Nakato laboratory

Publication List

Ozawa H, Kambe A, Hibi K, Murakami S, Oikawa A, Handa T, Fujiki K, Nakato R, Shirahige K, Kimura H, Shiraki N, Kume S.
Transient methionine deprivation triggers histone modification and potentiates differentiation of induced pluripotent stem cells,
Stem Cells, vol 41, issue 3, 271-286, 2023.
Wang J, Nakato R.
CohesinDB: a comprehensive database for decoding cohesin-related epigenomes, 3D genomes and transcriptomes in human cells,
Nucleic Acids Research, vol 51, issue D1, D70-D79, 2023.
Fujimoto M, Takii R, Matsumoto M, Okada M, Nakayama KI, Nakato R, Fujiki K, Shirahige K, Nakai A.
HSF1 phosphorylation establishes an active chromatin state via the TRRAP-TIP60 complex and promotes tumorigenesis,
Nature Communications, vol 13, issue 1, 2022.
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,
Science Advances, vol 8, issue 23, 2022.
Wang J, Bando M, Shirahige K, Nakato R.
Large-scale multi-omics analysis suggests specific roles for intragenic cohesin in transcriptional regulation,
Nature Communications, vol 13, issue 1, 2022.
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 (preprint), 2022.
Kawabata A, Hayashi T, Akasu-Nagayoshi Y, Yamada A, Shimizu N, Yokota N, Nakato R, Shirahige K, Okamoto A, Akiyama T.
CRISPR/Cas9 Screening for Identification of Genes Required for the Growth of Ovarian Clear Cell Carcinoma Cells,
Current issues in molecular biology, vol. 44, issue 4, 1587-1596, 2022.
Akasu-Nagayoshi Y, Hayashi T, Kawabata A, Shimizu N, Yamada A, Yokota N, Nakato R, Shirahige K, Okamoto A, Akiyama T.
PHOSPHATE exporter XPR1/SLC53A1 is required for the tumorigenicity of epithelial ovarian cancer,
Cancer science, vol. 113, issue 6, 2034-2043, 2022.
Machino H, Kaneko S, Komatsu M, Ikawa N, Asada K, Nakato R, Shozu K, Dozen A, Sone K, Yoshida H, Kato T, Oda K, Osuga Y, Fujii T, von Keudell G, Saloura V, Hamamoto R.
The metabolic stress-activated checkpoint LKB1-MARK3 axis acts as a tumor suppressor in high-grade serous ovarian carcinoma,
Communications biology, vol. 5, issue 1, 39-39, 2022.
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 & Development, vol. 36, issue 1-2, 84-102, 2022.
Cona B, Hayashi T, Yamada A, Shimizu N, Yokota N, Nakato R, Shirahige K, Akiyama T.
The splicing factor DHX38/PRP16 is required for ovarian clear cell carcinoma tumorigenesis, as revealed by a CRISPR-Cas9 screen,
FEBS Open Bio, vol. 12, issue 3, 582-593, 2021.
Koui Y, Himeno M, Mori Y, Nakano Y, Saijou E, Tanimizu N, Kamiya Y, Anzai H, Maeda N, Wang L, Yamada T, Sakai Y, Nakato R, Miyajima A, Kido T.
Development of human iPSC-derived quiescent hepatic stellate cell-like cells for drug discovery and in vitro disease modeling,
Stem Cell Reports, vol. 16, issue 12, 3050-3063, 2021.
Wang J, Nakato R.
HiC1Dmetrics: framework to extract various one-dimensional features from chromosome structure data,
Briefings in Bioinformatics, vol. 23, issue 1, bbab509, 2021.
Nakajima N, Hayashi T, Fujiki K, Shirahige K, Akiyama T, Akutsu T, Nakato R.
Codependency and mutual exclusivity for gene community detection from sparse single-cell transcriptome data,
Nucleic Acids Research, vol. 49, issue 18, e104, 2021.
Nakajima N, Akutsu T, Nakato R.
Databases for Protein-Protein Interactions,
Methods in Molecular Biology (Springer), vol. 2021, issue. 2361, 229-248, 2021.
Shinkai S, Onami S, Nakato R.
Toward understanding the dynamic state of 3D genome,
Computational and Structural Biotechnology Journal, vol. 18, 2259-2269, 2020.
Tanaka S, Ise W, Inoue T, Ito A, Ono C, Shima Y, Sakakibara S, Nakayama M, Fujii K, Miura I, Sharif J, Koseki H, Koni P.A, Raman I, Li Q, Kubo M, Fujiki K, Nakato R, Shirahige K, Araki H, Miura F, Ito T, Kawakami E, Baba Y, Kurosaki T.
Tet2 and Tet3 in B cells are required to repress CD86 and prevent autoimmunity,
Nature Immunology, vol.21, issue 8, 950-961, 2020.
Seong KH, Ly NH, Katou Y, Yokota N, Nakato R, Murakami S, Hirayama A, Fukuda S, Kang S, Soga T, Shirahige K, Ishii S.
Paternal restraint stress affects offspring metabolism via ATF-2 dependent mechanisms in Drosophila melanogaster germ cells,
Communications Biology, vol. 3, issue 208, 2020.
Nakato R, Sakata T.
Methods for ChIP-seq analysis: A practical workflow and advanced applications,
Methods, vol. 187, 44-53, 2020.
Shinkai S, Nakagawa M, Sugawara T, Togashi Y, Ochiai H, Nakato R, Taniguchi Y, Onami S.
PHi-C: deciphering Hi-C data into polymer dynamics,
NAR Genomics and Bioinformatics, vol. 2, issue 2, 2020.
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, vol. 12, issue 1, 77, 2019.
Fiordaliso SK, Iwata-Otsubo A, Ritter AL, Quesnel-Vallières M, Fujiki K, Nishi E, Hancarova M, Miyake N, Morton JEV, Lee S, Hackmann K, Bando M, Masuda K, Nakato R, Arakawa M, Bhoj E, Li D, Hakonarson H, Takeda R, Harr M, Keena B, Zackai EH, Okamoto N, Mizuno S, Ko JM, Valachova A, Prchalova D, Vlckova M, Pippucci T, Seiler C, Choi M, Matsumoto N, Di Donato N, Barash Y, Sedlacek Z, Shirahige K, Izumi K.
Missense Mutations in NKAP Cause a Disorder of Transcriptional Regulation Characterized by Marfanoid Habitus and Cognitive Impairment,
Am J Hum Genet, vol. 105, issue 5, 987-995, 2019.
Kawasaki Y, Miyamoto M, Oda T, Matsumura K, Negishi L, Nakato R, Suda S, Yokota N, Shirahige K, Akiyama T.
The novel lncRNA CALIC upregulates AXL to promote colon cancer metastasis,
The EMBO Reports, vol. 20, e47052, 2019.
Ueda S, Cordeiro IR, Moriyama Y, Nishimori C, Kai KI, Yu R, Nakato R, Shirahige K, Tanaka M.
Cux2 refines the forelimb field by controlling expression of Raldh2 and Hox genes,
Biology Open, vol. 8, issue 2, 2019.
Nakato R, Shirahige K.
Sensitive and robust assessment of ChIP-seq read distribution using a strand-shift profile,
Bioinformatics, vol. 34, issue 14, 2356-2363, 2018.
Kuroki S, Nakai Y, Maeda R, Okashita N, Akiyoshi M, Yamaguchi Y, Kitano S, Miyachi H, Nakato R, Ichiyanagi K, Shirahige K, Kimura H, Shinkai Y, Tachibana M.
Combined Loss of JMJD1A and JMJD1B Reveals Critical Roles for H3K9 Demethylation in the Maintenance of Embryonic Stem Cells and Early Embryogenesis,
Stem Cell Reports, vol. 10, issue 4, 1340-1354, 2018.
Nakato R, Shirahige K.
Statistical Analysis and Quality Assessment of ChIP-seq Data with DROMPA,
Methods in Molecular Biology (Springer), 1672, 631-643, 2018.
Fujimoto M, Takii R, Takaki E, Katiyar A, Nakato R, Shirahige K, Nakai A.
The HSF1-PARP13-PARP1 complex facilitates DNA repair and promotes mammary tumorigenesis,
Nature Communications, vol.8, issue 1, 2017.
Bleuyard JY, Fournier M, Nakato R, Couturier AM, Katou Y, Ralf C, Hester SS3, 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. (PNAS), vol. 114, issue 29, 7671-7676, 2017.
Sakai A, Nakato R, Ling Y, Hou X, Hara N, Iijima T, Yanagawa Y, Kuwano R, Okuda S, Shirahige K, Sugiyama S.
Genome-Wide Target Analyses of Otx2 Homeoprotein in Postnatal Cortex,
Frontiers in Neuroscience, 11:307, 2017.
Murakami S, Minami-Ohtsubo M, Nakato R, Shirahige K, Tabata T.
Two components of aversive memory in Drosophila, anesthesia-sensitive and anesthesia-resistant memory, require distinct domains within the Rgk1 small GTPase,
The Journal of Neuroscience, vol. 37, issue 22, 5496-5510, 2017.
Fujita Y, Masuda K, Bando M, Nakato R, Katou Y, Tanaka T, Nakayama M, Takao K, 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
The Journal of Experimental Medicine, vol. 214, issue 5, 1431-1452, 2017.
Nakato R, Shirahige K.
Recent advances in ChIP-seq analysis: from quality management to whole-genome annotation,
Briefings in Bioinformatics, vol. 18, issue 2, 279-290, 2017.
Kubota T, Katou Y, Nakato R, Shirahige K, Donaldson AD.
Replication-Coupled PCNA Unloading by the Elg1 Complex Occurs Genome-wide and Requires Okazaki Fragment Ligation,
Cell Reports, vol. 12, issue 5, 774-787, 2015.
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,
Nature Communications, vol. 6, issue 7815, 2015.
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., vol. 290, issue 35, 21713-23, 2015.
Balint A, Kim T, Gallo D, Cussiol JR, Bastos de Oliveira FM, Yimit A1, Ou J, Nakato R, Gurevich A, Shirahige K, Smolka MB, Zhang Z, Brown GW.
Assembly of Slx4 signaling complexes behind DNA replication forks,
The EMBO Journal, vol. 34, issue 16, 2182-2197, 2015.
Minamino M, Ishibashi M, Nakato R, Akiyama K, Tanaka H, Kato Y, Negishi L, Hirota T, Sutani T, Bando M, Shirahige K.
Esco1 Acetylates Cohesin via a Mechanism Different from That of Esco2,
Current Biology, vol. 25, issue 13, 1694-1706, 2015.
Izumi K, Nakato R, Zhang Z, Edmondson AC, Noon S, Dulik MC, Rajagopalan R, Venditti CP, Gripp K, Samanich J, Zackai EH, Deardorff MA, Clark D, Allen JL, Dorsett D, Misulovin Z, Komata M, Bando M, Kaur M, Katou Y, Shirahige K, Krantz ID.
Germline gain-of-function mutations in AFF4 cause a developmental syndrome functionally linking the super elongation complex and cohesin,
Nature Genetics, vol. 47, issue 4, 338-344, 2015.
Takii R, Fujimoto M, Tan K, Takaki E, Hayashida N, Nakato R, Shirahige, K, Nakai A.
ATF1 modulates the heat shock response by regulating the stress-inducible HSF1-transcription complex,
Molecular and Cellular Biology, vol. 30, issue 1, 11-25, 2015.
Jeppsson K, Carlborg KK, Nakato R, Berta DG, Lilienthal I, Kanno T, Lindqvist A, Brink MC, Dantuma NP, Katou Y, Shirahige K, Sjögren C.
The chromosomal association of the Smc5/6 complex depends on cohesion and predicts the level of sister chromatid entanglement,
PLOS Genetics vol. 10, issue 10, e1004680, 2014.
Suda N, Itoh T, Nakato R, Shirakawa D, Bando M, Katou Y, Kataoka K, Shirahige K, Tickle C, Tanaka M.
Dimeric combinations of MafB, cFos and cJun control the apoptosis-survival balance in limb morphogenesis
Development vol. 141, issue 14, 2885-2894, 2014.
Yata K, Bleuyard JY, Nakato R, Ralf C, Katou Y, Schwab RA, Niedzwiedz W, Shirahige K, Esashi F.
BRCA2 coordinates the activities of cell-cycle kinases to promote genome stability,
Cell Reports, vol. 7, issue 5, 1547-1559, 2014.
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, vol. 14, issue 2, 217-227, 2014.
Zuin J, Franke V, van Ijcken WF, van der Sloot A, Krantz ID, van der Reijden MI, Nakato R, Lenhard B, Wendt KS.
A cohesin-independent role for NIPBL at promoters provides insights in CdLS
PLoS Genetics, Feb 13, 2014.
Gallego-Paez L.M, Tanaka H, Bando M, Takahashi M, Nozaki N, Nakato R, Shirahige K, Hirota T.
Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells,
Molecular Biology of the Cell, vol.25, issue 2, Nov. 20, 2013.
Müller C.A, Hawkins M, Retkute R, Malla S, Wilson R, Blythe M.J, Nakato R, Komata M, Shirahige K, Moura A, Nieduszynski C.A.
The dynamics of genome replication using deep sequencing,
Nucleic Acids Research, vol. 42, issue 1, Oct. 1, 2013.
Kon A, Shih LY, Minamino M, Sanada M, Shiraishi Y, Nagata Y, Yoshida K, Okuno Y, Bando M, Nakato R, Ishikawa S, Sato-Otsubo A, Nagae G, Nishimoto A, Haferlach C, Nowak D, Sato Y, Alpermann T, Nagasaki M, Shimamura T, Tanaka H, Chiba K, Yamamoto R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Nakamaki T, Ishiyama K, Nolte F, Hofmann WK, Miyawaki S, Chiba S, Mori H, Nakauchi H, Koeffler HP, Aburatani H, Haferlach T, Shirahige K, Miyano S, Ogawa S.
Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms,
Nature Genetics, vol. 45, issue 10, 2013.
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 to Cells, vol. 18, issue 7, 589-601, 2013.
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, vol. 12, issue 3, 368-382, 2013.
Foltman M, Evrin C, De Piccoli G, Jones R.C, Edmondson R.D, Katou Y, Nakato R, Shirahige K, Labib K.
Eukaryotic replisome components cooperate to process histones during chromosome replication,
Cell Rep., vol. 3, issue 3, 892-904, 2013.
Tazumi A, Fukuura M, Nakato R, Kishimoto A, Takenaka T, Ogawa S, Song J.H, Takahashi T.S, Nakagawa T, Shirahige K, Masukata H.
Telomere-binding protein Taz1 controls global replication timing through its localization near late replication origins in fission yeast,
Genes & Development, vol. 26, issue 18, 2012.
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, vol. 489, issue 7415, 313-317, 2012.
*These authors contributed equally to this work.
De Piccoli, G, Katou, Y, Itoh, T, Nakato, R, Shirahige, K, Labib, K.
Replisome stability at defective DNA replication forks is independent of S-phase checkpoint kinases,
Molecular Cell, vol. 45, issue 5, 696-704, 2012.
Masumoto H, Nakato R, Kanemaki M, Shirahige K, Hachinohe M.
The inheritance of histone modifications depends upon the location in the chromosome in Saccharomyces cerevisiae,
PLoS ONE, vol. 6, issue 23, e28980, 2011.
Tanaka S, Nakato R, Katou Y, Shirahige K, Araki H.
Origin Association of Sld3, Sld7, and Cdc45 Proteins Is a Key Step for Determination of Origin-Firing Timing,
Current Biology, vol. 21, issue 24, 2055-2063, 2011.
Nakato R, Gotoh O.
Cgaln: fast and space-efficient whole-genome alignment,
BMC Bioinformatics, Vol. 11, 224, 2010.