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Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C]

ABSTRACT: Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C]

PROVIDER: PRJNA421280 | ENA |

REPOSITORIES: ENA

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Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Project description:Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

| PRJNA421963 | ENA

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Hi-C]

Project description:Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Hi-C]

| PRJNA421970 | ENA

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Tri-C]

Project description:Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Tri-C]

| PRJNA421281 | ENA

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Capture-C]

Project description:The genome is organized into self-interacting chromatin domains containing genes and the cis-regulatory elements controlling their expression. How these domains form and how elements within them interact is not fully understood. We have developed Tri-C, a sensitive, high-resolution Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions in single cells. Combining Tri-C with conventional 3C and polymer modeling, we show that, rather than folding into stable pre-formed loops, self-interacting domains form dynamic compartmentalized chromatin structures, delimited by CTCF/Cohesin boundaries. Within these tissue-specific domains, all regions of chromatin contact each other, but preferential structures are formed in which multiple enhancers and promoters interact simultaneously. Flanking CTCF/Cohesin-bound elements are excluded from these interactions and form distinct structures. These observations are best explained by a dynamic loop extrusion mechanism and subsequent stabilization of enhancer-promoter interactions, rather than the current view of long-range interactions occurring via the formation of discrete pre-formed chromatin loops.

2018-08-17 | GSE107753 | GEO

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Hi-C]

Project description:The genome is organized into self-interacting chromatin domains containing genes and the cis-regulatory elements controlling their expression. How these domains form and how elements within them interact is unknown. We have developed Tri-C, a sensitive, high-resolution Chromosome Conformation Capture (3C) approach to identify concurrent chromatin interactions in single cells. Combining Tri-C with conventional 3C and polymer modeling, we show that, rather than folding into stable pre-formed loops, self-interacting domains form dynamic compartmentalized chromatin structures, delimited by CTCF/Cohesin boundaries. Within these tissue-specific domains, all regions of chromatin contact each other, but preferential structures are formed in which multiple enhancers and promoters interact simultaneously. Flanking CTCF/Cohesin-bound elements are excluded from these interactions and form distinct structures. These observations are best explained by a dynamic loop extrusion mechanism and subsequent stabilization of enhancer-promoter interactions, rather than the current view of long-range interactions occurring via the formation of discrete pre-formed chromatin loops.

2018-08-17 | GSE107939 | GEO

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains [Tri-C]

2018-08-17 | GSE107755 | GEO

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Project description: Not available

| S-EPMC6265079 | biostudies-literature

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-08-17 | GSE107940 | GEO

Systematic mapping of nuclear domain-associated transcripts reveals speckles and lamina as hubs of functionally distinct retained introns

Project description:The nucleus is highly compartmentalized through the formation of distinct classes of membraneless domains, yet the composition and function of many of these structures is not well understood. Using APEX2-mediated proximity labelling and RNA sequencing, we surveyed transcripts associated with nuclear speckles, several additional domains, and the lamina. Remarkably, speckles and lamina are associated with distinct classes of retained introns enriched in genes that function in RNA processing, translation, and the cell cycle. In contrast to the lamina-proximal introns, retained introns associated with speckles are relatively short, GC-rich, and enriched for functional sites of RNA binding proteins that are concentrated in these domains. They are also highly differentially regulated across diverse cellular contexts, including the cell cycle. Our study thus provides a resource of nuclear domain-associated transcripts and further reveals speckles and lamina as hubs of distinct populations of retained introns linked to gene regulation and cell cycle progression.

2022-02-18 | GSE176439 | GEO

Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation

Project description:Streptomyces are among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear genome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetics compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the genome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an ‘open’ to a rather ‘closed’ conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal that S. ambofacien's linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution

2021-07-01 | GSE162865 | GEO

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