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| Status |
Public on Oct 03, 2015 |
| Title |
Canonical poly(A) polymerase activity promotes the decay of a wide variety of mammalian nuclear RNAs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The human nuclear poly(A)-binding protein PABPN1 has been implicated in the decay of nuclear noncoding RNAs (ncRNAs). In addition, PABPN1 stimulates hyperadenylation by poly(A) polymerase, and this activity is thought to be required for decay. Here, we inactivated hyperadenylation by two distinct mechanisms and examined changes in gene expression in HEK293 cells by RNAseq. We observed the upregulation of various ncRNAs, including snoRNA host genes, primary miRNA transcripts, and upstream antisense RNAs, confirming that hyperadenylation is broadly required for the degradation of PABPN1-targets. In addition, we found that mRNAs with retained introns are susceptible to PABPN1 and PAPα/γ-mediated decay (PPD). Transcripts are targeted for degradation due to inefficient export, which is a consequence of reduced intron number or incomplete splicing. We conclude that PPD is an important mammalian nuclear RNA decay pathway for the removal of poorly spliced and nuclear-retained transcripts.
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| Overall design |
Poly(A)+ RNA from HEK293 cells was analyzed by next generation sequencing following depletion of PAPα and PAPγ or expression of a dominant negative allele of PABPN1 (LALA) designed to inhibit polyadenylation. For each condition, we collected both total RNA and a nuclear-enriched sample. Each sample was collected in duplicate.
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| Contributor(s) |
Bresson SM, Hunter OV, Hunter AC, Conrad NK |
| Citation(s) |
26484760 |
| |
| Submission date |
Oct 02, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Bresson |
| E-mail(s) |
stefan.bresson@gmail.com
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| Organization name |
University of Edinburgh
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| Department |
Wellcome Trust Centre for Cell Biology
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| Lab |
Tollervey Lab
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| Street address |
Max Born Crescent, Swann 5.1
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| City |
Edinburgh |
| State/province |
Scotland |
| ZIP/Postal code |
EH9 3BF |
| Country |
United Kingdom |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (10)
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| Relations |
| BioProject |
PRJNA297633 |
| SRA |
SRP064410 |
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