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Long-distance association of topological boundaries through nuclear condensates (ChIP-Seq)

ABSTRACT: Long-distance association of topological boundaries through nuclear condensates (ChIP-Seq)

PROVIDER: PRJNA801255 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR17786623.fastq.gz	Fastqsanger.gz
	SRR17786624.fastq.gz	Fastqsanger.gz
	SRR17786625.fastq.gz	Fastqsanger.gz
	SRR17786626.fastq.gz	Fastqsanger.gz
	SRR17786627.fastq.gz	Fastqsanger.gz

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Long-distance association of topological boundaries through nuclear condensates

Project description:Long-distance association of topological boundaries through nuclear condensates

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

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Long-distance association of topological boundaries through nuclear condensates (GRO-Seq)

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Long-distance association of topological boundaries through nuclear condensates (PRO-Seq)

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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

Long-distance association of topological boundaries through nuclear condensates (PRO-Seq)

2022-06-15 | GSE195563 | GEO

Long-distance association of topological boundaries through nuclear condensates (GRO-Seq)

2022-06-15 | GSE195562 | GEO

Long-distance association of topological boundaries through nuclear condensates (ChIP-Seq)

2022-06-15 | GSE195561 | GEO

Long-distance association of topological boundaries through nuclear condensates

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

2022-06-13 | GSE195566 | GEO

Long-distance association of topological boundaries through nuclear condensates.

Project description:The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.

| S-EPMC9371644 | biostudies-literature

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