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Hi-C following CTCF RNAi in LNCaP cells to determine changes to topological domains

ABSTRACT: Hi-C following CTCF RNAi in LNCaP cells to determine changes to topological domains

PROVIDER: PRJNA518744 | ENA |

REPOSITORIES: ENA

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Hi-C following CTCF RNAi in LNCaP cells to determine changes to topological domains

Project description:This study aimed to ascertain the effect of CTCF RNAi on gene expression, chromatin conformation and the chromatin environment in prostate cancer cell line, LNCaP

2020-01-01 | GSE125640 | GEO

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [Hi-C]

| PRJNA780175 | ENA

Setdb1 regulates Cohesin at H3K9me3-independent topological domains

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains

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Epigenetic maintenance of topological domains in the rearranged gibbon genome [Hi-C]

Project description:Epigenetic maintenance of topological domains in the rearranged gibbon genome [Hi-C]

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Long-distance association of topological boundaries through nuclear condensates (Hi-C)

Project description:Chromatin is partitioned into distinct topological domains in an activity-dependent manner, with topological boundaries limiting the interaction between adjacent domains. Recent studies support the concept that several well-established nuclear compartments are assembled as ribonucleoprotein condensates. Here we ask whether the physical processes driving the assembly of the nuclear condensates play any role in three-dimensional chromatin architecture. We report that the insulation of approximately 20% of topological boundaries in human embryonic stem cells is substantially weakened following brief treatment with 1,6-hexanediol, a chemical known to disrupt several nuclear condensates. The disrupted boundaries are characterized by a high level of transcription, striking spatial clustering, and the augmented presence of transcription units widely expressed in diverse cell types. These topological boundary regions tend to be spatially associated, even inter-chromosomally, and segregate with nuclear speckles. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring widely-expressed transcription units and associated transcriptional condensates.

2022-06-15 | GSE195565 | GEO

Conserved Topological Domains in Mammalian Genomes Identified by High-resolution Analysis of Chromatin Interactions

Project description:The spatial organization of the genome is intimately linked to its biological function, yet our understanding of higher order genomic structure is limited. Here we present high-resolution analyses of chromosomal organization in pluripotent and differentiated human and murine cell types determined using the Hi-C technique. We find that the mammalian genome is composed of over 1000 topological domains, which are stable among different cell types and highly conserved across species. These megabase-long genomic structures, defined by prominent local chromatin interactions and separated by narrow boundary regions, likely function to restrict regulatory interactions between cis-acting elements and limit the spreading of heterochromatin during cellular differentiation. Interestingly, the boundaries are enriched not only for binding sites of the insulator protein CTCF, but also for promoters of house keeping genes, supporting a role for both CTCF and housekeeping genes in the establishment or maintenance of the topological domains. Hi-C experiment were conducted in mESC, hESC and IMR90 cells

2012-04-10 | E-GEOD-35156 | biostudies-arrayexpress

Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [ChIP-Seq]

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Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

Project description:Setdb1 regulates Cohesin at H3K9me3-independent topological domains [RNA-Seq]

| PRJNA507945 | ENA

Epigenetic maintenance of topological domains in the rearranged gibbon genome

Project description:Epigenetic maintenance of topological domains in the rearranged gibbon genome

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Regions of very low H3K27me3 partition the Drosophila genome into topological domains

Project description:This SuperSeries is composed of the SubSeries listed below. We have investigated boundaries of topologically associated domains (TADs) in the Drosophila genome and find that they can be identified as domains of very low H3K27me3. The genome-wide H3K27me3 profile partitions into two states; very low H3K27me3 identifies Depleted (D) domains that contain housekeeping genes and their regulators such as the histone acetyltransferase-containing NSL complex, whereas domains containing mid-to-high levels of H3K27me3 (Enriched or E domains) are associated with regulated genes, irrespective of whether they are active or inactive. The D domains correlate with the boundaries of TADs and are enriched in a subset of architectural proteins, particularly Chromator, BEAF-32, and Z4. However, rather than being clustered at the borders of these domains, these proteins bind throughout the H3K27me3-depleted regions and are much more strongly associated with the TSSs of the housekeeping genes than with the H3K27me3 domain boundaries. We suggest that the D domain chromatin state, characterised by very low H3K27me3 and established by housekeeping gene regulators, acts to separate topological domains thereby setting up the domain architecture of the genome.

2017-05-02 | GSE85504 | GEO

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