Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (TT-Seq)

ABSTRACT: Accurate regulation of RNA Polymerase II (RNAPII) transcriptional termination is a prerequisite for correct gene expression. Here we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation sites (PASs). The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) modified on both Ser2 and Ser5, and are detected at early, alternative PASs. Concomitant knockout of human SCAF4 and SCAF8 results in altered PAS selection, leading to expression of truncated mRNAs and proteins lacking functional domains, and is cell-lethal. While SCAF4 and SCAF8 thus work redundantly to suppress early termination, they also have independent, non-essential functions. SCAF8 is a positive RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, directing PAS selection to ensure correct RNAPII transcriptional termination in human cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE121822 | GEO | 2019/05/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (DRB-Seq)

Project description:Accurate regulation of RNA Polymerase II (RNAPII) transcriptional termination is a prerequisite for correct gene expression. Here we describe a role for SCAF4 and SCAF8 as anti-terminators, suppressing the use of early, alternative polyadenylation sites (PASs). The SCAF4/8 proteins bind the hyper-phosphorylated RNAPII C-terminal repeat domain (CTD) modified on both Ser2 and Ser5, and are detected at early, alternative PASs. Concomitant knockout of human SCAF4 and SCAF8 results in altered PAS selection, leading to expression of truncated mRNAs and proteins lacking functional domains, and is cell-lethal. While SCAF4 and SCAF8 thus work redundantly to suppress early termination, they also have independent, non-essential functions. SCAF8 is a positive RNAPII elongation factor, whereas SCAF4 is required for correct termination at canonical transcription termination sites in the presence of SCAF8. Together, SCAF4 and SCAF8 coordinate the transition between elongation and termination, directing PAS selection to ensure correct RNAPII transcriptional termination in human cells.

2019-05-16 | GSE121817 | GEO

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (3'-Seq)

2019-05-16 | GSE121816 | GEO

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (mRNA-Seq)

2019-05-16 | GSE121824 | GEO

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (mNET-Seq)

2019-05-16 | GSE121823 | GEO

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins (PAR-CLIP)

2019-05-16 | GSE121821 | GEO

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

Transcription elongation has a tissue-specific impact in alternative cleavage and polyadenylation in Drosophila melanogaster

Project description:Alternative cleavage and polyadenylation (APA) is a mechanism generating multiple mRNA isoforms with different 3'UTRs and/or coding sequences from a single gene. Here we used 3' Region Extraction And Deep Sequencing (3'READS) to systematically map cleavage and polyadenylation sites (PAS) in Drosophila and analyzsed APA in the RpII215 C4 mutant strain, which harbors a mutant RNA polymerase II (RNAPII) with a slower elongation rate. We found that about two thirds of mRNA genes in fly undergo APA and cis element analysis indicates that fly PASs are associated with downstream UGUG elements to a lesser degree than mammalian PASs. The head tissue tends to use distal PASs compared to the body, leading to preferential expression of long 3'UTR isoforms and transcripts using distal terminal exons. Gene Ontology analysis correlates brain-specific APA events with neuronal functions, indicating their functional relevance. We also found that the distance between the proximal and distal PASs and intron locations might play important roles for brain APA. Analysis of the RpII215 C4 mutant strain, reveals that a 50% decrease in transcriptional elongation rate leads to shortened 3'UTRs in the fly body, but not in the head. This correlates with an upregulation of Ssu72 specifically in RpII215 C4 bodies, suggesting that the mechanism underlying those observations involves another layer of regulation by RNAPII termination factors. By contrast, more significant activation of intronic PASs was observed in the head compared to the body when RNAPII speed is slow. Together, our results reveal that in Drosophila RNAPII elongation impacts on PAS choice in a context-specific manner.

2017-08-23 | GSE85368 | GEO

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

Project description:Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-coding genes is limited by unknown mechanisms. In particular, although RNA polymerase II (RNAPII) initiates divergently from most active gene promoters, productive elongation occurs primarily in the sense-coding direction. Here we show in mouse embryonic stem cells that asymmetric sequence determinants flanking gene transcription start sites control promoter directionality by regulating promoter-proximal cleavage and polyadenylation. We find that upstream antisense RNAs are cleaved and polyadenylated at poly(A) sites (PASs) shortly after initiation. De novo motif analysis shows PAS signals and U1 small nuclear ribonucleoprotein (snRNP) recognition sites to be the most depleted and enriched sequences, respectively, in the sense direction relative to the upstream antisense direction. These U1 snRNP sites and PAS sites are progressively gained and lost, respectively, at the 5' end of coding genes during vertebrate evolution. Functional disruption of U1 snRNP activity results in a dramatic increase in promoter-proximal cleavage events in the sense direction with slight increases in the antisense direction. These data suggest that a U1-PAS axis characterized by low U1 snRNP recognition and a high density of PASs in the upstream antisense region reinforces promoter directionality by promoting early termination in upstream antisense regions, whereas proximal sense PAS signals are suppressed by U1 snRNP. We propose that the U1-PAS axis limits pervasive transcription throughout the genome. 3' end sequencing of poly (A) + RNAs in mouse ES cells with and without U1 snRNP inhibition using antisense morpholino oligonucleotides (AMO). Each with two biological replicates.

2013-06-28 | E-GEOD-46433 | biostudies-arrayexpress

The Sen1 Helicase Prevents Spurious Transcription by Controlling Genome-Wide Transcription Termination by RNAPII

Project description:RNA Polymerase II (RNAPII) termination for transcripts containing a polyadenylation signal (PAS) is thought to differ mechanistically from termination for PAS-independent RNAPII transcripts such as sn(o)RNAs. In a screen for factors required for PAS-dependent termination, we identified Sen1, a putative helicase known primarily for its role in PAS-independent termination. We show that Sen1 is required for termination on hundreds of protein-coding genes and suppresses cryptic transcription from nucleosome-free regions on a genomic scale. These effects often overlap with but are also often distinct from those caused by Nrd1 depletion, which also impacts termination of protein-coding and cryptic transcripts, including many genic antisense transcripts. Sen1 controls termination through its helicase activity and stimulates recruitment of factors previously implicated in both PAS-dependent (Rna14, Rat1) and PAS-independent (Nrd1) termination. Thus, RNAPII termination for both protein-coding genes and cryptic transcripts is dependent on multiple pathways. The 2 RNAPII datasets were produced in duplicates and the Sen1 and Nrd1 datasets in triplicates (all IP/Input).

2011-06-01 | E-GEOD-19015 | biostudies-arrayexpress

SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins

Project description:SCAF4 and SCAF8, Transcriptional Anti-Terminator Proteins

| PRJNA498525 | ENA