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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-poly(A) termination Pathway: Nrd1, Nab3 and Sen1

ABSTRACT: We report here the transcriptome-wide distribution of yeast Rpb2, Sen1, Nrd1 and Nab3 binding sites. These data sets provide highresolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3'-antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link to many expected ncRNAs but surprisingly binds to pre-mRNA transcripts suggesting a role in 3' end formation and/or termination. Six samples by adaptation of PAR-ClIP procedure

ORGANISM(S): Saccharomyces cerevisiae

SUBMITTER: Jeff Corden

PROVIDER: E-GEOD-31764 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing.

Jamonnak Nuttara N Creamer Tyler J TJ Darby Miranda M MM Schaughency Paul P Wheelan Sarah J SJ Corden Jeffry L JL

RNA (New York, N.Y.) 20110927 11

RNA polymerase II transcribes both coding and noncoding genes, and termination of these different classes of transcripts is facilitated by different sets of termination factors. Pre-mRNAs are terminated through a process that is coupled to the cleavage/polyadenylation machinery, and noncoding RNAs in the yeast Saccharomyces cerevisiae are terminated through a pathway directed by the RNA-binding proteins Nrd1, Nab3, and the RNA helicase Sen1. We have used an in vivo cross-linking approach to map ...[more]

PMID: 21954178

Similar Datasets

Transcriptome-Wide Binding Sites for Components of the Saccharomyces cerevisiae Non-poly(A) termination Pathway: Nrd1, Nab3 and Sen1

Project description:We report here the transcriptome-wide distribution of yeast Rpb2, Sen1, Nrd1 and Nab3 binding sites. These data sets provide highresolution definition of non-poly(A) terminators, identify novel genes regulated by attenuation of nascent transcripts close to the promoter, and demonstrate the widespread occurrence of Nrd1-bound 3'-antisense transcripts on genes that are poorly expressed. In addition, we show that Sen1 does not cross-link to many expected ncRNAs but surprisingly binds to pre-mRNA transcripts suggesting a role in 3' end formation and/or termination.

2011-09-08 | GSE31764 | GEO

Characterization of extended transcripts by RNA-Seq suggests that Rrp6 influences Nrd1-dependent termination

Project description:RNAPII is responsible for transcription of protein-coding genes and short, regulatory RNAs. In Saccharomyces cerevisiae, termination of RNAPII-transcribed RNAs ≤1000 bases requires the NNS complex (comprised of Nrd1, Nab3, and Sen1) processing by the exosome, and the nuclear specific catalytic subunit, Rrp6. It has been shown that Rrp6 interacts directly with Nrd1, but whether or not Rrp6 is required for NNS-dependent termination is unclear. Loss of Rrp6 function may result in extension (or inhibition of termination) of NNS-dependent transcripts, or Rrp6 may only function after the fact to carry out RNA 3’ end processing. Here, we performed in-depth differential expression analyses and compare RNA-sequencing data of transcript length and abundance in cells lacking RRP6 to previously published sequencing data measuring the length of RNAs in Nrd1-depleted cells. We find many transcripts that were defined as unterminated upon loss of Nrd1 activity are of similar length in rrp6Δ, and expression levels of downstream genes are significantly decreased. This suggests a similar transcription interference mechanism occurs in cells lacking either Nrd1 or Rrp6, supporting the hypothesis that Rrp6 activity is required for proper NNS termination in vivo. Four biological replicates each for deletion mutant (RRP6) and reference cells (WT)

2015-04-14 | E-GEOD-57155 | biostudies-arrayexpress

Characterization of extended transcripts by RNA-Seq suggests that Rrp6 influences Nrd1-dependent termination

2015-04-14 | GSE57155 | GEO

Pol II chromatin immunoprecipitation in S. cerevisiae

Project description:In Saccharomyces cerevisiae short non-coding RNA (ncRNA) generated by RNA Polymerase II (Pol II) are terminated by the NRD complex consisting of Nrd1, Nab3 and Sen1. We now show that Pcf11, a component of the cleavage and polyadenylation complex (CPAC), is generally required for NRD-dependent transcription termination through the action of its CTD interacting domain (CID). Pcf11 localizes downstream of Nrd1 on NRD terminators, and its recruitment depends on Nrd1. Furthermore mutation of the Pcf11 CID results in Nrd1 retention on chromatin, delayed degradation of ncRNA and restricts Pol II CTD Ser2 phosphorylation and Sen1-Pol II interaction. Finally, the pcf11-13 and sen1-1 mutant phenotypes are very similar as both accumulate RNA:DNA hybrids and display Pol II pausing downstream of NRD terminators. We predict a mechanism whereby Nrd1 and Pcf11 exchange on chromatin facilitates Pol II pausing and CTD Ser2-P phosphorylation. This in turn promotes Sen1 activity that is required for NRD-dependent transcription termination in vivo.

2015-04-02 | GSE67483 | GEO

Pol II chromatin immunoprecipitation in S. cerevisiae

2015-04-02 | E-GEOD-67483 | biostudies-arrayexpress

Genetic and pharmacological evidence for kinetic competition between alternative poly(A) sites in yeast - NNS complex

Project description:PAT-seq approach was used to determine changes to 3'UTR length in yeast upon mutation of NNS subunits Nrd1 (nrd1-5), Nab3 (nab3-11) and Sen1 (sen1-1) compared to wild type cells

2021-06-25 | GSE160567 | GEO

Genome-wide mapping of yeast RNA polymerase II termination

Project description:Using a modification of the yeast anchor away and PAR-CLIP protocols, we have mapped the position of Pol II genome-wide in living yeast cells after depletion of components of either the polyadenylation (pA) or non-pA termination complexes. Depletion of Ysh1 from the nucleus does not lead to readthrough transcription. In contrast, depletion of the termination factor Nrd1 leads to widespread runaway elongation of non-pA transcripts. Depletion of Sen1 also leads to readthrough at non-pA terminators but in contrast to Nrd1 this readthrough appears less processive. Examination of PAR-CLIP sequencing data of Pol II after removal of different transcriptional termination factors.

2014-07-24 | E-GEOD-56435 | biostudies-arrayexpress

Genome-wide mapping of yeast RNA polymerase II termination

2014-07-24 | GSE56435 | GEO

Transcription profiling of S. cerevisiae Nab3 and Nrd1 mutants

Project description:Nrd1 and Nab3 are two yeast RNA binding proteins which have been shown to be involved in transcription termination of non poly(A) genes. We have used expression profiling of a Nab3 mutant to discover novel RNA targets of the Nrd1 and Nab3 transcription termination pathway. Failure to terminate RNA polymerase II by Nab3 leads to continued transcription well beyond the correct termination sites, altering the expression of adjacent downstream genes. Using this concept, our microarray uncovered the up-regulation of numerous genes that are located downstream of âcryptic unstable transcriptsâ, transcripts that are transcribed, terminated and rapidly degraded by Nrd1, Nab3, and the nuclear exosome. Experiment Overall Design: Four yeast total RNA samples where analyzed in this study. These RNAs come from two separate strains of yeast, each strain at either the permissive temperature (25C) or the non-permissive temperature (37C). One of these strains is a wild type strain of yeast used as a control. The other strain has a mutation in the Nab3 protein that confers temperature sensitivity at the non-permissive temperature of 37C. After two hours at the non-permissive temperature, we observe disruptions in the Nrd1/Nab3 transcription termination pathway and this is the scheme that we followed for our microarray experiment. Our goal was to observe the global expression changes after 2 hours without Nab3 function.

2008-06-13 | E-GEOD-4657 | biostudies-arrayexpress

Molecular basis for coupling transcription termination to non-coding RNA degradation

Project description:The Nrd1-Nab3-Sen1 (NNS) complex plays a pivotal role in the control of pervasive transcription and the generation of sn- and snoRNAs in S. cerevisiae. The NNS-complex terminates transcription of non-coding RNA genes and promotes processing/degradation of transcripts by the nuclear exosome. To assess the role of the Nrd1p CTD-interacting domain (CID) in the function of the NNS-complex, we re-examined whether this domain is required for efficient transcription termination by the NNS pathway. We compared the RNA polymerase II distribution by ChIP and tiling arrays (ChIP-chip) in wild type and nrd1 deltaCID cells. Moreover, we compared the genome-wide chromatin distribution of Nrd1p in the presence and the absence of the CID by ChIP-chip analysis. ChIP of RNA polymerase II was performed using an anti-Rpb3 antibody (1Y26, Neoclone). ChIP of Nrd1 was performed using TAP-tagged S. cerevisiae strains. For details see protocols. To download the wild-type Pol II and Nrd1 data go to E-MTAB-1626 and E-MTAB-1060, respectively.

2014-04-24 | E-MTAB-2175 | biostudies-arrayexpress

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