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Extensive folding variability between homologous chromosomes in mammalian cells [ChIP-Seq]

ABSTRACT: Extensive folding variability between homologous chromosomes in mammalian cells [ChIP-Seq]

PROVIDER: PRJNA1071563 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27805695.fastq.gz	Fastqsanger.gz
	SRR27805696.fastq.gz	Fastqsanger.gz
	SRR27805697.fastq.gz	Fastqsanger.gz

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Similar Datasets

Extensive folding variability between homologous chromosomes in mammalian cells

Project description:Extensive folding variability between homologous chromosomes in mammalian cells

| PRJNA1071571 | ENA

Extensive folding variability between homologous chromosomes in mammalian cells [GAM]

Project description:Extensive folding variability between homologous chromosomes in mammalian cells [GAM]

| PRJNA1071570 | ENA

Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq]

Project description:Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq]

| PRJNA1071503 | ENA

Extensive folding variability between homologous chromosomes in mammalian cells [GAM]

Project description:Genetic variation and 3D chromatin structure have major roles in gene regulation. Structural differences between genotypically different chromosomes and their effects on gene expression remain ill understood, due to challenges in mapping 3D genome structure with allele-specific resolution. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (ESC) line with high SNP density. Given its high efficiency of haplotype phasing, GAM resolves allele-specific 3D genome structures with high sensitivity. We discovered extensive genotype-specific folding of chromosomes in compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts and CTCF loops, often coinciding with allele-specific gene expression in association with Polycomb repression. We show that histone genes are expressed with allelic imbalance and involved in allele-specific chromatin contacts marked by H3K27me3. Functional analysis through conditional Ezh2- or Ring1b-knockdown shows a role for Polycomb repression in tuning histone protein levels. Our work reveals that the homologous chromosomes have highly distinct 3D folding structures, and their intricate relationships with gene-specific mechanisms of allelic expression imbalance.

2025-01-29 | GSE254717 | GEO

Extensive folding variability between homologous chromosomes in mammalian cells

Project description:Genetic variation and 3D chromatin structure have major roles in gene regulation. Structural differences between genotypically different chromosomes and their effects on gene expression remain ill understood, due to challenges in mapping 3D genome structure with allele-specific resolution. Here, we applied Genome Architecture Mapping (GAM) to a hybrid mouse embryonic stem cell (ESC) line with high SNP density. Given the high efficiency of GAM in haplotype phasing, we could resolve allele-specific 3D genome structures with high sensitivity. We discovered extensive genotype-specific folding of chromosomes in compartments, topologically associating domains (TADs), long-range enhancer-promoter contacts and CTCF loops, often coinciding with allele-specific gene expression in association with Polycomb repression. We show that histone genes are expressed with allelic imbalance in ESCs, and involved in allele-specific chromatin contacts marked by H3K27me3. Functional analysis through conditional Ezh2- or Ring1b-knockdown shows a role for Polycomb repression in tuning histone protein levels. Our work reveals that the homologous chromosomes have highly distinct 3D folding structures, and their intricate relationships with gene-specific mechanisms of allelic expression imbalance.

2025-01-30 | PXD048969 | Pride

Extensive folding variability between homologous chromosomes in mammalian cells [ChIP-Seq]

2025-01-29 | GSE254710 | GEO

Extensive folding variability between homologous chromosomes in mammalian cells [RNA-seq]

2025-01-29 | GSE254675 | GEO

Extensive folding variability between homologous chromosomes in mammalian cells

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

2025-01-29 | GSE254723 | GEO

Extensive mutual influences of SMC complexes shape 3D genome folding

Project description:Extensive mutual influences of SMC complexes shape 3D genome folding

| PRJNA1124163 | ENA

Interphase chromosome conformation is specified by distinct folding programs inherited via mitotic chromosomes or through the cytoplasm [Hi-C]

Project description:Identity-specific interphase chromosome conformation must be re-established each time a cell divides. To understand how interphase folding is inherited, we developed an experimental approach that physically segregates mediators of G1 folding that are intrinsic to mitotic chromosomes from cytoplasmic factors. Proteins essential for nuclear transport, RanGAP1 and Nup93, were degraded in pro-metaphase arrested DLD-1 cells to prevent the establishment of nucleo-cytoplasmic transport during mitotic exit and isolate the decondensing mitotic chromatin of G1 daughter cells from the cytoplasm. Using this approach, we discover a transient folding intermediate entirely driven by chromosome-intrinsic factors. In addition to conventional compartmental segregation, the chromosome-intrinsic folding program leads to prominent genome-scale microcompartmentalization of mitotically bookmarked and cell type-specific cis-regulatory elements. The microcompartment conformation is formed during telophase and subsequently modulated by a second folding program driven by factors inherited through the cytoplasm in G1. This nuclear import-dependent folding program includes cohesin and factors involved in transcription and RNA processing. The combined and inter-dependent action of chromosome-intrinsic and cytoplasmic inherited folding programs determines the interphase chromatin conformation as cells exit mitosis.

2025-11-06 | GSE277875 | GEO

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