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Genome-wide analysis of replication timing in ESC and 2CLC during 2CLC emergence [transitional]

ABSTRACT: The timing of DNA replication is an important developmentally regulated regional property that is correlated with gene expression, chromatin state, GC content, subnuclear structure. These correlations reflect the variable accessibility of origins to a limited pool of initiation factors within different context, and the extent to which changes in replication timing occur during differentiation. Therefore, temporal order of genome replication could be sufficient to identify the cell type. A lot of studies for characterizing DNA replication have been done using many different types of cells, however, the pattern of it in the totipotent cells is still entirely unknown. In this study, we try to understand the molecular basis underlying totipotency by identifying specific DNA replication features found exclusively in totipotent cells.

ORGANISM(S): Mus musculus

PROVIDER: GSE136227 | GEO | 2022/01/18

REPOSITORIES: GEO

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Genome-wide analysis of replication timing in ESC and 2CLC [stable]

Project description:The timing of DNA replication is an important developmentally regulated regional property that is correlated with gene expression, chromatin state, GC content, subnuclear structure. These correlations reflect the variable accessibility of origins to a limited pool of initiation factors within different context, and the extent to which changes in replication timing occur during differentiation. Therefore, temporal order of genome replication could be sufficient to identify the cell type. Several studies for characterizing DNA replication have been done using many different types of cells, however, the pattern of it in the totipotent cells is still entirely unknown. In this study, we try to understand the molecular basis underlying totipotency by identifying specific DNA replication features found exclusively in totipotent cells.

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Project description:Faithful DNA replication is essential for genome integrity. Under-replicated DNA leads to chromosome segregation defects, which are reportedly common during embryogenesis. However, DNA replication regulation remains poorly understood in early mammalian embryos. Here, we constructed a single-cell genome-wide DNA replication atlas of pre-implantation mouse embryos and discovered an abrupt replication program switch accompanied by a transient period of genomic instability. In 1- and 2-cell embryos, we observed the complete absence of a replication timing (RT) program, and the entire genome replicated gradually and uniformly using extremely slow-moving forks. In 4-cell embryos, a somatic-cell-like RT program commenced abruptly. However, the fork speed was still slow, S-phase was extended, and SLX4 DNA repair foci increased during G2/M, which was followed by a transient increase in chromosome segregation errors. Importantly, live imaging captured longer S-phase of error cells, and the breakpoints identified by single-cell genome sequencing were enriched in late-replicating regions. By the 8-cell stage, forks gained speed, S-phase was no longer extended, and chromosome aberrations disappeared. Thus, a transient period of genomic instability exists during normal mouse development, which is preceded by a fragile S-phase lacking the coordination between replisome-level regulation and megabase-scale RT regulation, implicating the importance of their coordination for genome integrity.

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G9a selectively represses a class of late-replicating genes at the nuclear periphery (Expression)

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