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Elongation factor-specific capture of RNA polymerase II complexes

ABSTRACT: Elongation factor-specific capture of RNA polymerase II complexes

PROVIDER: PRJNA856248 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19997408.fastq.gz	Fastqsanger.gz
	SRR19997409.fastq.gz	Fastqsanger.gz
	SRR19997410.fastq.gz	Fastqsanger.gz
	SRR19997411.fastq.gz	Fastqsanger.gz
	SRR19997412.fastq.gz	Fastqsanger.gz

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Elongation factor-specific capture of RNA polymerase II complexes

Project description:Transcription of protein-coding genes is regulated by dynamic association of co-factors with RNA polymerase II (RNAPII). The function of these factors and their relationship with RNAPII is often poorly understood. Here, we present an approach for elongation factor-specific mNET capture (EMCAP) of RNA polymerase II complexes for sequencing and mass spectrometry analysis, for investigating the function of such RNAPII regulatory proteins. As proof of principle, we apply EMCAP to the RNAPII-associated proteins SCAF4 and SCAF8, which share an essential role as mRNA anti-terminators but have individual roles at the 3’end of genes. Mass spectrometry analysis shows that both SCAF4 and SCAF8 are part of RNAPII elongation complexes containing 3’end processing factors but depleted of splicing components. Importantly, the EMCAP-seq profiles of SCAF4- and SCAF8-RNAPII complexes reflect their function as mRNA-anti-terminators and their competing functions at the end of genes where they prevent or promote transcriptional readthrough.

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MDC1 maintains active elongation complexes of RNA polymerase II

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Elongation factor-specific capture of RNA polymerase II complexes.

Project description:Transcription of protein-coding genes is regulated by dynamic association of co-factors with RNA polymerase II (RNAPII). The function of these factors and their relationship with RNAPII is often poorly understood. Here, we present an approach for elongation-factor-specific mNET capture (ELCAP) of RNAPII complexes for sequencing and mass spectrometry analysis aimed at investigating the function of such RNAPII regulatory proteins. As proof of principle, we apply ELCAP to the RNAPII-associated proteins SCAF4 and SCAF8, which share an essential role as mRNA anti-terminators but have individual roles at the 3' end of genes. Mass spectrometry analysis shows that both SCAF4 and SCAF8 are part of RNAPII elongation complexes containing 3' end processing factors but depleted of splicing components. Importantly, the ELCAP sequencing (ELCAP-seq) profiles of SCAF4- and SCAF8-RNAPII complexes nicely reflect their function as mRNA-anti-terminators and their competing functions at the end of genes, where they prevent or promote transcriptional readthrough.

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NDF Is a Transcription Factor that Stimulates Elongation by RNA Polymerase II

Project description:RNA polymerase II (Pol II) elongation is a critical step in gene expression. Here we find that NDF, which was identified as a bilaterian nucleosome-destabilizing factor, is also a Pol II transcription factor that stimulates elongation with plain DNA templates in the absence of nucleosomes. NDF binds directly to Pol II and enhances elongation by a different mechanism than does transcription factor TFIIS. Moreover, yeast Pdp3, which is related to NDF, binds to Pol II and stimulates elongation. Thus, NDF is a Pol II-binding transcription elongation factor that is localized over gene bodies and is conserved from yeast to humans.

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