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| Status |
Public on Oct 02, 2023 |
| Title |
PAP-gamma associates with PAXT nuclear exosome to control the abundance of PROMPT ncRNAs |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
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| Summary |
Pervasive transcription of the human genome generates an abundance of RNAs that must be processed and degraded. The nuclear RNA exosome is the main RNA degradation machinery in the nucleus. However, nuclear exosome must be recruited to its substrates by targeting complexes, such as NEXT or PAXT. By proteomic analysis, we have identified additional subunits of PAXT, including many orthologs of MTREC found in S. pombe. In particular, we show that polyA polymerase gamma was associated with PAXT. Genome-wide mapping of the binding sites of ZFC3H1, RBM26 and PAPgamma, showed that PAXT is recruited to the TSS of hundreds of genes. Loss of ZFC3H1 abolished recruitment of PAXT subunits including PAPgamma to TSSs and concomitantly increased the abundance of PROMPTs at the same sites. Moreover, PAPgamma polyadenylated PROMPTs and modulated their stability. Our results thus provide key insights into the direct targeting and degradation of PROMPT ncRNAs by PAXT, at their genomic sites and depending on polyadenylation of RNAs.
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| Overall design |
We used the technology of ChIP-seq to quantify occupancy of PAXT subunits, ZFC3H1, RBM26 and a newly identified subunit, PAPgamma, as well as RNA polymerase II in control cells. Localization of PAXT subunits was also identified by ChIP-seq in cells expressing shRNAs targeting ZFC3F1 or a non-targeting control.
We used the RNA-seq technology to quantify RNA expression changes upon loss of PAP-Gamma using siRNA.
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| Contributor(s) |
Contreras X, Depierre D, Akkawi C, Cuvier O, Kiernan R |
| Citation(s) |
37875486 |
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| Submission date |
Nov 18, 2021 |
| Last update date |
Nov 13, 2023 |
| Contact name |
Rosemary Kiernan |
| Organization name |
UMR9002 CNRS-UM
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| Lab |
Gene Regulation lab
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| Street address |
141 rue de la cardonille
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| City |
Montpellier |
| ZIP/Postal code |
34396 |
| Country |
France |
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| Platforms (2) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (26)
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| Relations |
| BioProject |
PRJNA781729 |
| SRA |
SRP346829 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE189157_RAW.tar |
9.7 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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