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The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection

ABSTRACT: The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection

PROVIDER: PRJEB14500 | ENA |

REPOSITORIES: ENA

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The Nrd1-like protein Seb1 coordinates co-transcriptional 3â end processing and polyadenylation site selection

Project description:Termination of RNAPII transcription is associated with RNA 3â end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in S. cerevisiae do not rely on RNA cleavage for termination, but instead terminate via a pathway that requires the Nrd1-Nab3-Sen1 (NNS) complex. Here we show that the S. pombe ortholog of Nrd1, Seb1, does not function in NNS-like termination, but promotes polyadenylation site selection of coding and noncoding genes. We found that Seb1 associates with 3â end processing factors, is enriched at the 3â end of genes, and binds RNA motifs downstream of cleavage sites. Importantly, a deficiency in Seb1 resulted in widespread changes in 3â UTR length as a consequence of increased alternative polyadenylation. Given that Seb1 levels affected the recruitment of conserved 3â end processing factors, our findings indicate that the conserved RNA-binding protein Seb1 co-transcriptionally controls alternative polyadenylation. Two biological replicates of Seb1 and Control (parental strain) CRAC experiments

2016-07-22 | E-GEOD-82326 | biostudies-arrayexpress

The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection

Project description:Termination of RNAPII transcription is associated with RNA 3’ end formation. For coding genes, termination is initiated by the cleavage/polyadenylation machinery. In contrast, a majority of noncoding transcription events in S. cerevisiae do not rely on RNA cleavage for termination, but instead terminate via a pathway that requires the Nrd1-Nab3-Sen1 (NNS) complex. Here we show that the S. pombe ortholog of Nrd1, Seb1, does not function in NNS-like termination, but promotes polyadenylation site selection of coding and noncoding genes. We found that Seb1 associates with 3’ end processing factors, is enriched at the 3’ end of genes, and binds RNA motifs downstream of cleavage sites. Importantly, a deficiency in Seb1 resulted in widespread changes in 3’ UTR length as a consequence of increased alternative polyadenylation. Given that Seb1 levels affected the recruitment of conserved 3’ end processing factors, our findings indicate that the conserved RNA-binding protein Seb1 co-transcriptionally controls alternative polyadenylation.

2016-07-22 | GSE82326 | GEO

The Nrd1-like protein Seb1 coordinates co-transcriptional 3â?? end processing and polyadenylation site decision

Project description:Seb1 promotes co-transcriptional 3â?? end processing events that influence polyadenylation site decision knockdown experiments of Seb1 in Pombe

2016-05-31 | E-GEOD-75753 | biostudies-arrayexpress

The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site decision

Project description:Seb1 promotes co-transcriptional 3’ end processing events that influence polyadenylation site decision

2016-05-31 | GSE75753 | GEO

The Nrd1-like protein Seb1 coordinates co-transcriptional 3 end processing and polyadenylation site selection

Project description:Three studies comprising of a strand specific RNA-seq analysis of the fission yeast transcriptome upon depletion of the termiantion factor Seb1 (2 repeats). RNAPII ChIP-seq in fission yeast upon depletion of the termiantion factor Seb1 (1 IP and 1 input). Seb1 ChIP-seq in fission yeast (HTP, 2 IP and 2 input).

2016-07-31 | E-MTAB-4827 | biostudies-arrayexpress

The Nrd1-like protein Seb1 coordinates cotranscriptional 3' end processing and polyadenylation site selection.

Project description: Not available

| S-EPMC4949328 | biostudies-literature

Schizosaccharomyces pombe

Project description:The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site decision

| PRJNA305270 | ENA

Schizosaccharomyces pombe

Project description:The Nrd1-like protein Seb1 coordinates co-transcriptional 3’ end processing and polyadenylation site selection

| PRJNA324654 | ENA

Regulation of alternative cleavage and polyadenylation by 3’ end processing and splicing factors

Project description:Alternative cleavage and polyadenylation (APA) results in mRNA isoforms containing different 3’ untranslated regions (3’UTRs) and/or coding sequences. How core cleavage and polyadenylation (C/P) factors regulate APA is not well understood. Using siRNA knockdown coupled with deep sequencing, we found that several C/P factors can play significant roles in 3’UTR-APA. Whereas Pcf11 and Fip1 enhance usage of proximal poly(A) sites (pAs), CFI-25/68, PABPN1, and PABPC1 promote usage of distal pAs. Strong cis element biases were found for pAs regulated by CFI or Fip1, and the distance between pAs plays an important role in APA regulation. In addition, intronic pAs are substantially regulated by splicing factors, with U1 mostly influencing C/P events in 5’ introns and U2 impacting those in efficiently spliced introns. Furthermore, PABPN1 regulates expression of transcripts with pAs near the transcription start site, a property possibly related to its role in RNA degradation. Finally, we found that groups of APA events regulated by C/P factors are also modulated in cell differentiation and development with distinct trends. Together, our results indicate that the abundance of different C/P factors and splicing factors plays diverse roles in APA, and is relevant to APA regulation in biological conditions. knockdown experiments of 23 C/P factors, 3 splicing factors and U1D in mouse C2C12 myoblast cells

2015-04-01 | E-GEOD-62001 | biostudies-arrayexpress

The Nrd1 CTD-interaction domain contributes to the choice of RNA polymerase II termination pathway and couples to RNA processing by the nuclear exosome

Project description:The RNA polymerase II (RNApII) C-terminal domain (CTD)-interacting domain (CID) proteins are involved in two distinct termination pathways and recognize different phosphorylated forms of CTD. To investigate the role of differential CTDM-^VCID interactions in the choice of termination pathway, we altered the CTD-binding specificity of Nrd1 by domain swapping. ChIP-chip was performed to examine the effect of Nrd1 CID swapping on genome-wide RNA polymerase II (Rpb3 antibody, Neoclone) occupancy. Nrd1 with the CID from Rtt103 (Nrd1[CID-Rtt103]; strain YSB2445) causes read-through transcription at many genes, but can trigger termination where multiple Nrd1/Nab3-binding sites and serine 2 phosphorylated CTD co-exist.

2013-12-04 | E-MTAB-1626 | biostudies-arrayexpress

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