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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

ABSTRACT: Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

PROVIDER: PRJNA1007628 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25721700_1.fastq.gz	Fastqsanger.gz
	SRR25721700_2.fastq.gz	Fastqsanger.gz
	SRR25723300_1.fastq.gz	Fastqsanger.gz
	SRR25723300_2.fastq.gz	Fastqsanger.gz
	SRR25721701_1.fastq.gz	Fastqsanger.gz

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [RNA-Seq]

Project description:The ZFX transcriptional activator binds to CpG island promoters, with a major peak at ~200-250bp downstream from transcription start sites. Because ZFX binds within the transcribed region, we investigated whether it regulates transcriptional elongation. We used GRO-seq to show that loss or reduction of ZFX increased the pause ratio at ZFX-regulated promoters. To further investigate the mechanisms by which ZFX regulates transcription, we determined regions of the protein needed for transactivation and for recruitment to the chromatin. Interestingly, although ZFX has 13 grouped zinc fingers, deletion of the first 11 fingers produces a protein that can still bind to chromatin and activate transcription. We next used TurboID-MS to detect ZFX-interacting proteins, identifying ZNF593, proteins that interact with the N-terminal transactivation domain (e.g. histone modifying proteins), and proteins that interact with ZFX when it is bound to the chromatin (e.g. TAFs and other histone modifying proteins). Our studies support a model in which ZFX enhances elongation at target promoters by recruiting H4 acetylation complexes and reducing pausing.

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [ChIP-Seq]

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [ChIP-Seq]

Project description:Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [ChIP-Seq]

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [RNA-Seq]

Project description:Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [RNA-Seq]

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [GRO-seq]

Project description:Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters [GRO-seq]

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Reduction of ZFX levels decreases histone H4 acetylation and increases the pause ratio at target promoters

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Reduction of ZFX levels decreases histone H4 acetylation and increases Pol2 pausing at target promoters

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

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Total RNA Pol2 ChIP-seq in mES cells treated with flavopiridol (Cdk9 inhibitor) after DSIF and NELF knockdown

Project description:Recent studies have found that promoter-proximal pausing occurs at most Pol2-regulated genes. DSIF and NELF function as negative elongation factors and promote Pol2 pausing. P-TEFb, whose enzymatic activity lies in the kinase Cdk9, positively regulates the transition into productive elongation by phosphorylating subunits in DSIF, NELF and Pol2. To gain insights into the interplay between these factors in regulating transcriptional pause release, we tested if knockdown of either pausing factor could bypass P-TEFb function. We find that P-TEFb function is still required for transcriptional elongation after DSIF or NELF knockdown. mES cells were infected with a shRNA hairpin to knockdown Spt5, Spt4, NelfE or control. The resulting cells were then treated with flavopiridol (1uM for 60 minutes). DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. A sample of whole cell extract was sequenced and used as the background to determine enrichment. ChIP was performed using an antibody against total RNA Pol2 (Rpb1 N-terminus, Santa Cruz sc-899).

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Total RNA Pol2 ChIP-seq in mES cells treated with flavopiridol (Cdk9 inhibitor) after DSIF and NELF knockdown

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