Publication List
2024 |
2023 |
2022 |
2021 |
2020 |
2019
(* Corresponding author)
2024
- Springer Book "Computational Methods for 3D Genome Analysis" (Editors: Ryuichiro Nakato, non-peer-reviewed)
- *Saijou E, Kamiya Y, Fujiki K, Shirahige K, Nakato R.
Modulation of liver cholesterol homeostasis by choline supplementation during fibrosis resolution,
Heliyon, vol. 10, issue 17, e36727, 2024.
- Lee S, Lin C, Chen CY, *Nakato R.
ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach,
bioRxiv, July 26, 2024.
- 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 to Cells, vol. 29, issue 9, 722-734, 2024.
- Oba GM, *Nakato R.
Clover: An unbiased method for prioritizing differentially expressed genes using a data-driven approach,
Genes to Cells, vol. 29, issue 6, 456-470, 2024.
- 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,
Proceedings of the National Academy of Sciences (PNAS), vol. 121, Issue 13, 2024.
- *Nagai LAE, Lee S, *Nakato R.
Protocol for identifying differentially expressed genes using the RumBall RNA-seq analysis platform,
STAR Protocols, vol. 5, Issue 1, 2024.
- *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,
Science Advances, vol. 10, issue 8, 2024.
- *Jeppsson K, Pradhan B, Sutani T, Sakata T, Umeda-Igarashi M, Berta DG, Kanno T, Nakato R, Shirahige K, *Kim E, *Bjökegren C.
Loop-extruding Smc5/6 organizes transcription-induced positive DNA supercoils,
Molecular Cell, vol. 84, Issue 5, 867-882, 2024.
- Wang J, *Nakato R.
Churros: A docker-based pipeline for large-scale epigenomic analysis,
DNA Research, vol. 31, issue 1, 2024.
2023
- Li M, Nishimura T, Takeuchi Y, Hongu T, Wang Y, Shiokawa D, Wang K, Hirose H, Sasahara A, Yano M, Ishikawa S, Inokuchi M, Ota T, Tanabe M, Tada K, Akiyama T, Cheng X, Liu C, Yamashita T, Sugano S, Uchida Y, Chiba T, Asahara H, Nakagawa M, Sato S, Miyagi Y, Shimamura T, Nagai LAE, Kanai A, Katoh M, Nomura S, Nakato R, Suzuki Y, Tojo A, Voon D, Ogawa S, Okamoto K, Foukakis T, *Gotoh N.
FXYD3 functionally demarcates an ancestral breast cancer stem cell subpopulation with features of drug-tolerant persisters,
The Journal of Clinical Investigation, vol 133, issue 22, 2023.
- *Homma M, Nakato R, Niida A, Bando M, Fujiki K, Yokota N, Yamamoto S, Shibata T, Takagi M, Yamaki J, Kozuka-Hata H, Oyama M, Shirahige K, Homma Y.
Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexes,
Life Science Alliance, vol 7, issue 1, 2023.
- *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,
Nature Communications, vol 14, issue 1, 2023.
- *Nagai H, Nagai LAE, Tasaki S, Nakato R, Umetsu D, Kuranaga E, Miura M, *Nakajima Y.
Nutrient-driven dedifferentiation of enteroendocrine cells promotes adaptive intestinal growth in Drosophila,
Developmental Cell, vol 58, issue 18, P1764-1781, 2023.
- *Oka M, Otani M, Miyamoto Y, Oshima R, Adachi J, Tomonaga T, Asally M, Nagaoka Y, Tanaka K, Toyoda A, Ichikawa K, Morishita S, Isono K, Koseki H, *Nakato R, *Ohkawa Y, Yoneda Y.
Phase-separated nuclear bodies of nucleoporin fusions promote condensation of MLL1/CRM1 and rearrangement of 3D genome structure,
Cell Reports, vol 42, issue 8, 2023.
- Wang J, *Nakato R.
Comprehensive multiomics analyses reveal pervasive involvement of aberrant cohesin binding in transcriptional and chromosomal disorder of cancer cells,
iScience, vol 26, issue 6, 2023.
- Sorimachi Y, Kobayashi H, Shiozawa Y, Koide S, Nakato R, Shimizu Y, Okamura T, Shirahige K, Iwama A, Goda N, Takubo K, *Takubo K.
Mesenchymal loss of p53 alters stem cell capacity and models human soft tissue sarcoma traits,
Stem Cell Reports, vol 18, issue 5, 1211-1226, 2023.
- 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.
2022
- 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.
- 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.
2021
- 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.
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, 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.
2019
- 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.
