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

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

PROVIDER: PRJNA150781 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR400251_1.fastq.gz	Fastqsanger.gz
	SRR400251_2.fastq.gz	Fastqsanger.gz
	SRR400252_1.fastq.gz	Fastqsanger.gz
	SRR400252_2.fastq.gz	Fastqsanger.gz
	SRR400253_1.fastq.gz	Fastqsanger.gz

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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

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

2012-04-10 | GSE35156 | GEO

Topological domains in mammalian genomes identified by 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 coarse, fragmented and incomplete. In the nucleus of eukaryotic cells, interphase chromosomes occupy distinct chromosome territories, and numerous models have been proposed for how chromosomes fold within chromosome territories. These models, however, provide only few mechanistic details about the relationship between higher order chromatin structure and genome function. Recent advances in genomic technologies have led to rapid advances in the study of three-dimensional genome organization. In particular, Hi-C has been introduced as a method for identifying higher order chromatin interactions genome wide. Here we investigate the three-dimensional organization of the human and mouse genomes in embryonic stem cells and terminally differentiated cell types at unprecedented resolution. We identify large, megabase-sized local chromatin interaction domains, which we term 'topological domains', as a pervasive structural feature of the genome organization. These domains correlate with regions of the genome that constrain the spread of heterochromatin. The domains are stable across different cell types and highly conserved across species, indicating that topological domains are an inherent property of mammalian genomes. Finally, we find that the boundaries of topological domains are enriched for the insulator binding protein CTCF, housekeeping genes, transfer RNAs and short interspersed element (SINE) retrotransposons, indicating that these factors may have a role in establishing the topological domain structure of the genome.

| S-EPMC3356448 | biostudies-literature

Setdb1 regulates Cohesin at H3K9me3-independent topological domains

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

| PRJNA507948 | ENA

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

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

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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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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 [Hi-C]

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

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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

Regions of very low H3K27me3 partition the Drosophila genome into topological domains [HiC-seq]

Project description: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 | GSE85503 | GEO

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