Quality control of transcription start site selection by nonsense-mediated-mRNA decay
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 deficie...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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eLife Sciences Publications Ltd
2015-04-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/06722 |
| _version_ | 1811236934765248512 |
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| author | Christophe Malabat Frank Feuerbach Laurence Ma Cosmin Saveanu Alain Jacquier |
| author_facet | Christophe Malabat Frank Feuerbach Laurence Ma Cosmin Saveanu Alain Jacquier |
| author_sort | Christophe Malabat |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-12T12:17:41Z |
| format | Article |
| id | doaj.art-4fc0945da5244f8ab28e8f132e2e88d3 |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T12:17:41Z |
| publishDate | 2015-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-4fc0945da5244f8ab28e8f132e2e88d32022-12-22T03:33:23ZengeLife Sciences Publications LtdeLife2050-084X2015-04-01410.7554/eLife.06722Quality control of transcription start site selection by nonsense-mediated-mRNA decayChristophe Malabat0Frank Feuerbach1Laurence Ma2Cosmin Saveanu3Alain Jacquier4Institut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, FranceInstitut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, FrancePlate-Forme Génomique, Institut Pasteur, Paris, FranceInstitut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, FranceInstitut Pasteur, UMR3525, Génétique des Interactions Macromoléculaires, Centre National de la Recherche Scientifique, Paris, FranceNonsense-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.https://elifesciences.org/articles/06722non-coding RNARNA quality controlnon-sense mediated mRNA decaynuclear RNA degradationtranscription initiation |
| spellingShingle | Christophe Malabat Frank Feuerbach Laurence Ma Cosmin Saveanu Alain Jacquier Quality control of transcription start site selection by nonsense-mediated-mRNA decay eLife non-coding RNA RNA quality control non-sense mediated mRNA decay nuclear RNA degradation transcription initiation |
| title | Quality control of transcription start site selection by nonsense-mediated-mRNA decay |
| title_full | Quality control of transcription start site selection by nonsense-mediated-mRNA decay |
| title_fullStr | Quality control of transcription start site selection by nonsense-mediated-mRNA decay |
| title_full_unstemmed | Quality control of transcription start site selection by nonsense-mediated-mRNA decay |
| title_short | Quality control of transcription start site selection by nonsense-mediated-mRNA decay |
| title_sort | quality control of transcription start site selection by nonsense mediated mrna decay |
| topic | non-coding RNA RNA quality control non-sense mediated mRNA decay nuclear RNA degradation transcription initiation |
| url | https://elifesciences.org/articles/06722 |
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