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| Status |
Public on Apr 24, 2015 |
| Title |
Quality control of transcription start site selection by Nonsense-Mediated-mRNA Decay |
| Organism |
Saccharomyces cerevisiae BY4741 |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. Moreover, we found that the low specificity of RNA polymerase II TSSs selection generates, for 47% of the expressed genes, NMD-sensitive transcript isoforms carrying uORFs or starting downstream of the ATG START codon. Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.
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| |
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| Overall design |
5'-end profile of WT and NMD deficient yeast cells
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| |
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| Contributor(s) |
Feuerbach F, Malabat C, Ma L, Saveanu C, Jacquier A |
| Citation(s) |
25905671 |
| |
| Submission date |
Dec 12, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Alain Jacquier |
| E-mail(s) |
alain.jacquier@pasteur.fr
|
| Phone |
33-1-4061 3205
|
| Organization name |
Institut Pasteur
|
| Department |
Génomes & génétique
|
| Lab |
Génétique des Interactions macromoléculaires
|
| Street address |
25-28 rue du docteur roux
|
| City |
Paris cedex 15 |
| ZIP/Postal code |
75724 |
| Country |
France |
| |
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| Platforms (1) |
| GPL18330 |
Illumina HiSeq 2000 (Saccharomyces cerevisiae BY4741) |
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| Samples (40)
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| Relations |
| BioProject |
PRJNA270241 |
| SRA |
SRP051115 |
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