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Mus musculus

ABSTRACT: The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [Hi-C]

PROVIDER: PRJNA376128 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5274801_1.fastq.gz	Fastqsanger.gz
	SRR5274801_2.fastq.gz	Fastqsanger.gz
	SRR5274802_1.fastq.gz	Fastqsanger.gz
	SRR5274802_2.fastq.gz	Fastqsanger.gz
	SRR5274803_1.fastq.gz	Fastqsanger.gz

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The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture

Project description:The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture

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Mus musculus

Project description:The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq]

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The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

Project description:Here we show that HNRNPU, the major nuclear matrix attachment factor, is necessary to maintain proper nuclear architecture in mouse hepatocytes. Upon HNRNPU depletion, the interactions between chromatin and nuclear lamina have been changed dramatically；chromatin organization is globally changed; boundaries of topologically associating domains (TADs) become weaker; inter-TAD interactions are increased; thousands of genes are significantly altered coincident with 3D chromatin changes. Mechanically, HNRNPU interacts with CTCF and RAD21, which affects the binding of RAD21 to the chromatin significantly, whereas CTCF bindings are almost unchanged, what’ more, the decrease of binding strengths are highly correlated with the weakness of loop bounded by Rad21. Taken together, we identify HNRNPU as a key regulator of chromatin architecture, and our data suggest the importance of nuclear matrix associating factors in 3D genome organization.

2017-12-03 | GSE104098 | GEO

Mus musculus

Project description:The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 1]

| PRJNA376127 | ENA

The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

Project description:The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 2]

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The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [ChIP-Seq 1]

Project description:Higher-order chromatin conformation plays critical role in regulating gene expression and biological development, here we show that HNRNPU, a nuclear matrix attachment factor, is a regulator of 3D genome architecture at multiple levels in mouse hepatocytes. We demonstrate that depletion of HNRNPU results into a global reorganization of nuclear bodies and re-localization of chromatin towards nuclear periphery. Additionally, upon HNRNPU depletion, chromatin interactions between A-type (active) and B-type (inactive) compartments increase significantly but those among same types of compartments decrease significantly, which associate with global gene expression changes. While TADs remain largely invariant, both inter- and intra-TAD interactions increase significantly in A-type compartments but decrease in B-type compartments. Mechanically, HNRNPU complexes with structural proteins CTCF and RAD21; depletion of HNRNPU specifically weakens the bindings of RAD21 to the chromatin, which is highly correlated with the weakness of chromatin loops.

2017-12-03 | GSE95113 | GEO

The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [Hi-C]

2017-12-03 | GSE95112 | GEO

The nuclear matrix associating protein HNRNPU functions as a key regulator of 3D genome architecture [RNA-Seq]

2017-12-03 | GSE95111 | GEO

Genome-wide maps of nuclear lamina interactions in AML12 cells upon HNRNPU KD [DamID]

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Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3 [RNA-Seq]

Project description:Polycomb Repressive Complex 1 (PRC1) forms nuclear condensates that organize target chromatin domains. SUMOylation modulates PRC1 clustering, but its impact on condensate properties and 3D genome architecture remains unclear. Here, we show that depletion of SUMO in Drosophila wing imaginal discs transforms PRC1 condensates into large structures with reduced molecular dynamics. Strikingly, this biophysical reorganization occurs without global loss of the H3K27me3 mark. Instead, Hi-C reveals widespread rewiring of topologically associating domain (TAD) interactions. PRC1-bound TADs lose specific long-range contacts with each other while gaining ectopic interactions with active chromatin. These topological shifts correlate with gene misregulation independently of changes in canonical Polycomb histone modifications. Our results establish SUMOylation as a critical regulator of PRC1 condensates, demonstrating that post-translational control of biomolecular condensation dictates 3D genome architecture and transcriptional output through mechanisms separable from histone mark deposition.

2026-08-17 | GSE320239 | GEO

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