{"id":280,"date":"2017-03-13T16:45:50","date_gmt":"2017-03-13T07:45:50","guid":{"rendered":"http:\/\/www2.med.osaka-u.ac.jp\/wwwmed\/eng\/activities\/research\/genome\/molecular-genetics"},"modified":"2026-11-06T13:13:14","modified_gmt":"2026-11-06T04:13:14","slug":"developmental_epigenetics","status":"publish","type":"page","link":"https:\/\/www.med.osaka-u.ac.jp\/eng\/introduction\/research\/genome\/developmental_epigenetics","title":{"rendered":"Developmental Epigenetics"},"content":{"rendered":"<ul class=\"linkBar clearfix\">\n<li><a href=\"https:\/\/www.bdr.riken.jp\/en\/research\/labs\/hiratani-i\/index.html\" target=\"_blank\" rel=\"noopener\">\u7814\u7a76\u5ba4\u30a6\u30a7\u30d6\u30b5\u30a4\u30c8<\/a><\/li>\n<li><a href=\"https:\/\/www.med.osaka-u.ac.jp\/introduction\/research\/genome\/developmental_epigenetics\">Text in Japanese<\/a><\/li>\n<p><!-- \n\n<li><a href=\"#\" target=\"_blank\" class=\"pdf\" rel=\"noopener\">\u5927\u5b66\u9662\u751f\u5411\u3051\u7814\u7a76\u6982\u8981<\/a><\/li>\n\n --><\/ul>\n<div class=\"index\">\n<div class=\"title\">Unraveling the spatiotemporal regulation of 3D genome organization that underlies diverse biological functions<\/div>\n<ul>\n<li>Investigating the establishment of somatic-type DNA replication timing program during development and differentiation<\/li>\n<li>Cross-species comparison of DNA replication timing and 3D genome organization dynamics<\/li>\n<li>Comprehensive analysis of genome dynamics using single-cell multiomics approaches<\/li>\n<li>Development of high-resolution scRepli-seq for single-cell genome-wide DNA replication profiling<\/li>\n<\/ul>\n<\/div>\n<div class=\"profile\">\n<div class=\"clearfix\">\n<div class=\"fl photo\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone wp-image-10008 size-medium\" src=\"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001-375x400.jpg?_t=1793846673\" alt=\"\" width=\"375\" height=\"400\" srcset=\"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001-375x400.jpg 375w, https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001-960x1024.jpg 960w, https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001-768x819.jpg 768w, https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001-1440x1536.jpg 1440w, https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/09\/hiratani20261001.jpg 1578w\" sizes=\"(max-width: 375px) 100vw, 375px\" \/><\/div>\n<div class=\"name\"><span class=\"position\">Professor <\/span>Ichiro Hiratani<\/div>\n<div class=\"member\">Developmental Epigenetics<\/div>\n<div class=\"description\">We seek to understand the spatiotemporal regulation of 3D genome organization, which underlies divese genome functions, including gene expression, using DNA replication timing as a key entry point. Building on our original single-cell genome-wide DNA replication profiling technology, we aim to uncover how diverse cell types balance genome function with genome integrity.<\/div>\n<\/div>\n<\/div>\n<h3>Unraveling how diverse cell types maintain and faithfully transmit their genomes while ensuring proper genome function, using our unique single-cell technologies<\/h3>\n<p>During development from a fertilized egg into a multicellular organism, DNA replication, 3D genome organization, and transcription undergo dynamic changes, gradually establishing somatic-type genome regulatory programs. However, genome-wide analysis of cells in vivo has been technically challenging, and the dynamics of these processes have remained poorly understood at the single-cell level. Because the spatiotemporal regulation of DNA replication closely reflects 3D genome organization (Figure, top panel), DNA replication timing serves as a useful index to study genome architecture. In 2008, we developed a genome-wide DNA replication timing profiling method, which we subsequently extended into a single-cell technology, scRepli-seq, in collaboration with our colleagues in 2019 (Takahashi et al., Nat Genet 2019; Figure, middle panel). This unique approach has enabled us, for the first time, to characterize DNA replication dynamics during development and differentiation at the single-cell level and to infer changes in 3D genome organization.<\/p>\n<p>Using embryonic stem cell differentiation, early mouse embryogenesis, and X chromosome inactivation as model systems, we have demonstrated that DNA replication regulation is far more diverse and flexible than previously appreciated (Miura et al., Nat Genet 2019; Poonperm et al., Nat Struct Mol Biol 2023; Takahashi et al., Nature 2024; Figure, bottom panel, illustrating the discovery of multiple previously unrecognized modes of DNA replication regulation in early mouse embryos). More recently, we have also shown that the re-establishment of an orderly 3D chromosome organization during G1\/S following cell division plays an important role in regulating subsequent DNA replication (Oji et al., Nat Commun 2026).<\/p>\n<p class=\"figure\"><img decoding=\"async\" class=\"imgC\" src=\"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-content\/uploads\/2026\/11\/hiratani_eng_fig.jpg\" alt=\"\" \/> <span class=\"caption\">Figure<\/span><\/p>\n<p>Together, our studies clearly demonstrate that 3D genome organization and DNA replication regulation undergo flexible changes depending on developmental stage and cell type. These changes are strongly interconnected, raising the possibility that the two processes are coordinately regulated. Disruption of such coordinated regulation may lead to chromosomal abnormalities, making this an important area of investigation with medical relevance. Moving forward, with a particular focus on early mouse embryos, we aim to uncover the molecular basis and biological significance of this flexibility and coordination, and to understand how diverse cell types faithfully maintain and transmit their genomes while ensuring proper genome function.<\/p>\n<p>To observe what other researchers have not been able to see or even recognize, we need flexible thinking, unwavering determination, and unique technologies. Building on our single-cell genome-wide DNA replication profiling technology, scRepli-seq, we will continue to develop new single-cell analytical approaches.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>\u7814\u7a76\u5ba4\u30a6\u30a7\u30d6\u30b5\u30a4\u30c8 Text in Japanese Unraveling the spatiotemporal regulation of 3D genome organization that underlies d [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":76,"menu_order":192,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"_links":{"self":[{"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/280"}],"collection":[{"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/comments?post=280"}],"version-history":[{"count":7,"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/280\/revisions"}],"predecessor-version":[{"id":10286,"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/280\/revisions\/10286"}],"up":[{"embeddable":true,"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/pages\/76"}],"wp:attachment":[{"href":"https:\/\/www.med.osaka-u.ac.jp\/eng\/wp-json\/wp\/v2\/media?parent=280"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}