Nakato laboratory

Publication List

Jeppsson K., Sakata T., Nakato R., Milanova S., Shirahige K., Bjoerkegren C.
Transcription and replication organize cohesin-dependent chromosome loops
bioRxiv (preprint), 2020.
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, S1046-2023, issue 20, 30059-1, 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,Volume 2, Issue 2, June 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-Vallieres 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, 87-995, 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, 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
Mol. Cell. Biol., 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., Sjogren 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.
Muller 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.