Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Yeast RNase III triggers polyadenylation independent transcription termination

ABSTRACT: Transcription termination of messenger RNA (mRNA) is normally achieved by polyadenylation followed by Rat1p dependent 5’-3’ exoribonuleolytic degradation of the downstream transcript. Here we show that the yeast orthologue of the dsRNA-specific ribonuclease III (Rnt1p) may trigger Rat1p dependent termination of RNA transcripts that fail to terminate near polyadenylation signals. Rnt1p cleavage sites were found downstream of several genes and the deletion of RNT1 resulted in transcription read-through. Inactivation of Rat1p impaired Rnt1p dependent termination and resulted in the accumulation of 3’ end cleavage products. These results support a new model for transcription termination in which co-transcriptional cleavage by Rnt1p provides access for exoribonucleases in the absence of polyadenylation signals.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE16784 | GEO | 2009/10/09

SECONDARY ACCESSION(S): PRJNA117539

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

Project description:Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements, thus representing cornerstones of genomic regulation in eukaryotes. Restrictor, a complex conserved from worms to humans and composed of the RNA-binding protein ZC3H4 and of WDR82, a Pol II-carboxyterminal repeat domain (CTD)-interacting protein, is required to suppress long-range, processive transcription at thousands of extragenic sites, with instead comparatively limited effects on gene transcription. Restrictor contains no RNA cleavage subunit and does not coopt known cleavage complexes, indicating alternative termination mechanisms. Here we show that Restrictor-driven termination involves Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent, phosphatase-dependent termination of non-coding RNAs in yeast. Competition among Restrictor, the cleavage and polyadenylation specificity complex (CPSF) and the histone cleavage complex for a limited pool of Symplekin resulted in mutual regulation, thus revealing unexpected regulatory interactions among multiple transcription termination pathways and a general role of Symplekin in both genic and extragenic cleavage-independent termination pathways.

2023-12-14 | GSE240357 | GEO

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

2023-12-14 | GSE237459 | GEO

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

2023-12-14 | GSE237458 | GEO

Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription

2023-12-14 | GSE237457 | GEO

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals

Project description:Here we present complete genomic and biochemical annotations of the signals required for RNA degradation by the dsRNA specific ribonuclease III (Rnt1p) and examine its impact on transcriptome expression. Rnt1p cleavage signals are randomly distributed in the yeast genome and encompass wide variety of sequence indicating that transcriptome stability is not determined by the recurrence of a fixed cleavage motif. Instead, RNA reactivity is defined by the sequence and structural context in which the cleavage sites are located. Reactive signals are often associated with transiently expressed genes and their impact on RNA expression is linked to growth conditions. Together the data suggest that Rnt1p reactivity is triggered by malleable RNA degradation signals that permit dynamic response to changes in growth conditions. Total RNA and whole cell extract from rnt1d strain was divided in two samples. One sample was treated with purified Rnt1p. The other was only incubated with buffer. The two samples were then treated with recombinant Xrn1p.

2015-02-16 | E-GEOD-57447 | biostudies-arrayexpress

Transcriptome wide annotation of eukaryotic RNase III reactivity and degradation signals [Expression 2]

2015-02-16 | GSE57447 | GEO

Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT-Seq)

Project description:The best-studied mechanism of eukaryotic RNA polymerase II (RNAPII) transcriptional termination is at protein-coding genes and involves endonucleolytic cleavage of the nascent RNA at the polyadenylation site. The RNAPII-associated cleavage product is then degraded 5'→3’ by XRN2 to elicit termination. In contrast, prokaryotic RNAP and eukaryotic RNAPIII often terminate directly over T-tracts in the non-template DNA strand. Here, we demonstrate a similar capability for mammalian RNAPII. This mechanism terminates snRNA transcription, which we unexpectedly show to be Integrator-independent. It is more generally employed where RNAPII elongation competence is low, especially in promoter-proximal regions and downstream of some protein-coding genes. In contrast, RNAPII within gene bodies does not terminate at T-tracts. Finally, XRN2-dependent, and T-tract termination are usually independent: the former acts following polyadenylation site cleavage, whereas the latter is employed where XRN2 cannot be engaged. Overall, we propose that RNAP’s retain the potential to terminate over T-rich sequences throughout evolution

2024-11-28 | GSE264717 | GEO

Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT5-Seq)

2024-11-28 | GSE264716 | GEO