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Series GSE189157 Query DataSets for GSE189157
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
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.
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.
Contributor(s) Contreras X, Depierre D, Akkawi C, Cuvier O, Kiernan R
Citation(s) 37875486
Submission date Nov 18, 2021
Last update date Nov 13, 2023
Contact name Rosemary Kiernan
Organization name UMR9002 CNRS-UM
Lab Gene Regulation lab
Street address 141 rue de la cardonille
City Montpellier
ZIP/Postal code 34396
Country France
Platforms (2)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (26)
GSM5695517 Z1_shCtrl
GSM5695519 PAPgamma_shCtrl
GSM5695520 RBM26_shCtrl
BioProject PRJNA781729
SRA SRP346829

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Supplementary file Size Download File type/resource
GSE189157_RAW.tar 9.7 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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