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| Status |
Public on Nov 28, 2024 |
| Title |
Widespread termination of mammalian RNA polymerase II at T-rich DNA sequences (RNA-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
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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| Overall design |
Comparative meta and gene expression analysis of nuclear RNA sequencing (RNA-Seq) for EXOSC3-dTAG, XRN2-dTAG and parental HCT116 degron cell lines (with or without KD)
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| Contributor(s) |
Davidson L, Rouvière JO, Sousa-Luís R, Nojima T, Proudfoot N, Heick Jensen T, West S |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 21, 2024 |
| Last update date |
Nov 28, 2024 |
| Contact name |
Steven West |
| E-mail(s) |
[email protected]
|
| Phone |
0044(0)1392727458
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| Organization name |
University of Exeter
|
| Department |
Living Systems Institute
|
| Street address |
Stocker Rd
|
| City |
Exeter |
| State/province |
Devon |
| ZIP/Postal code |
EX4 4QD |
| Country |
United Kingdom |
| |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
|
| Samples (12)
|
| GSM8219024 |
3' QUANT-Seq HCT116 plus dTAGv-1 minus EPAP rep 1 |
| GSM8219025 |
3' QUANT-Seq HCT116 plus dTAGv-1 minus EPAP rep 2 |
| GSM8219026 |
3' QUANT-Seq HCT116 plus dTAGv-1 plus EPAP rep 1 |
| GSM8219027 |
3' QUANT-Seq HCT116 plus dTAGv-1 plus EPAP rep 2 |
| GSM8219028 |
3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 minus EPAP rep 1 |
| GSM8219029 |
3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 minus EPAP rep 2 |
| GSM8219030 |
3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 plus EPAP rep 1 |
| GSM8219031 |
3' QUANT-Seq EXOSC3-dTAG plus dTAGv-1 plus EPAP rep 2 |
| GSM8219032 |
3' QUANT-Seq XRN2-dTAG plus dTAGv-1 minus EPAP rep 1 |
| GSM8219033 |
3' QUANT-Seq XRN2-dTAG plus dTAGv-1 minus EPAP rep 2 |
| GSM8219034 |
3' QUANT-Seq XRN2-dTAG plus dTAGv-1 plus EPAP rep 1 |
| GSM8219035 |
3' QUANT-Seq XRN2-dTAG plus dTAGv-1 plus EPAP rep 2 |
|
| Relations |
| BioProject |
PRJNA1102851 |
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