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

• Daskeviciute D, Chappell-Maor L, Sainty B, Arnaud P, Iglesias-Platas I, Simon C, Okae H, Arima T, Vassena R, Lartey J, Monk D.
  Non-canonical imprinting, manifesting as post-fertilization placenta-specific parent-of-origin dependent methylation, is not conserved in humans.
  Hum Mol Genet. (2025) in press.
• Gonçalves IM, Afzal M, Kennedy N, Moita A, Lima R, Ostrovidov S, Hori T, Nashimoto Y, Kaji H.
  Placental microphysiological systems: new advances on promising platforms that mimic the microenvironment of the human placenta.
  Lab Chip. (2025) 25:979-995.
• Shukla V, Iqbal K, Okae H, Arima T, Soares MJ.
  Effects Of Aryl Hydrocarbon Receptor Ligand TCDD On Human Trophoblast Cell Development.
  bioRxiv. (2025) 2024.08.27.609205.
• Toh H, Okae H, Shirane K, Sato T, Hamada H, Kikutake C, Saito D, Arima T, Sasaki H, Suyama M.
  Epigenetic dynamics of partially methylated domains in human placenta and trophoblast stem cells.
  BMC Genomics. (2024) 25:1050.
• Okae H, Shibata S, Arima T.
  Common and uncommon findings in marmoset and human trophoblast stem cells.
  Cell Stem Cell. (2024) 31:1387-1388.
• Shukla V, Moreno-Irusta A, Varberg KM, Kuna M, Iqbal K, Galligos AM, Aplin JD, Choudhury RH, Okae H, Arima T, Soares MJ.
  NOTUM-mediated WNT silencing drives extravillous trophoblast cell lineage development.
  Proc Natl Acid Sci USA. (2024) 21: e2403003121.
• Varberg KM, Moreno-Irusta A, Novoa A, Musser B, Varberg JM, Goering JP, Saadi I, Iqbal K, Okae H, Arima T, Williams J 3rd, Pisarska MD, Soares MJ.
  Leveraging chorionic villus biopsies for the derivation of patient-specific trophoblast stem cells.
  medRxiv. (2024) 2022.12.07.22283218.
• Shibata S, Endo S, Nagai LAE, H Kobayashi E, Oike A, Kobayashi N, Kitamura A, Hori T, Nashimoto Y, Nakato R, Hamada H, Kaji H, Kikutake C, Suyama M, Saito M, Yaegashi N, Okae H, Arima T.
  Modeling embryo-endometrial interface recapitulating human embryo implantation.
  Sci Adv. (2024) 10:eadi4819.
• Hori T, Okae H, Shibata S, Kobayashi N, Kobayashi EH, Oike A, Sekiya A, Arima T, Kaji H.
  Trophoblast stem cell-based organoid models of the human placental barrier.
  Nat Commun. (2024) 15:962.
• Shao R, Suzuki T, Suyama M, Tsukada Y.
  The impact of selective HDAC inhibitors on the transcriptome of early mouse embryos.
  BMC Genomics. (2024) 25:143.
• Shimizu T, Oike A, Kobayashi EH, Sekiya A, Kobayashi N, Shibata S, Hamada H, Saito M, Yaegashi N, Suyama M, Arima T, Okae H.
  CRISPR screening in human trophoblast stem cells reveals both shared and distinct aspects of human and mouse placental development.
  Proc Natl Acad Sci USA. (2023) 120:e2311372120.
• Varberg KM, Dominguez EM, Koseva B, Varberg JM, McNally RP, Moreno-Irusta A, Wesley ER, Iqbal K, Cheung WA, Schwendinger-Schreck C, Smail C, Okae H, Arima T, Lydic M, Holoch K, Marsh C, Soares MJ, Grundberg E.
  Extravillous trophoblast cell lineage development is associated with active remodeling of the chromatin landscape.
  Nat Commun. (2023) 14:4826.
• Frost JM, Amante SM, Okae H, Jones EM, Ashley B, Lewis RM, Cleal JK, Caley MP, Arima T, Maffucci T, Branco MR.
  Regulation of human trophoblast gene expression by endogenous retroviruses.
  Nat Struct Mol Biol. (2023) 30:527-538.
• Kuna M, Dhakal P, Iqbal K, Dominguez EM, Kent LN, Muto M, Moreno-Irusta A, Kozai K, Varberg KM, Okae H, Arima T, Sucov HM, Soares MJ.
  CITED2 is a conserved regulator of the uterine-placental interface.
  Proc Natl Acad Sci USA. (2023) 120:e2213622120.
• Kobayashi EH, Shibata S, Oike A, Kobayashi N, Hamada H, Okae H, Arima T.
  Genomic imprinting in human placentation.
  Reprod Med Biol. (2022) 21:e12490.
• 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) 119:e2203071119.
• 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.

• Sekita T, Asano N, Kubo T, Totsuka H, Mitani S, Hattori N, Yoshida A, Kobayashi E, Komiyama M, Ushijima T, Nakayama R, Nakamura M, Kawai A, Ichikawa H.
  Early separation and parallel clonal selection of dedifferentiated and well-differentiated components in dedifferentiated liposarcoma.
  Neoplasia. (2025) 59:101074.
• Azechi T, Fukaya Y, Nitani C, Hara J, Kawamoto H, Taguchi T, Yoshimura K, Sato A, Hattori N, Ushijima T, Kimura T.
  Population Pharmacokinetics of Tamibarotene in Pediatric and Young Adult Patients with Recurrent or Refractory Solid Tumors.
  Curr Oncol. (2024) 31:7155-7164.
• Mori Y, Akizuki Y, Honda R, Takao M, Tsuchimoto A, Hashimoto S, Iio H, Kato M, Kaiho-Soma A, Saeki Y, Hamazaki J, Murata S, Ushijima T, Hattori N, Ohtake F.
  Intrinsic signaling pathways modulate targeted protein degradation.
  Nat Commun. (2024) 15:5379.
• Yamamoto Y, Watanabe T, Ureshino H, Kurahashi Y, Fukuda-Kurahashi Y, Kamachi K, Kawasoe K, Kidoguchi K, Yamashita S, Hattori N, Ushijima T, Kimura S.
  DNA demethylating agents for chemoprevention of oncovirus-associated leukemogenesis.
  Leukemia. (2024) 38:1613-1616.
• Sasaki A, Takeshima H, Yamashita S, Ichita C, Kawachi J, Naito W, Ohashi Y, Takeuchi C, Fukuda M, Furuichi Y, Yamamichi N, Ando T, Kobara H, Kotera T, Itoi T, Sumida C, Hamada A, Koizumi K, Ushijima T.
  Severe induction of aberrant DNA methylation by nodular gastritis in adults.
  J Gastroenterol. (2024) 59:442-456.
• Kobayashi M, Fujisaki J, Namikawa K, Hoteya S, Sasaki A, Shibagaki K, Yao K, Abe S, Oda I, Ueyama H, Isomoto H, Ito M, Sugimoto M, Kawai T, Kodama M, Murakami K, Adachi K, Matsuhashi N, Ohata K, Ushijima T, Kato M, Miyamoto S, Yoshimura D, Yao T, Yagi K, Iwaizumi M, Uemura N.
  Multicenter study of invasive gastric cancer detected after 10 years of Helicobacter pylori eradication in Japan: Clinical, endoscopic, and histopathologic characteristics.
  DEN Open. (2024) 4:e345.
• Takeuchi C, Sato J, Yamamichi N, Kageyama-Yahara N, Sasaki A, Akahane T, Aoki R, Nakajima S, Ito M, Yamamichi M, Liu YY, Sakuma N, Takahashi Y, Sakaguchi Y, Tsuji Y, Sakurai K, Tomida S, Niimi K, Ushijima T, Fujishiro M.
  Marked intestinal trans-differentiation by autoimmune gastritis along with ectopic pancreatic and pulmonary trans-differentiation.
  J. Gastroenterol. (2024) 59:95-108.
• Takeuchi C, Yamashita S, Liu YY, Takeshima H, Sasaki A, Fukuda M, Hashimoto T, Naka T, Ishizu K, Sekine S, Yoshikawa T, Hamada A, Yamamichi N, Fujishiro M, Ushijima T.
  Precancerous nature of intestinal metaplasia with increased chance of conversion and accelerated DNA methylation.
  Gut. (2024) 73:255-267.
• Nishiyama K, Nishinakamura H, Takeshima H, Yuyu L, Takeuchi C, Hattori N, Takeda H, Yamashita S, Wakabayashi M, Sato K, Obama K, Ushijima T.
  Mouse methylation profiles for leukocyte cell types, and estimation of leukocyte fractions in inflamed gastrointestinal DNA samples.
  PLoS One. (2023) 18:e0290034.
• Arai N, Hattori N, Yamashita S, Liu YY, Ebata T, Takeuchi C, Takeshima H, Fujii S, Kondo H, Mukai H, Ushijima T.
  HSD17B4 methylation enhances glucose dependence of BT-474 breast cancer cells and increases lapatinib sensitivity.
  Breast Cancer Res Treat. (2023) 201:317-328.
• Irie T, Yamada H, Takeuchi C, Liu YY, Charvat H, Shimazu T, Ando T, Maekita T, Abe S, Takamaru H, Kodama M, Murakami K, Sugimoto K, Sakamoto K, Ushijima T.
  The methylation level of a single cancer risk marker gene reflects methylation burden in gastric mucosa.
  Gastric Cancer. (2023) 26:667-676.
• Hattori N, Liu YY, Ushijima T.
  DNA Methylation Analysis.
  Methods Mol Biol. (2023) 2691:165-183.
• 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.

• Nagaoka Y, Nakato R.
  Analysis and Visualization of Multiple Hi-C and Micro-C Data with CustardPy.
  Methods Mol Biol. (2025) 2856:223-238.
• Nakato R.
  Exploring Contact Distance Distributions with Google Colaboratory.
  Methods Mol Biol. (2025) 2856:179-196.
• Saijou E, Kamiya Y, Fujiki K, Shirahige K, Nakato R.
  Modulation of liver cholesterol homeostasis by choline supplementation during fibrosis resolution.
  Heliyon. (2024) 10: e36727.
• Nagagaki Y, Kozakura Y, Mahandaran T, Fumoto Y, Nakato R, Shirahige K, Ishikawa F.
  Histone H3.3 chaperone HIRA renders stress-responsive genes poised for prospective lethal stresses in acquired tolerance.
  Genes Cells. (2024) 29:722-734.
• Oba GM, Nakato R.
  Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach.
  Genes Cells. (2024) 29:456-470.
• Uneme Y, Maeda R, Nakayama G, Narita H, Takeda N, Hiramatsu R, Nishihara H, Nakato R, Kanai Y, Araki K, Siomi MC, Yamanaka S.
  Morc1 reestablishes H3K9me3 heterochromatin on piRNA-targeted transposons in gonocytes.
  Proc Natl Acad Sci USA. (2024) 121: e2317095121.
• Nagai LAE, Lee S, Nakato R.
  Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform.
  STAR Protoc. (2024) 5:102926.
• Jeppsson K, Pradhan B, Sutani T, Sakata T, Umeda Igarashi M, Berta DG, Kanno T, Nakato R, Shirahige K, Kim E, Björkegren C.
  Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils.
  Mol Cell. (2024) 84:867-882.
• Wang J, Nakato R.
  Churros: a Docker-based pipeline for large-scale epigenomic analysis.
  DNA Res. (2024) 31:dsad026.
• Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K.
  Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors.
  Nat Commun. (2023) 14:5647.
• Wang J, Nakato R.
  Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells.
  iScience. (2023) 26:106908.
• Wang J, Nakato R.
  CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells.
  Nucleic Acids Res. (2022) 51:D70-D79.
• 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.
• 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.