Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA234285 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rif1 regulates the replication timing domains on the human genome
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Project description:Abnormal Developmental Control of Replication Timing Domains in Pediatric Acute Lymphoblastic Leukemia
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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
Project description:DNA replication timing and 3D chromatin organisation are associated with epigenomic changes across large domains during human differentiation and cancer progression. However, it is unclear if epigenome changes, in particular cancer-associated DNA hypomethylation, is a consequence or cause of changes observed in higher order genome architecture. Here, we compare replication timing profiles and three dimensional (3D) genome organisation, using Hi-C and single cell Repli-Seq in the DNMT1 and DNMT3B DNA methyltransferases double knockout hypomethylated DKO1 colorectal cancer cell line and its parental HCT116 cell line. We find that the hypomethylated cells show a profound loss of replication timing precision, gain of single cell replication timing heterogeneity and loss of chromatin conformation integrity. Discrete regions, that undergo a large change in replication timing in the hypomethylated cells, are associated with a loss of allelic replication timing and shrinking of late replicating Partially Methylated Domain (PMD) boundaries. In contrast, conservation of replication timing after DNA methylation depletion at PMDs is associated with the formation of new H3K9me3/H3K4me3 bivalent domains which may serve to prevent ectopic transcription and maintain cell viability. Together our results show that a loss of global methylation, a common hallmark of cancer, directly impacts on the precision of replication timing and contribute to deregulation of the 3D chromatin architecture.
2021-09-21 | GSE159663 | GEO
Project description: Not available
| S-EPMC2531291 | biostudies-literature
Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume. Deletion of RIf1 in mammalian cells causes an initial alteration of three-dimensional chromatin organization which impacts first on replication timing and genome stability, but has long-term indirect repercussions also on gene expression.
2015-12-24 | E-MTAB-3502 | biostudies-arrayexpress
Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume. Deletion of RIf1 in mammalian cells causes an initial alteration of three-dimensional chromatin organization which impacts first on replication timing and genome stability, but has long-term indirect repercussions also on gene expression.
2015-12-24 | E-MTAB-3500 | biostudies-arrayexpress
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. Profile comparison of fibroblast and T-cell cultures from trans-chromosomic mice and human and mouse controls.
2012-06-04 | E-GEOD-38472 | biostudies-arrayexpress
Project description:RNA extracted at 240min. Samples are rRNA depleted. Expression measurement of Homo sapiens genes.
2019-07-31 | GSE114179 | GEO