Genome-wide analysis of replication timing in ESC and 2CLC [stable]
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PROVIDER: PRJNA561657 | ENA |
REPOSITORIES: ENA
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Project description:Genome-wide analysis of replication timing in ESC and 2CLC
| PRJNA561656 | ENA
Project description:Genome-wide analysis of replication timing in ESC and 2CLC during 2CLC emergence [transitional]
| PRJNA561658 | ENA
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
Project description:Mouse ESC 46C replication timing has been assessed by repli-chip.
2017-07-28 | GSE95090 | GEO
Project description:Eukaryotic chromosomes replicate in a temporal order known as the replication-timing program. In mammals, replication timing is cell type-specific with at least half the genome switching replication timing during development, primarily in units of 400-800 kilobases ('replication domains;), whose positions are preserved in different cell types, conserved between species, and appear to confine long-range effects of chromosome rearrangements. Early and late replication correlate, respectively, with open and closed three-dimensional chromatin compartments identified by high-resolution chromosome conformation capture (Hi-C), and, to a lesser extent, late replication correlates with lamina-associated domains (LADs). Recent Hi-C mapping has unveiled substructure within chromatin compartments called topologically associating domains (TADs) that are largely conserved in their positions between cell types and are similar in size to replication domains. However, TADs can be further sub-stratified into smaller domains, challenging the significance of structures at any particular scale.Moreover, attempts to reconcile TADs and LADs to replication-timing data have not revealed a common, underlying domain structure. Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 mouse cell types. We demonstrate that, collectively, replication domain boundaries share a near one-to-one correlation with TAD boundaries, whereas within a cell type, adjacent TADs that replicate at similar times obscure replication domain boundaries, largely accounting for the previously reported lack of alignment. Moreover, cell-type-specific replication timing of TADs partitions the genome into two large-scale sub-nuclear compartments revealing that replication-timing transitions are indistinguishable from late-replicating regions in chromatin composition and lamina association and accounting for the reduced correlation of replication timing to LADs and heterochromatin. Our results reconcile cell-type-specific sub-nuclear compartmentalization and replication timing with developmentally stable structural domains and offer a unified model for large-scale chromosome structure and function.
2014-11-20 | GSE51334 | GEO
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. 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.
2022-01-18 | GSE136227 | GEO
Project description:Differentiation of mouse embryonic stem cells (mESCs) is accompanied by global changes in replication timing. To elucidate this reorganization process and explore its potential impact on mouse development, we constructed genome-wide replication-timing profiles of 15 independent mouse cell types representing nine different stages of early mouse development, including all three germ layers. Overall, 45% of the genome exhibits significant changes in replication timing between cell types, indicating that replication-timing regulation is more extensive than previously estimated from neural differentiation. Intriguingly, analysis of early and late epiblast cell culture models suggest that the earliest changes in development include extensive lineage-independent early-to-late replication switches that are completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (Oct4/Nanog/Sox2). These changes were stable in all subsequent lineages and involved a class of irreversibly silenced genes that were re-positioned closer to the nuclear periphery. Lineage-specific, late-to-early and early-to-late replication switches followed, which created cell-type specific replication profiles. Importantly, partially reprogrammed induced pluripotent stem cells (piPSCs) failed to restore ESC-specific replication timing and transcription programs particularly within regions of lineage-independent early-to-late replication changes, as well as the inactive X-chromosome. We conclude that lineage-independent, early-to-late replication-timing switches that occur in the post-implantation epiblast embody an epigenetic commitment to differentiation prior to germ layer specification. 22 cell lines, with a total of 36 individual replicates (i.e. 14 in duplicates, 8 in single replicates)
2010-05-19 | E-GEOD-17983 | biostudies-arrayexpress
Project description:Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of lineage-independent early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (Oct4/Nanog/Sox2) and coinciding with the emergence of compact chromatin near the nuclear periphery. These changes were conserved in all subsequent lineages and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X-chromosome. Taken together, we demonstrate that replication-timing changes are extensive during development. Moreover, a distinct set of lineage-independent, early-to-late changes completed in and stably maintained after the post-implantation epiblast stage is difficult to reprogram and therefore coincides with an epigenetic commitment to differentiation prior to germ layer specification. 8 cell lines, with a total of 14 individual replicates (i.e. 6 in duplicates, 2 in single replicates)
2010-05-19 | E-GEOD-17980 | biostudies-arrayexpress
Project description:Differentiation of mouse embryonic stem cells (mESCs) is accompanied by global changes in replication timing. To elucidate this reorganization process and explore its potential impact on mouse development, we constructed genome-wide replication-timing profiles of 15 independent mouse cell types representing nine different stages of early mouse development, including all three germ layers. Overall, 45% of the genome exhibits significant changes in replication timing between cell types, indicating that replication-timing regulation is more extensive than previously estimated from neural differentiation. Intriguingly, analysis of early and late epiblast cell culture models suggest that the earliest changes in development include extensive lineage-independent early-to-late replication switches that are completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (Oct4/Nanog/Sox2). These changes were stable in all subsequent lineages and involved a class of irreversibly silenced genes that were re-positioned closer to the nuclear periphery. Lineage-specific, late-to-early and early-to-late replication switches followed, which created cell-type specific replication profiles. Importantly, partially reprogrammed induced pluripotent stem cells (piPSCs) failed to restore ESC-specific replication timing and transcription programs particularly within regions of lineage-independent early-to-late replication changes, as well as the inactive X-chromosome. We conclude that lineage-independent, early-to-late replication-timing switches that occur in the post-implantation epiblast embody an epigenetic commitment to differentiation prior to germ layer specification.
2009-11-25 | GSE17983 | GEO
Project description:Human DNA Replication Timing Variation
| PRJNA598743 | ENA