Hi-C technology has revolutionized genome biology, revealing that mammalian chromosomes are partitioned into megabase-sized topologically associating domains (TADs). TADs can be in either A (active) or B (inactive) nuclear compartments, which exhibit early and late DNA replication timing (RT), respectively. Several years ago, we developed a single-cell DNA replication sequencing technology, scRepli-seq, which has allowed us to monitor genome-wide RT dynamics and infer 3D genome organization dynamics in single cells. In this seminar, I will discuss our ongoing efforts to leverage scRepli-seq to understand the regulatory principles of 3D genome organization through the lens of DNA replication regulation. Topics include the 3D genome and replication dynamics during mammalian development, X-chromosome inactivation, and cell cycle, as well as our ongoing effort to understand the mechanism and significance of RT/compartment regulation. 

References: 

Takahashi S, Kyogoku H, Hayakawa T, Miura H, Oji A, Kondo Y, Takebayashi SI, Kitajima TS, Hiratani I. Embryonic genome instability upon DNA replication timing program emergence. Nature 633:686-694 (2024)

Oji A, Choubani L, Miura H, and Hiratani I. Structure and dynamics of A/B compartments and subcompartments. Curr Opin Cell Biol 90:102406 (2024) https://doi.org/10.1016/j.ceb.2024.102406 

Poonperm R, Ichihara S, Miura H, Tanigawa A, Nagao K, Obuse C, Sado T, Hiratani I. Replication dynamics identifies the folding principles of the inactive X chromosome. Nat Struct Mol Biol 30:1224-1237 (2023) 

 Miura H and Hiratani I. Cell cycle dynamics and developmental dynamics of the 3D genome: toward linking the two timescales. Curr Opin Genet Dev 73:101898 (2022)  

 Poonperm R and Hiratani I. Formation of a multi-layered 3-dimensional structure of the heterochromatin compartment during early mammalian development. Dev Growth Differ 63:5-17 (2021) 

Miura H, Takahashi S, Shibata T, Nagao K, Obuse C, Okumura K, Ogata M, Hiratani I, Takebayashi SI. Mapping replication timing domains genome wide in single mammalian cells with single-cell DNA replication sequencing. Nat Protoc 15:4058-4100 (2020) 

Miura H, Takahashi S, Poonperm R, Tanigawa A, Takebayashi SI, Hiratani I. Single-cell DNA replication profiling identifies spatiotemporal developmental dynamics of chromosome organization. Nat Genet 51:1356-1368 (2019)

Takahashi S, Miura H, Shibata T, Nagao K, Okumura K, Ogata M, Obuse C, Takebayashi SI, Hiratani I. Genome-wide stability of the DNA replication program in single mammalian cells. Nat Genet 51:529-540 (2019)