Laboratory for
Epigenome Inheritance
RIKEN IMS, Yokohama, Japan
Featured publications
Full publications (2019~)
Click titles to jump to the article page.
Click PDF icon to download papers.
25. Mei H*, Kozuka C, Kumon M, Koseki H, and Inoue A*†. (2026) (*Equal contribution)
H2AK119ub1–MLL2 counteraction underlies heritable H3K27me3 formation in oocytes.
Molecular Cell 86, 1-17.doi.org/10.1016/j.molcel.2026.03.014
– プレスリリース「世代を超えるエピゲノムの確立機構を解明－卵の“遺伝子てんびん”が次世代の発生を支える－」
– 白根健次郎先生（大阪大学）による紹介記事
– Highlighted by BioArt
24. Kyogoku H†, Tarama M, Matsuwaka M, Mishina T, Harada A, Nakagawa R, Kumon M, Shimizu Y, Ohkawa Y, Shibata T, Inoue A, Kitajima TS†. (2026)
Cytoplasmic competition between separate parental pronuclei in zygotes.
Nature Apr 29. doi: 10.1038/s41586-026-10417-7.
*We contributed to this study by low-input ChIP-sequencing for histone modifications in zygotes.
– プレスリリース「命の始まりは父母ゲノムの「別居」から－父母ゲノム間の競合が受精卵の発生を助ける－」
23. Horii T†, Morita S, Hino S, Hino Y, Fukushima SH, Kobayashi R, Kimura M, Nakano M, Mizukami Y, Inoue A, Hatada I†. (2025)
Germline epigenome editing identifies H3K9me3 as a mediator of intergenerational DNA methylation recovery in mice.
Nature Communications Dec 25;16(1):11200. doi: 10.1038/s41467-025-67488-9.
*We contributed to this study by low-input ChIP-sequencing for histone modifications in early embryos.
22. Kozuka C†. (2025)
The Journal of Biochemistry, Nov 19:mvaf070. doi: 10.1093/jb/mvaf070.
21. Nosaka Y, Nagano M, Yabuta Y, Nakakita B, Nagaoka SI, Okamoto I, Sasada H, Mizuta K, Umemura F, Kuma H, Okochi Y, Katou Y, de Massy B, Inoue A, Horie A, Mandai M, Ohta H, Saitou M†. (2025)
Developmental Cell, Jun 27:S1534-5807(25)00363-6. doi: 10.1016/j.devcel.2025.06.008
*We contributed to this study by low-input ChIP-sequencing for histone modifications in in vitro produced oocytes.
20. Mei H*, Hayashi R*, Kozuka C, Kumon M, Koseki H, Inoue A† (2025) (*Equal contribution)
Nature Structural & Molecular Biology, 32(10):1883-1893. doi: 10.1038/s41594-025-01573-x
– プレスリリース「卵子成熟に必須のエピゲノム因子を発見－ヒストンH2A.Zが卵特有のヒストン修飾の確立を促す」
– 石内崇士先生（山梨大学）による紹介記事
– Research Highlight"Identifying a critical component for eggs in mice"
19. Fukushima SH† and Takeda H†. (2025)
Nature Communications 16:5222. https://doi.org/10.1038/s41467-025-60246-x
– プレスリリース「初期発生における遺伝子発現の仕組みを解明－複数種類のヒストン修飾が協調的に遺伝子発現 を制御」
– Research Highlight"How embryos first regulate their genes"
18. Takao T, Matsui A, Kikutake C, Kan-O K, Inoue A, Suyama M, Okamoto I, Ito M†. (2025)
Nature Communications 13;16(1):631. doi: 10.1038/s41467-025-55941-8
*We contributed to this study by low-input ChIP-sequencing for histone modifications in ILC2.
17. Matsuwaka M, Kumon M, Inoue A†. (2025)
Nature Cell Biology 27(1): 28–38, doi: 10.1038/s41556-024-01553-1
– Highlighted by Nat Cell Biol, Building the epigenetic fortress with PRC2.2
– プレスリリース「発生最初期の遺伝子スイッチの作り方－不育症メカニズムの解明に向けて－」
– 大保和之先生（横浜市立大学）による紹介記事
16. Mori M, Koshiguchi M, Takenouchi O, Mukose MA, Takase HM, Mishina T, Mei H, Kihara M, Abe T, Inoue A, Kitajima TS†. (2024)
Aging-associated reduction of chromosomal histones in mammalian oocytes.
Genes to Cells 29(10):808-819. doi: 10.1111/gtc.13146
*We contributed to this study by low-input MNase-sequencing in oocytes.
15. Toriyama K, Au Yeung WK, Inoue A, Kurimoto K, Yabuta Y, Saitou M, Nakamura T, Nakano T, Sasaki H†. (2024)
DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells.
BMC Genomics 25(1):344. doi: 10.1186/s12864-024-10192-7.
14. Fukuda K, Shimi T, Shimura C, Ono T, Suzuki T, Onoue K, Okayama S, Miura H, Hiratani I, Ikeda K, Okada Y, Dohmae N, Yonemura S, Inoue A, Kimura H, Shinkai Y†. (2023)
Epigenetic plasticity safeguards heterochromatin configuration in mammals.
Nucleic Acid Research 7;51(12):6190-6207 doi: 10.1093/nar/gkad387.
*We contributed to this study by low-input ChIP-sequencing for histone modifications in MEFs.
13. Richard Albert J, Kobayashi T, Inoue A, Monteagudo-Sánchez A, Kumamoto S, Takashima T, Miura A, Oikawa M, Miura F, Takada S, Hirabayashi M, Korthauer K, Kurimoto K, Greenberg MVC, Lorincz M, Kobayashi H†. (2023)
Conservation and divergence of canonical and non-canonical imprinting in murids.
Genome Biology 24(1):48. doi: 10.1186/s13059-023-02869-1.
*We contributed to this study by low-input ChIP-sequencing for histone modifications in rat oocytes.
12. Inoue A†. (2023)
Noncanonical imprinting: Intergenerational epigenetic inheritance mediated by Polycomb complexes.
Current Opinion in Genetics & Development. 78:102015, 1-9
11. Hayashi R, Inoue A†. (2023)
Low-input CUT&RUN for Mouse Oocytes and Preimplantation Embryos.
Methods Mol Biol 2577:83-92. doi: 10.1007/978-1-0716-2724-2_6.
10. Kai Y*†, Mei H*, Kawano H, Nakajima N, Takai A, Kumon M, Inoue A†, Yamashita N. (2022) (*Equal contribution)
PLoS One Dec 1;17(12):e0278663. doi: 10.1371/journal.pone.0278663 *Co-first, †Co-corresponding
*We contributed to this study by RNA-sequencing in human blastocyst embryos.
9. Miyao T, Miyauchi M, Kelly ST, Terooatea TW, Ishikawa T, Oh E, Hirai S, Horie K, Takakura Y, Ohki H, Hayama M, Maruyama Y, Seki T, Ishii H, Yabukami H, Yoshida M, Inoue A, Sakaue-Sawano A, Miyawaki A, Muratani M, Minoda A, Akiyama N, Akiyama T†. (2022)
Integrative analysis of scRNA-seq and scATAC-seq revealed transit-amplifying thymic epithelial cells expressing autoimmune regulator.
eLife May 17;11:e73998. doi: 10.7554/eLife.73998.
8. Matoba S*, Kozuka C*, Miura K, Inoue K, Kumon M, Hayashi R, Ohhata T, Ogura A, Inoue A*†. (2022) (*Equal contribution)
Noncanonical imprinting sustains embryonic development and restrains placental overgrowth.
Genes & Development 36(7-8):483-494. doi: 10.1101/gad.349390.122.
– プレスリリース「母親ゲノムの記憶が胎児を育む－胎盤と胚発生に重要な刷り込み遺伝子を同定」
– 立花誠先生（大阪大学）による紹介記事
– Highlighted by Discover Magazine, New research helps us understand miscarriage and placenta
development
– 日刊工業新聞2022.5.19「胚・胎盤形成 遺伝子を同定 理研 不妊症の原因解明期待」
7. Kusuyama J, Makarewicz NS, Albertson BG, Alves-Wagner AB, Conlin RH, Prince NB, Alves CRR, Ramachandran K, Kozuka C, Xiudong Y, Xia Y, Hirshman MF, Hatta T, Nagatomi R, Nozik ES, Goodyear LJ. (2022)
Maternal Exercise-Induced SOD3 Reverses the Deleterious Effects of Maternal High Fat Diet on Offspring Metabolism Through Stabilization of H3K4me3 and Protection Against WDR82 Carbonylation.
Diabetes 71(6):1170-1181. doi: 10.2337/db21-0706.
6. Kozuka C, Efthymiou V, Sales VM, Zhou L, Osataphan S, Yuchi Y, Chimene-Weiss J, Mulla C, Isganaitis E, Desmond J, Sanechika S, Kusuyama J, Goodyear L, Shi X, Gerszten RE, Aguayo-Mazzucato C, Carapeto P, Teixeira SD, Sandoval D, Alonso-Curbelo D, Wu L, Qi J, Patti ME. (2022)
Bromodomain Inhibition Reveals FGF15/19 as a Target of Epigenetic Regulation and Metabolic Control.
Diabetes 71(5), 1023-1033
5. Mei H*, Kozuka C, Hayashi R, Kumon M, Koseki H, Inoue A*†. (2021) (*Equal contribution)
H2AK119ub1 guides maternal inheritance and zygotic deposition of H3K27me3 in mouse embryos.
Nature Genetics 53, 539-550.
– Highlighted by Nat Genet, The Polycomb landscape in mouse development
– プレスリリース 「卵の記憶は胎盤へ –卵のエピジェネティック修飾が次世代に伝承される機構を解明」
– 塩見春彦先生（慶應義塾大学）による紹介記事
4. Kusuyama J, Alves-Wagner AB, Conlin RH, Makarewicz NS, Albertson BG, Prince NB, Kobayashi S, Kozuka C, Møller M, Bjerre M, Fuglsang J, Miele E, Middelbeek RJW, Xiudong Y, Xia Y, Garneau L, Bhattacharjee J, Aguer C, Patti ME, Hirshman MF, Jessen N, Hatta T, Ovesen PG, Adamo KB, Nozik-Grayck E, Goodyear LJ. (2021)
Placental superoxide dismutase 3 mediates benefits of maternal exercise on offspring health.
Cell Metabolism 33, 939-956.e8.
3. Chen Z, Yin Q, Inoue A, Zhang C, Zhang Y†. (2019)
Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells.
Science Advances 5, eaay7246.
2. Yang KT*, Inoue A*, Lee YJ, Jiang CL, Lin FJ†. (2019) (*Equal contribution)
Loss of Ikbkap/Elp1 in mouse oocytes causes spindle disorganization, developmental defects in preimplantation embryos and impaired female fertility.
Scientific Reports 9(1), 18875. *Co-first
1. Shishikura K, Kuroha S, Matsueda S, Iseki H, Matsui T, Inoue A, Arita M†. (2019)
Acyl-CoA synthetase 6 regulates long-chain polyunsaturated fatty acid composition of membrane phospholipids in spermatids and supports normal spermatogenic processes in mice.
The FASEB Journal 33(12), 14194-203.
Selected PUBLICATIONS (~2018)
17. Inoue A*, Chen Z*, Yin Q, Zhang Y. (2018)
Genes Dev 32, 1-12 *Co-first.
16. Djekidel MN*, Inoue A*, Matoba S, Suzuki T, Zhang C, Lu F, Jiang L, Zhang Y. (2018)
Cell Reports 23, 1939-47. *Co-first.
15. Inoue A#, Jiang L, Lu F, Zhang Y. (2017) #Corresponding
Genomic imprinting of Xist by maternal H3K27me3.
Genes Dev 31, 1927-32.
14. Inoue A*, Jiang L*, Lu F*, Suzuki T, Zhang Y. (2017)
Maternal H3K27me3 controls DNA methylation-independent imprinting.
Nature 547(7664), 419-24. *Co-first.
Highlighted by Nat Rev MCB, Getting instructions from mum.
Highlighted by Nat Struct Mol Biol, Oocyte-derived histone H3 lysine 27 methylation controls gene
expression in the early embryo.
Highlighted by Genome Biol, Genomic imprinting beyond DNA methylation: a role for maternal histones.
Highlighted by BioArt, 重大发现：张毅组Nature揭示基因印迹的新机制【附朱冰点评】丨BioArt特别推荐
Highlighted by Nat Rev MCB, Imprints in the history of epigenetics.
Highlighted by AASJ論文ウォッチ (2017年7月26日), 「もう一つのインプリンティング」
13. Lu F*, Liu Y*, Inoue A*, Suzuki T, Zhao K, Zhang Y. (2016)
Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development.
Cell 165(6), 1375-88. *Co-first.
12. Inoue A, Shen L, Matoba S, Zhang Y. (2015)
Cell Reports 10(4), 763-70.
11. Shen L*,Inoue A*, He J, Liu Y, Lu F, Zhang Y. (2014)
Cell Stem Cell 15, 459-70. *Co-first.
10. Inoue A#, Sunaga K, Aoki F, Zhang Y. (2014) #Corresponding
siRNA-mediated depletion of stable proteins in mouse oocytes.
Protocol Exchange. doi:10.1038/protex.2014.024
9. Inoue A#, Zhang Y. (2014) #Corresponding
Nucleosome assembly is required for nuclear pore complex assembly in mouse zygotes.
Nature Structural & Molecular Biology 21, 609-16.
8. Inoue A, Matoba S, Zhang Y. (2012)
Cell Research 22(12):1640-9.
7. Inoue A, Shen L, Dai Q, He C, Zhang Y. (2011)
Cell Research 21(12):1670-6.
Selected as the cover of the issue and as an Editor’s Choice 2011
6. Inoue A, Zhang Y. (2011)
Replication-dependent loss of 5-hydroxymethylcytosine in mouse preimplantation embryos.
Science 334(6053):194.
5. Inoue A, Ogushi S, Saitou M, Suzuki GM, Aoki F. (2011)
Involvement of mouse nucleoplasmin 2 in the decondensation of sperm chromatin after fertilization.
Biol Reprod 85(1):70-7.
4. Inoue A, Aoki F. (2010)
The FASEB Journal 24(2):485-94.
3. Inoue A, Murata Y, Takahashi H, Tsuji N, Fujisaki S, Kato J. (2008)
Involvement of an essential gene, mviN, in murein synthesis in Escherichia coli.
J Bacteriol 190(21):7298-301.
2. Inoue A, Nakajima R, Nagata M, Aoki F. (2008)
Human Reproduction 23(6):1377-84.
1. Inoue A, Akiyama T, Nagata M, and Aoki F. (2007)
The perivitelline space-forming capacity of mouse oocytes is associated with meiotic competence.
J Reprod Dev 53(5):1043-52.