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

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

PROVIDER: PRJNA559545 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9942480_1.fastq.gz	Fastqsanger.gz
	SRR9942480_2.fastq.gz	Fastqsanger.gz
	SRR9942490.fastq.gz	Fastqsanger.gz
	SRR9942481_1.fastq.gz	Fastqsanger.gz
	SRR9942481_2.fastq.gz	Fastqsanger.gz

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

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

| PRJNA559548 | 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)

| PRJNA559549 | ENA

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

Project description: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

Project description:Schwann cells play critical roles in peripheral neuropathies, however, the regulatory mechanisms of their homeostasis remain largely unknown. Here we show that nucleoporin Seh1, a component of nuclear pore complex, is important for Schwann cell homeostasis and loss of Seh1 led to necroptosis of non-myelinating Schwann cell and degeneration of sensory neurons. While myelinogenesis, myelinating Schwann cell, and wrapped large fibers were not affected, mice with depletion of Seh1 in Schwann cell lineage developed progressive reduction of non-myelinating Schwann cells in sciatic nerves, followed by the degeneration of unmyelinated small sensory fibers and malfunction of the sensory system. Mechanistically, Seh1 safeguards genome stability by mediating the interaction between SETDB1 and KAP1. The disrupted interaction after ablation of Seh1 derepresses endogenous retroviruses, which triggers ZBP1-dependent necroptosis in non-myelinating Schwann cells. Collectively, our results reveal that Seh1 is required for homeostasis of Schwann cells and suggest that decrease of nucleoporins as aging may participate in the pathogenesis of periphery neuropathies.

2023-01-03 | GSE222015 | GEO

Quantitative proteomics of liver from PCB 153 exposed Atlantic cod

Project description:In order to investigate the underlying mechanisms of PCB 153 mediated toxicity to Atlantic cod (Gadus morhua), we analyzed the liver proteome of fish exposed to various doses of PCB 153 (0, 0.5, 2 and 8mg/kg body weight) for two weeks and examined the effects on expression of liver proteins using quantitative proteomics. Label-free mass spectrometry enabled quantification of 1272 proteins, and 78 were differentially regulated between PCB 153 treated samples and controls. Two proteins downregulated due to PCB 153 treatment, Glutathione S-transferase theta 1 (GSTT1) and sulfotransferase family protein 1 (ST2B1), were verified using selected reaction monitoring (SRM). Supported by bioinformatics analyses, we concluded that PCB 153 perturbs lipid metabolism in the Atlantic cod liver and that increased levels of lipogenic enzymes indicate increased synthesis of fatty acids and triglycerides.

2017-01-17 | PXD004362 | Pride

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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