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Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (POINT-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: GSE264717 | 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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