■ Books and Articles
|
1. |
Article |
Recent advances in methodologies of epigenomics Epigenomics pp.1-19 (Collaboration) 2025/11 |
| Language | English | | Publication Date | 2025/11 | | Type | Review Article or Commentary (Scientific Journal) | | Peer Review | With peer review | | Invitation | With invitation | | Title | Recent advances in methodologies of epigenomics | | Contribution Type | Joint Work | | Journal | Epigenomics | | Journal Type | Another Country | | Volume, Issue, Pages | pp.1-19 | | Authorship | Last author,Corresponding author | | Author and coauthor | Hiroaki Ohishi, Wan Kin Au Yeung | | Details | Rapid methodological breakthroughs over the past ten years have transformed epigenomics from bulk, population-averaged assays into single-cell, multi-omic, and intracellular spatial investigations. This review surveys the interconnected technology pillars that now map the epigenome with unprecedented breadth and resolution. First, advances in next-generation and long-read sequencing empower investigators to chart chromatin accessibility, histone and DNA modifications, and three-dimensional higher-order chromatin structure in thousands of individual cells while retaining allele-specific information across kilobase-long molecules. Second, live-cell fluorescence probes and multiplexed chromatin tracing enable visualizing the dynamic organization of epigenetic marks and genome architecture of intact nuclei and tissues. Third, integrative platforms merge base-level reads with their native 3D coordinates, providing a holistic view of gene regulation in physiologic context. We distill key biological insights yielded by each methodology, discuss unresolved and persistent limitations, and outline future directions toward routine, cost-effective investigations. Together, these innovations are redefining how we interrogate chromatin biology in health and disease. | | DOI | 10.1080/17501911.2025.2571391 | |
|
2. |
Article |
A deletion at the X-linked ARHGAP36 gene locus is associated with the orange coloration of tortoiseshell and calico cats Current Biology 35(12),pp.2816-2825 (Collaboration) 2025/05 |
| Language | English | | Publication Date | 2025/05 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | A deletion at the X-linked ARHGAP36 gene locus is associated with the orange coloration of tortoiseshell and calico cats | | Contribution Type | Joint Work | | Journal | Current Biology | | Journal Type | Another Country | | Volume, Issue, Pages | 35(12),pp.2816-2825 | | Authorship | Lead author | | Author and coauthor | Hidehiro Toh, Wan Kin Au Yeung, Motoko Unoki, Yuki Matsumoto, Yuka Miki, Yumiko Matsumura, Yoshihiro Baba, Takashi Sado, Yasukazu Nakamura, Miho Matsuda, Hiroyuki Sasaki | | DOI | 10.1016/j.cub.2025.03.075 | | PMID | 40378840 | |
|
3. |
Article |
DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells BMC Genomics 25(1) (Collaboration) 2024/04 |
| Language | English | | Publication Date | 2024/04 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells | | Contribution Type | Joint Work | | Journal | BMC Genomics | | Journal Type | Another Country | | Publisher | Springer Science and Business Media LLC | | Volume, Issue, Pages | 25(1) | | Authorship | Corresponding author | | Author and coauthor | Keisuke Toriyama,Wan Kin Au Yeung,Azusa Inoue,Kazuki Kurimoto,Yukihiro Yabuta,Mitinori Saitou,Toshinobu Nakamura,Toru Nakano,Hiroyuki Sasaki | | DOI | 10.1186/s12864-024-10192-7 | | ISSN | /1471-2164 | | PermalinkURL | https://link.springer.com/content/pdf/10.1186/s12864-024-10192-7.pdf | | URL for researchmap | https://link.springer.com/article/10.1186/s12864-024-10192-7/fulltext.html | |
|
4. |
Article |
The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes PLOS Genetics 19(8),pp.e1010855-e1010855 (Collaboration) 2023/08 |
| Language | English | | Publication Date | 2023/08 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes | | Contribution Type | Joint Work | | Journal | PLOS Genetics | | Journal Type | Another Country | | Publisher | Public Library of Science (PLoS) | | Volume, Issue, Pages | 19(8),pp.e1010855-e1010855 | | Author and coauthor | Ryuji Uehara,Wan Kin Au Yeung,Keisuke Toriyama,Hiroaki Ohishi,Naoki Kubo,Hidehiro Toh,Isao Suetake,Kenjiro Shirane,Hiroyuki Sasaki | | DOI | 10.1371/journal.pgen.1010855 | | ISSN | /1553-7404 | | PermalinkURL | https://dx.plos.org/10.1371/journal.pgen.1010855 | |
|
5. |
Article |
Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with distinctive genome-wide DNA hypomethylation Human molecular genetics 32(9),pp.1439-1456 (Collaboration) 2022/12 |
| Language | English | | Publication Date | 2022/12 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability, and facial anomalies (ICF) syndrome with distinctive genome-wide DNA hypomethylation | | Contribution Type | Joint Work | | Journal | Human molecular genetics | | Journal Type | Another Country | | Volume, Issue, Pages | 32(9),pp.1439-1456 | | Author and coauthor | Motoko Unoki,Guillaume Velasco,Satomi Kori,Kyohei Arita,Yasukazu Daigaku,Wan Kin Au Yeung,Akihiro Fujimoto,Hirofumi Ohashi,Takeo Kubota,Kunio Miyake,Hiroyuki Sasaki | | DOI | 10.1093/hmg/ddac291 | | PMID | 36458887 | |
|
6. |
Article |
CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers BMC bioinformatics 23(1),pp.371-371 (Collaboration) 2022/09 |
| Language | English | | Publication Date | 2022/09 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers | | Contribution Type | Joint Work | | Journal | BMC bioinformatics | | Journal Type | Another Country | | Volume, Issue, Pages | 23(1),pp.371-371 | | Authorship | Corresponding author | | Author and coauthor | Osamu Maruyama,Yinuo Li,Hiroki Narita,Hidehiro Toh,Wan Kin Au Yeung,Hiroyuki Sasaki | | DOI | 10.1186/s12859-022-04916-3 | | PMID | 36096737 | |
|
7. |
Book |
Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification (Collaboration) 2022/07 |
| Language | English | | Publication Date | 2022/07 | | Type | Scholarly Book | | Peer Review | With peer review | | Title | Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification | | Contribution Type | Joint Work | | Journal Type | Another Country | | Publisher | Springer Nature | | Authorship | Lead author,Corresponding author | | Author and coauthor | Wan Kin Au Yeung,Hiroyuki Sasaki | | PermalinkURL | https://link.springer.com/protocol/10.1007/978-1-0716-2380-0_14 | |
|
8. |
Article |
Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters Nature Cell Biology (Collaboration) 2021/09 |
|
|
|
9. |
Article |
A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns BMC bioinformatics 22(1),pp.341-341 (Collaboration) 2021/06 |
| Language | English | | Publication Date | 2021/06 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns | | Contribution Type | Joint Work | | Journal | BMC bioinformatics | | Journal Type | Another Country | | Volume, Issue, Pages | 22(1),pp.341-341 | | Authorship | Lead author,Corresponding author | | Author and coauthor | Wan Kin Au Yeung,Osamu Maruyama,Hiroyuki Sasaki | | DOI | 10.1186/s12859-021-04272-8 | | PMID | 34162326 | |
|
10. |
Article |
Reprogramming of the histone H3.3 landscape in the early mouse embryo Nature structural & molecular biology 28(1),pp.38-49 (Collaboration) 2021/01 |
| Language | English | | Publication Date | 2021/01 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Reprogramming of the histone H3.3 landscape in the early mouse embryo | | Contribution Type | Joint Work | | Journal | Nature structural & molecular biology | | Journal Type | Another Country | | Volume, Issue, Pages | 28(1),pp.38-49 | | Author and coauthor | Takashi Ishiuchi,Shusaku Abe,Kimiko Inoue,Wan Kin Au Yeung,Yuka Miki,Atsuo Ogura,Hiroyuki Sasaki | | DOI | 10.1038/s41594-020-00521-1 | | PMID | 33169018 | |
|
11. |
Article |
A Rice Immunophilin Homolog, OsFKBP12, Is a Negative Regulator of Both Biotic and Abiotic Stress Responses International journal of molecular sciences 21(22) (Collaboration) 2020/11 |
| Language | English | | Publication Date | 2020/11 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | A Rice Immunophilin Homolog, OsFKBP12, Is a Negative Regulator of Both Biotic and Abiotic Stress Responses | | Contribution Type | Joint Work | | Journal | International journal of molecular sciences | | Journal Type | Another Country | | Volume, Issue, Pages | 21(22) | | International coauthorship | International coauthorship | | Author and coauthor | Ming-Yan Cheung,Wan Kin Au Yeung,Kwan-Pok Li,Hon-Ming Lam | | DOI | 10.3390/ijms21228791 | | PMID | 33233855 | |
|
12. |
Article |
Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo Nature communications 11(1),pp.5417-5417 (Collaboration) 2020/10 |
| Language | English | | Publication Date | 2020/10 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo | | Contribution Type | Joint Work | | Journal | Nature communications | | Journal Type | Another Country | | Volume, Issue, Pages | 11(1),pp.5417-5417 | | International coauthorship | International coauthorship | | Author and coauthor | Julien Richard Albert,Wan Kin Au Yeung,Keisuke Toriyama,Hisato Kobayashi,Ryutaro Hirasawa,Julie Brind'Amour,Aaron Bogutz,Hiroyuki Sasaki,Matthew Lorincz | | DOI | 10.1038/s41467-020-19279-7 | | PMID | 33110091 | |
|
13. |
Article |
Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos Molecular cell 77(4),pp.825-839 (Collaboration) 2020/02 |
| Language | English | | Publication Date | 2020/02 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos | | Contribution Type | Joint Work | | Journal | Molecular cell | | Journal Type | Another Country | | Volume, Issue, Pages | 77(4),pp.825-839 | | International coauthorship | International coauthorship | | Author and coauthor | Zhenhai Du,Hui Zheng,Yumiko K Kawamura,Ke Zhang,Johanna Gassler,Sean Powell,Qianhua Xu,Zili Lin,Kai Xu,Qian Zhou,Evgeniy A Ozonov,Nathalie Véron,Bo Huang,Lijia Li,Guang Yu,Ling Liu,Wan Kin Au Yeung,Peizhe Wang,Lei Chang,Qiujun Wang,Aibin He,Yujie Sun,Jie Na,Qingyuan Sun,Hiroyuki Sasaki,Kikuë Tachibana,Antoine H F M Peters,Wei Xie | | DOI | 10.1016/j.molcel.2019.11.011 | | PMID | 31837995 | |
|
14. |
Article |
Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells Genes to cells : devoted to molecular & cellular mechanisms 25(1),pp.54-64 (Collaboration) 2020/01 |
| Language | English | | Publication Date | 2020/01 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells | | Contribution Type | Joint Work | | Journal | Genes to cells : devoted to molecular & cellular mechanisms | | Journal Type | Another Country | | Volume, Issue, Pages | 25(1),pp.54-64 | | Authorship | Lead author | | Author and coauthor | Hiroaki Ohishi,Wan Kin Au Yeung,Motoko Unoki,Kenji Ichiyanagi,Kei Fukuda,Shoji Maenohara,Kenjiro Shirane,Hatsune Chiba,Takashi Sado,Hiroyuki Sasaki | | DOI | 10.1111/gtc.12736 | | PMID | 31733167 | |
|
15. |
Article |
Histone H3K9 Methyltransferase G9a in Oocytes Is Essential for Preimplantation Development but Dispensable for CG Methylation Protection Cell reports 27(1),pp.282-293 (Collaboration) 2019/04 |
| Language | English | | Publication Date | 2019/04 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | Histone H3K9 Methyltransferase G9a in Oocytes Is Essential for Preimplantation Development but Dispensable for CG Methylation Protection | | Contribution Type | Joint Work | | Journal | Cell reports | | Journal Type | Another Country | | Volume, Issue, Pages | 27(1),pp.282-293 | | Authorship | Lead author | | International coauthorship | International coauthorship | | Author and coauthor | Wan Kin Au Yeung,Julie Brind'Amour,Yu Hatano,Kazuo Yamagata,Robert Feil,Matthew C Lorincz,Makoto Tachibana,Yoichi Shinkai,Hiroyuki Sasaki | | DOI | 10.1016/j.celrep.2019.03.002 | | PMID | 30943408 | |
|
16. |
Book |
Drought Stress and Tolerance in Soybean (Collaboration) 2013/01 |
| Language | English | | Publication Date | 2013/01 | | Type | Scholarly Book | | Peer Review | With peer review | | Title | Drought Stress and Tolerance in Soybean | | Contribution Type | Joint Work | | Journal Type | Another Country | | Publisher | IntechOpen | | International coauthorship | International coauthorship | | Author and coauthor | Yee Shan Ku,Wan Kin Au Yeung,Yuk Lin Yung,Man Wah Li,Chaoqing Wen,Xueyi Liu,Hon Ming Lam | | PermalinkURL | https://www.intechopen.com/chapters/40090 | |
|
17. |
Article |
The GCN2 homologue in Arabidopsis thaliana interacts with uncharged tRNA and uses Arabidopsis eIF2α molecules as direct substrates Plant biology (Stuttgart, Germany) 15(1),pp.13-8 (Collaboration) 2013/01 |
| Language | English | | Publication Date | 2013/01 | | Type | Research Paper (Scientific Journal) | | Peer Review | With peer review | | Title | The GCN2 homologue in Arabidopsis thaliana interacts with uncharged tRNA and uses Arabidopsis eIF2α molecules as direct substrates | | Contribution Type | Joint Work | | Journal | Plant biology (Stuttgart, Germany) | | Journal Type | Another Country | | Volume, Issue, Pages | 15(1),pp.13-8 | | Author and coauthor | M-W Li,Wan Kin Au Yeung,H-M Lam | | Details | Phosphorylation of eIF2α is an important strategy for living organisms to adapt to metabolic and physiological changes that are often associated with external stimuli. GCN2 is one of the well-studied eIF2α kinases in yeast and mammals, which is responsible for the survival of the organism under amino acid starvation. Despite the downstream reactions being quite divergent, AtGCN2 exhibits a high primary sequence similarity to its yeast and animal counterparts. In this study, we provide experimental evidence to show that AtGCN2 shares similar biochemical properties to the yeast and animal homologues. Our in vitro assays demonstrate the binding of the C-terminus of AtGCN2 to uncharged tRNA molecules and the enzymatic activities of AtGCN2 on both eIF2α homologues in A. thaliana, thus providing essential information for further understanding the functions of plant general control non-repressible (GCN) homologues. | | DOI | 10.1111/j.1438-8677.2012.00606.x | | PMID | 22672016 | |
|
Hide details for all
|
|
Display details for all
|
|
Display 5 items
|
|
Display all(17)
|
|
