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

ABSTRACT: 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

ORGANISM(S): Homo sapiens

PROVIDER: GSE264716 | GEO | 2024/11/28

REPOSITORIES: GEO

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Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (nuclear RNA-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.

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

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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

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

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Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity

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