashita A, Okae H, Miura K, Shikata D, Arima T, Shirahige K, Hiratani I, Ogura A.
    Highly rigid H3.1/H3.2-H3K9me3 domains set a barrier for cell fate reprogramming in trophoblast stem cells.
    Genes Dev. (2022) 36, 84-102.
  • Gonçalves IM, Rodrigues RO, Moita AS, Hori T, Kaji H, Lima RA, Minas G.
    Recent trends of biomaterials and biosensors for organ-on-chip platforms.
    Bioprinting. (2022) 26, e00202.
  • Gonçalves IM, Carvalho V, Rodrigues RO, Pinho D, Teixeira SCF, Moita A, Hori T, Kaji H, Lima R, Minas G.
    Organ-on-a-chip platforms for drug screening and delivery in tumor cells: a systematic review.
    Cancers. (2022) 4, 935.
  • Kikutake C, Suyama M.
    Pan-cancer analysis of mutations in open chromatin regions and their possible association with cancer pathogenesis.
    Cancer Med. (2022) 11, 3902-3916.
  • Kubota N, Suyama M.
    Mapping of promoter usage QTL using RNA-seq data reveals their contributions to complex traits.
    PLoS Comput. Biol. (2022) 18, e1010436.
  • Varberg KM, Iqbal K, Muto M, Simon ME, Scott RL, Kozai K, Choudhury RH, Aplin JD, Biswell R, Gibson M, Okae H, Arima T, Vivian JL, Grundberg E, Soares MJ.
    ASCL2 reciprocally controls key trophoblast lineage decisions during hemochorial placenta development.
    Proc Natl Acad Sci USA. (2021) 10, e2016517118.
  • Raut B, Chen L, Hori T, Kaji H.
    An open-source add-on EVOM® device for real-time transepithelial/endothelial electrical resistance measurements in multiple transwell samples.
    Micromachines. (2021) 12, 282.
  • Shibata S, Kobayashi E, Kobayashi N, Oike A, Okae H, Arima T.
    Unique features and emerging in vitro models of human placental development.
    Reprod Med Biol. (2020) 19, 301-313.
  • Jessica KC, Sin YK, Guo Y, Hossain I, Sirois J, Russett CS, Tseng HW, Okae H, Arima T, Duchaine TF, Liu W, Pastor WA.
    Naive human embryonic stem cells can give rise to cells with a trophoblast-like transcriptome and methylome.
    Stem Cell Reports. (2020) 20, 30224.
  • Jaju Bhattad G, Jeyarajah MJ, McGill MG, Dumeaux V, Okae H, Arima T, Lajoie P, Bérubé NG, Renaud SJ.
    Histone deacetylase 1 and 2 drive differentiation and fusion of progenitor cells in human placental trophoblasts.
    Cell Death Dis. (2020) 5, 311.
  • Bhattacharya B, Home P, Ganguly A, Ray S, Ghosh A, Islam MR, French V, Marsh C, Gunewardena S, Okae H, Arima T, Paul S.
    Atypical protein kinase C iota (PKCλ/ι) ensures mammalian development by establishing the maternal-fetal exchange interface.
    Proc Natl Acad Sci U S A. (2020) 25,14280-14291.
  • Takahashi S, Okae H, Kobayashi N, Kitamura A, Kumada K, Yaegashi N, Arima T.
    Loss of p57KIP2 expression confers resistance to contact inhibition in human androgenetic trophoblast stem cells.
    Proc Natl Acad Sci USA. (2019) 116, 26606-26613.
  • Hattori H, Hiura H, Kitamura A, Miyauchi N, Kobayashi N, Takahashi S, Okae H, Kyono K, Kagami M, Ogata T, Arima T.
    Association of four imprinting disorders and ART.
    Clinical Epigenetics. (2019) 1, 21.

Team Ushijima

  • Ueda S, Yamashita S, Nakajima M, Kumamoto T, Ogawa C, Liu YY, Yamada H, Kubo E, Hattori N, Takeshima H, Wakabayashi M, Iida N, Shiraishi Y, Noguchi M, Sato Y, Ushijima T.
    A quantification method of somatic mutations in normal tissues and their accumulation in pediatric patients with chemotherapy.
    Proc Natl Acad Sci USA. (2022) 119, e2123241119.
  • Yamada H, Takeshima H, Fujiki R, Yamashita S, Sekine S, Ando T, Hattori N, Okabe A, Yoshikawa T, Obama K, Katai H, Kaneda A, Ushijima T.
    ARID1A loss-of-function induces CpG island methylator phenotype.
    Cancer Lett. (2022) 532, 215587.
  • Tsuyuki S, Takeshima H, Sekine S, Yamagata Y, Ando T, Yamashita S, Maeda S, Yoshikawa T, Ushijima T.
    Comparable genetic alteration profiles between gastric cancers with current and past Helicobacter pylori infection.
    Sci Rep. (2021) 11, 23443.
  • Ushijima T, Clark SJ, Tan P.
    Mapping genomic and epigenomic evolution in cancer ecosystems.
    Science. (2021) 373, 1474-1479.

Team Nakato

  • Wang J, Nakato R.
    CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.
    Nucleic Acids Res. (2022) in press.
  • Jeppsson K, Sakata T, Nakato R, Milanova S, Shirahige K, Bjökegren C.
    Cohesin-dependent chromosome loop extrusion is limited by transcription and stalled replication forks.
    Sci Adv. (2022) 8, eabn7063.
  • Wang J, Bando M, Shirahige K, Nakato R.
    Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation.
    Nat Commun. (2022) 13, 3218.
  • Nakato R, Sakata T, Wang J, Nagai LAE, Oba GM, Bando M, Shirahige K.
    Context-dependent 3D genome regulation by cohesin and related factors.
    bioRxiv. (2022) preprint.
  • Wang J, Nakato R.
    HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data.
    Brief Bioinform. (2021) 23, bbab509.
  • Nakato R, Sakata T.
    Methods for ChIP-seq analysis: A practical workflow and advanced applications.
    Methods. (2020) 187, 44-53.
  • Nakato R, Wada Y, Nakaki R, Nagae G, Katou Y, Tsutsumi S, Nakajima N, Fukuhara H, Iguchi A, Kohro T, Kanki Y, Saito Y, Kobayashi M, Izumi-Taguchi A, Osato N, Tatsuno K, Kamio A, Hayashi-Takanaka Y, Wada H, Ohta S, Aikawa M, Nakajima H, Nakamura M, McGee RC, Heppner KW, Kawakatsu T, Genno M, Yanase H, Kume H, Senbonmatsu T, Homma Y, Nishimura S, Mitsuyama T, Aburatani H, Kimura H, Shirahige K.
    Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells.
    Epigenetics Chromatin. (2019) 12, 77.

Publications before 2019