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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.

2022-01-18 | GSE136226 | GEO

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

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

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Project description:Human DNA Replication Timing Variation

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

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

Project description:We have investigated the role of the histone methyltransferase G9a in the establishment of silent nuclear compartments. Following conditional knockout of the G9a methyltransferase in mouse ESCs, 167 genes were significantly up-regulated, and no genes were strongly down-regulated. A partially overlapping set of 119 genes were up-regulated after differentiation of G9a-depleted cells to neural precursors. Promoters of these G9a-repressed genes were AT rich and H3K9me2 enriched but H3K4me3 depleted and were not highly DNA methylated. Representative genes were found to be close to the nuclear periphery, which was significantly enriched for G9a-dependent H3K9me2. Strikingly, although 73% of total genes were early replicating, more than 71% of G9a-repressed genes were late replicating, and a strong correlation was found between H3K9me2 and late replication. However, G9a loss did not significantly affect subnuclear position or replication timing of any non-pericentric regions of the genome, nor did it affect programmed changes in replication timing that accompany differentiation. We conclude that G9a is a gatekeeper for a specific set of genes localized within the late replicating nuclear periphery. 4 cell states each in duplicate (i.e. a total of 8 individual replicates)

2010-06-20 | E-GEOD-18076 | biostudies-arrayexpress

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

2009-11-02 | E-GEOD-18079 | biostudies-arrayexpress

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

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

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Replication-Timing Boundaries Facilitate Cell-type and Species-specific Regulation of a Rearranged Human Chromosome in Mouse

Project description:In multicellular organisms, developmental changes to replication timing occur in 400- 800 kb domains across half the genome. While clear examples of epigenetic control of replication timing have been described, a role for DNA sequence in mammalian replication timing has not been substantiated. To assess the role of DNA sequences in directing these changes, we profiled replication timing in mice carrying a genetically rearranged Human Chromosome 21 [Hsa21]. In two distinct mouse cell types, Hsa21 sequences maintained human-specific replication timing, except at points of Hsa21 rearrangement. Changes in replication timing at rearrangements extended up to 900 kb and consistently reconciled with the wild-type replication pattern at developmental boundaries of replication-timing domains. Our results demonstrate DNA sequencedriven regulation of Hsa21 replication timing during development and provide evidence that mammalian chromosomes consist of multiple independent units of replication timing regulation.

2012-06-05 | GSE38472 | GEO

Replication-Timing Boundaries Facilitate Cell-type and Species-specific Regulation of a Rearranged Human Chromosome in Mouse

2012-06-04 | E-GEOD-38472 | biostudies-arrayexpress

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