Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
| Autor: | Katja Baerenfaller, Martin Crespi, Julia Bailey-Serres, Jérémie Bazin, Brian D. Gregory, Sager J. Gosai |
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| Přispěvatelé: | University of Zurich, Bailey-Serres, Julia, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Department of Biology, University of Pennsylvania [Philadelphia], Marie Curie European Economic Community Fellowship [PIOF-GA-2012-327954], National Science Foundation (NSF) [MCB-1021969], Eidgenossische Technische Hochschule, Zurich, NSF [DBI-1429826], National Institutes of Health [S10-OD016290-01A1], University of California (UC), University of Pennsylvania |
| Jazyk: | angličtina |
| Rok vydání: | 2017 |
| Předmět: |
0301 basic medicine
RNA Untranslated phosphate deficiency Arabidopsis thaliana long noncoding RNA ribosome footprint profiling small peptides Arabidopsis Plant Biology 610 Medicine & health Biology Plant Roots Phosphates 03 medical and health sciences Open Reading Frames 10183 Swiss Institute of Allergy and Asthma Research Gene Expression Regulation Plant Translational regulation Protein biosynthesis [SDV.BV]Life Sciences [q-bio]/Vegetal Biology RNA Messenger Gene Genetics Messenger RNA 1000 Multidisciplinary Vegetal Biology Multidisciplinary Gene Expression Profiling RNA Translation (biology) Biological Sciences Long non-coding RNA Open reading frame 030104 developmental biology PNAS Plus Seedlings Starvation Protein Biosynthesis Mutation RNA Long Noncoding Transcriptome Ribosomes Biologie végétale |
| Zdroj: | Proceedings of the National Academy of Sciences of the United States of America Proceedings of the National Academy of Sciences of the United States of America, National Academy of Sciences, 2017, 114 (46), pp.E10018-E10027. ⟨10.1073/pnas.1708433114⟩ Proceedings of the National Academy of Sciences of the United States of America, 114 (46) Proceedings of the National Academy of Sciences of the United States of America 46 (114), E10018-E10027. (2017) Proceedings of the National Academy of Sciences of the United States of America, 2017, 114 (46), pp.E10018-E10027. ⟨10.1073/pnas.1708433114⟩ |
| ISSN: | 1091-6490 0027-8424 |
| DOI: | 10.1073/pnas.1708433114⟩ |
| Popis: | Eukaryotic transcriptomes contain a major non–protein-coding component that includes precursors of small RNAs as well as long noncoding RNA (lncRNAs). Here, we utilized the mapping of ribosome footprints on RNAs to explore translational regulation of coding and noncoding RNAs in roots of Arabidopsis thaliana shifted from replete to deficient phosphorous (Pi) nutrition. Homodirectional changes in steady-state mRNA abundance and translation were observed for all but 265 annotated protein-coding genes. Of the translationally regulated mRNAs, 30% had one or more upstream ORF (uORF) that influenced the number of ribosomes on the principal protein-coding region. Nearly one-half of the 2,382 lncRNAs detected had ribosome footprints, including 56 with significantly altered translation under Pi-limited nutrition. The prediction of translated small ORFs (sORFs) by quantitation of translation termination and peptidic analysis identified lncRNAs that produce peptides, including several deeply evolutionarily conserved and significantly Pi-regulated lncRNAs. Furthermore, we discovered that natural antisense transcripts (NATs) frequently have actively translated sORFs, including five with low-Pi up-regulation that correlated with enhanced translation of the sense protein-coding mRNA. The data also confirmed translation of miRNA target mimics and lncRNAs that produce trans-acting or phased small-interfering RNA (tasiRNA/phasiRNAs). Mutational analyses of the positionally conserved sORF of TAS3a linked its translation with tasiRNA biogenesis. Altogether, this systematic analysis of ribosome-associated mRNAs and lncRNAs demonstrates that nutrient availability and translational regulation controls protein and small peptide-encoding mRNAs as well as a diverse cadre of regulatory RNAs. Proceedings of the National Academy of Sciences of the United States of America, 114 (46) ISSN:0027-8424 ISSN:1091-6490 |
| Databáze: | OpenAIRE |
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