RIKEN Center for Biosystems Dynamics Research Laboratory for Developmental Epigenetics

Team Director: Ichiro Hiratani (Ph.D.)

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Research Summary

Understanding the 3D organization of the genomic DNA, which is the source of heredity, is essential for life science because it would lead to a fundamental understanding of various genome functions. However, many difficult questions remain unresolved. We are tackling these challenging questions by focusing on DNA replication regulation, which reflects the 3D genome structure. In particular, we aim to understand the regulation of the 3D genome organization during development, differentiation, and disease progression by combining advanced technologies such as scRepli-seq, our homemade genome-wide single-cell DNA replication sequencing technology, and Hi-C, a genome-wide methodology for analyzing the 3D genome architecture.

Main Research Fields

Biology

Related Research Fields

Biological Sciences

Keywords

3D genome organization
Epigenetics
DNA replication timing
Embryonic stem cell differentiation
Single-cell genome-wide sequencing technology

Selected Publications

1.Choubani L, Miura H, Ichinose T, et al.
"Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase."
eLife 15, RP110073 (2026) doi: 10.7554/eLife.110073
2.Elumalai J, Hiratani I.
"Single-cell mapping of chromosome breaks identifies multiple fragile site classes with distinct DNA replication timing landscapes."
Nature Communications 17, 9055 (2026) doi: 10.1038/s41467-026-76451-1
3.Oji A, Yusa K, Noda I, et al.
"Nuclear compartmentalization at the G1/S transition plays a key role in DNA replication control."
Nature Communications 17, 6961 (2026) doi: 10.1038/s41467-026-75264-6
4.Hiratani I.
"Regulation of DNA replication and 3D genome organization during early embryogenesis."
Current Opinion in Genetics & Development 98, 102469 (2026) doi: 10.1016/j.gde.2026.102469
5.Poonperm R, Yoneda T, Imada T, et al.
"scRepli-RamDA-seq: a multi-omics technology enabling the analysis of gene expression dynamics during S-phase."
Nature Communications 16, 10902 (2025) doi: 10.1038/s41467-025-64688-1
6.Takahashi S, Kyogoku H, Hayakawa T, et al.
"Embryonic genome instability upon DNA replication timing program emergence."
Nature 633, 686-694 (2024) doi: 10.1038/s41586-024-07841-y
7.Poonperm R, Ichihara S, Miura H, et al.
"Replication dynamics identifies the folding principles of the inactive X chromosome."
Nature Structural & Molecular Biology 30, 1224-1237 (2023) doi: 10.1038/s41594-023-01052-1
8.Miura H, Takahashi S, Shibata T, et al.
"Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing."
Nature Protocols 15, 4058-4100 (2020) doi: 10.1038/s41596-020-0378-5
9.Miura H, Takahashi S, Poonperm R, et al.
"Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization."
Nature Genetics 51, 1356-1368 (2019) doi: 10.1038/s41588-019-0474-z
10.Takahashi S, Miura H, Shibata T, et al.
"Genome-wide stability of the DNA replication program in single mammalian cells."
Nature Genetics 51, 529-540 (2019) doi: 10.1038/s41588-019-0347-5