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Genome-wide assay of Vezf1 and RNA Polymerase II binding

ABSTRACT: Genome-wide assay of Vezf1 and RNA Polymerase II binding

PROVIDER: PRJNA151057 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR402361.fastq.gz	Fastqsanger.gz
	SRR402362.fastq.gz	Fastqsanger.gz
	SRR402363.fastq.gz	Fastqsanger.gz
	SRR402364.fastq.gz	Fastqsanger.gz
	SRR402365.fastq.gz	Fastqsanger.gz

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Genome-wide assay of Vezf1 and RNA Polymerase II binding

Project description:The protein Vezf1 plays multiple roles important for embryonic development. In Vezf1-/- mouse embryonic stem (MES) cells our earlier data showed widespread changes in gene expression profiles, including decreased expression of the full length active isoform of Dnmt3b methyltransferase and concomitant genome wide reduction in DNA methylation. Here we show that, in HeLaS3 cells, there is a strong genome-wide correlation between Vezf1 binding and peaks of elongating Ser2-P Pol ll, reflecting Vezf1 dependent slowing of elongation. In Wt MES cells the elongating form of RNA polymerase II accumulates near Vezf1 binding sites within the dnmt3b gene and at several other Vezf1 sites, and this accumulation is significantly reduced at these sites in Vezf1-/- MES cells. Depending upon genomic location, Vezf1 mediated Pol II pausing can have different regulatory roles in transcription and splicing. We find examples of genes in which Vezf1 binding sites are located near cassette exons, and in which loss of Vezf1 leads to a change in the relative abundance of alternatively spliced messages. We further show that Vezf1 interacts with Mrg15/Mrgbp, a protein that recognizes H3K36 tri-methylation, consistent with the role of histone modifications at alternatively spliced sites. Comparison of Vezf1 and RNA Pol II binding in mouse and human cells.

2012-03-09 | E-GEOD-34785 | biostudies-arrayexpress

Genome-wide assay of Vezf1 and RNA Polymerase II binding

2012-03-09 | GSE34785 | GEO

Genome-wide mapping of RNA Polymerase II binding sites

Project description:Protein coding genes and some of the non-coding RNA genes in eucaryotes are transcribed by RNA Polymerase II. A transcription machinery complex consists of RNA Pol II and many other proteins including transcription factors, activators and repressors of transcription. Pol II binding sites are found in actively transcribing genes and many which are not actively transcribing. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf Map binding sites of RNA Polymerase II in the genome of K562 & NB4 cells

2008-10-02 | E-GEOD-13008 | biostudies-arrayexpress

Polymerase II binding analysis during nutrient restriction using targeted DamID

Project description:Polymerase II binding analysis during nutrient restriction using targeted DamID

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NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization

Project description:NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization

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NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization

Project description:NDF/GLYR1 Promotes RNA Polymerase II Processivity via Pol II Binding and Nucleosome Destabilization

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Genome-wide mapping of RNA Polymerase II binding sites

2008-10-02 | GSE13008 | GEO

Activation of GPCR ligand binding genes revealed through degradation of RNA polymerase II

Project description:RNA polymerase II drives mRNA gene expression, yet our understanding of global Pol II repression is limited. Using auxin-inducible degron, we degraded Pol II's RPB1 subunit in mESCs, resulting in global repression, yet certain genes exhibited increased RNA levels post-degradation. These genes are associated with GPCR ligand binding and are characterized by being less paused and comprising polycomb-bound short genes. RPB1 degradation globally increased KDM6B binding, which was insufficient to explain specific gene activation. In contrast, RPB2 degradation repressed nearly all genes, accompanied by decreased H3K9me3 and SUV39H1 occupancy. We observed a specific increase in serine 2 phosphorylated Pol II at Pol II degradation-upregulated genes, indicating their resistance to degradation. Additionally, a-amanitin or UV treatment resulted in RPB1 degradation and global gene repression, unveiling subsets of upregulated genes. Our findings highlight the activation of signaling genes as a potential mechanism for cells to counter global transcription shutdown during stress.

2024-05-28 | PXD048023 |

Genome-wide map of DNA Polymerase II binding in the adult Drosophila melanogaster gut in control and infected conditions

Project description:In order to gain insight into gene regulation in the Drosophila gut following oral infection, we performed the genome-wide DNA Polymerase II binding data for Polymerase II in the fly gut.

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Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II

Project description:Spt5 histone binding activity preserves chromatin during transcription by RNA polymerase II

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