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Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

ABSTRACT: Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

PROVIDER: PRJNA870926 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21129100.fastq.gz	Fastqsanger.gz
	SRR21129200.fastq.gz	Fastqsanger.gz
	SRR21129101.fastq.gz	Fastqsanger.gz
	SRR21129201.fastq.gz	Fastqsanger.gz
	SRR21129102.fastq.gz	Fastqsanger.gz

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Replication dynamics identifies the folding principles of the inactive X chromosome

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome

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Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]

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Replication dynamics identifies the folding principles of the inactive X chromosome [scRepli-seq]

Project description:Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase upon X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other, and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization on heterochromatin stability and gene regulation.

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Replication dynamics identifies the folding principles of the inactive X chromosome [BrdU-IP Repli-seq]

Project description:Replication dynamics identifies the folding principles of the inactive X chromosome [BrdU-IP Repli-seq]

| PRJNA870924 | ENA

Replication dynamics identifies the folding principles of the inactive X chromosome

2023-07-11 | GSE211574 | GEO

Replication dynamics identifies the folding principles of the inactive X chromosome [4C]

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Replication dynamics identifies the folding principles of the inactive X chromosome.

Project description:Chromosome-wide late replication is an enigmatic hallmark of the inactive X chromosome (Xi). How it is established and what it represents remains obscure. By single-cell DNA replication sequencing, here we show that the entire Xi is reorganized to replicate rapidly and uniformly in late S-phase during X-chromosome inactivation (XCI), reflecting its relatively uniform structure revealed by 4C-seq. Despite this uniformity, only a subset of the Xi became earlier replicating in SmcHD1-mutant cells. In the mutant, these domains protruded out of the Xi core, contacted each other and became transcriptionally reactivated. 4C-seq suggested that they constituted the outermost layer of the Xi even before XCI and were rich in escape genes. We propose that this default positioning forms the basis for their inherent heterochromatin instability in cells lacking the Xi-binding protein SmcHD1 or exhibiting XCI escape. These observations underscore the importance of 3D genome organization for heterochromatin stability and gene regulation.

| S-EPMC10442229 | biostudies-literature

Replication dynamics identifies the folding principles of the inactive X chromosome [RNA-seq]

2023-07-11 | GSE211571 | GEO

Principles of 3D chromosome folding and evolutionary genome reshuffling in mammals

Project description:Here we describe the principles of 3D genome folding dynamics in vertebrates and show how lineage-specific patterns of genome reshuffling can result in different chromatin configurations. We (i) identified different patterns of chromosome folding across vertebrate species, (ii) reconstructed ancestral marsupial and afrotherian genomes analyzing whole-genome sequences of 10 species representative of the major therian phylogroups, (iii) detected lineage-specific chromosome rearrangements and (iv) identified the dynamics of the structural properties of genome reshuffling through therian evolution.

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