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Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding [RNA-Seq]

ABSTRACT: Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding [RNA-Seq]

PROVIDER: PRJNA559548 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9942477.fastq.gz	Fastqsanger.gz
	SRR9942478.fastq.gz	Fastqsanger.gz
	SRR9942479.fastq.gz	Fastqsanger.gz

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Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding

Project description:Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding

| PRJNA559545 | ENA

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding (ChIP-Seq)

Project description:Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding (ChIP-Seq)

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Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding (ChIP-Seq)

Project description:Establishment of cell lineage specification, maintenance of cellular states and cellular responses to developmental cues rely on gene regulation and spatial genome organization during early development. Emerging data point to highly coordinated activity between epigenetic mechanisms that involve nuclear architecture, chromatin structure and chromatin organization. We show that the nuclear pore complex (NPC) basket protein, Nucleoporin 153 (NUP153) interacts with the nuclear architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements in pluripotent mouse embryonic stem (ES) cells. NUP153 depletion results in altered occupancy of architectural proteins coupled with differential changes in transcription. This affect is most prevalent at the bivalent genes. To provide molecular insights onto NUP153-mediated gene regulation, we utilized Epidermal Growth Factor (EGF)-inducible immediate early gene (IEG) loci, which we identified as NUP153 targets. IEG transcription is regulated through a POL II pause-release mechanism. We provide evidence that NUP153 is critical for CTCF and cohesin occupancy and subsequent POL II recruitment to the IEG proximal-promoter sites during the paused state. In particular, establishment of a poised IEG chromatin environment relies on co-regulatory function of NUP153 and CTCF, which underlies efficient and timely IEG transcription at the NPC. Our results uncover a key role for the mammalian NPC in distribution of chromatin architectural proteins and demonstrate that NUP153 acts as a cis-acting factor that causally links the NPC to chromatin organization during transcription regulation.

2020-05-21 | GSE135646 | GEO

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding [RNA-Seq]

2020-05-21 | GSE135645 | GEO

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding.

Project description:Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation. Nevertheless, the molecular mechanisms in mammalian cells are not well understood. Here, we report that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin binding and differential gene expression - specifically at the bivalent developmental genes. To investigate the molecular mechanism, we utilize epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We find that NUP153 controls CTCF and cohesin binding at the cis-regulatory elements and POL II pausing during the basal state. Furthermore, efficient IEG transcription relies on NUP153. We propose that NUP153 links the nuclear pore complex (NPC) to chromatin architecture allowing genes that are poised to respond rapidly to developmental cues to be properly modulated.

| S-EPMC7248104 | biostudies-literature

Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding

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

2020-05-21 | GSE135647 | GEO

Nucleoporin downregulation modulates keratinocyte differentiation independent of nuclear pore numbers

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Nucleoporin Seh1 Maintain Schwann Cell Homeostasis by Regulating Genome Stability and Necroptosis

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Quantitative proteomics of liver from PCB 153 exposed Atlantic cod

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Probing the trypanosome nuclear pore by TurboID proximity labelling – Part2

Project description:Previous BioID experiments targeting the nucleoporin (NUP) NUP158 (PMID: 36410438; PXD031245), as well as NUP110, NUP76 and NUP96 (PMID: 39206942; PXD047268) indicated that proximity labelling delivers highly specific interactome data in the confined localisation of the nuclear pore, with a labelling radius well below the size of the nuclear pore. The resulting proximity data allowed to assign NUPs and nuclear transport factors to specific subregions of the pore. Here we extended this approach to target NUP75 and transport factors MEX67 and Ran.

2024-09-20 | PXD055934 | Pride

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