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

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

PROVIDER: PRJNA769120 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR16227420.fastq.gz	Fastqsanger.gz
	SRR16227421_1.fastq.gz	Fastqsanger.gz
	SRR16227421_2.fastq.gz	Fastqsanger.gz
	SRR16227422_1.fastq.gz	Fastqsanger.gz
	SRR16227422_2.fastq.gz	Fastqsanger.gz

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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.

2022-03-10 | GSE185464 | GEO

Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters

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Elongation factor-specific capture of RNA polymerase II complexes

Project description:Elongation factor-specific capture of RNA polymerase II complexes

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Unphosphorylated SR-like Protein Npl3 Stimulates RNA Polymerase II Elongation

Project description:The production of a functional mRNA is regulated at every step of transcription. An area not well-understood is the transition of RNA polymerase II from elongation to termination. The S. cerevisiae SR-like protein Npl3 functions to negatively regulate transcription termination by antagonizing the binding of polyA/termination proteins to the mRNA. In this study, Npl3 is shown to interact with the CTD and have a direct stimulatory effect on the elongation activity of the polymerase. The interaction is inhibited by phosphorylation of Npl3. In addition, Casein Kinase 2 was found to specifically phosphorylate Npl3 and affect its ability to compete against Rna15 (Cleavage Factor I) for binding to polyA signals. Our results suggest that phosphorylation of Npl3 promotes its dissociation from the mRNA/RNAP II, and contributes to the association of the polyA/termination factor Rna15. This work defines a novel role for Npl3 in elongation and its regulation by phosphorylation. Keywords: Gene expression on a tiling array

2008-09-06 | GSE12677 | GEO

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

Project description:CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

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CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

Project description:CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

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CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

Project description:Cyclin-dependent kinase 12 (CDK12) phosphorylates the carboxyl-terminal domain (CTD) of RNA polymerase II (pol II) but its roles in transcription beyond the expression of DNA damage response genes remain unclear. Here, we have used TT-seq and mNET-seq to monitor the direct effects of rapid CDK12 inhibition on transcription activity and CTD phosphorylation in human cells. CDK12 inhibition causes a genome-wide defect in transcription elongation and a global reduction of CTD Ser2 and Ser5 phosphorylation. The elongation defect is explained by the loss of the elongation factors LEO1 and CDC73, part of PAF1 complex, and SPT6 from the newly-elongating pol II. Our results indicate that CDK12 is a general activator of pol II transcription elongation and indicate that it targets both Ser2 and Ser5 residues of the pol II CTD.

2020-06-18 | GSE133156 | GEO

CDK12 globally stimulates RNA polymerase II transcription elongation and carboxyl-terminal domain phosphorylation

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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.

2022-12-08 | GSE207568 | GEO

Molecular Determinants for RNA Polymerase II Elongation Rate and Acceleration

Project description:Recent studies reveal a striking phenomenon that RNA Polymerase II (Pol II) appears to travel on gene body in an accelerated fashion, but the mechanism has remained unknown. We performed synchronized transcription coupled with deep sequencing, observing an inverse relationship between initial rate and acceleration in different cell types. We directly tested several correlative events and detected a positive contribution of the splicing commitment factor SRSF2 to Pol II acceleration, suggesting a functional benefit of co-transcriptional pre-mRNA splicing in transcription elongation. Unexpectedly, we found that perturbation of Pol II Ser2 phosphorylation had little impact on Pol II elongation or acceleration. While H3K79me2 has been positively correlated with Pol II elongation, we showed that reduction of this histone modification event actually accelerated Pol II elongation. Together, these data suggest a combined effect of gradual gain-of-competence and gradual lost-of-epigenetic barriers as the mechanism for accelerated Pol II elongation. DRB time-course releasing assay under functional perturbation

2015-12-31 | E-GEOD-66021 | biostudies-arrayexpress

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