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Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation
- Source :
- 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⟩
- Publication Year :
- 2017
- Publisher :
- National Academy of Sciences, 2017.
-
Abstract
- 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.<br />Proceedings of the National Academy of Sciences of the United States of America, 114 (46)<br />ISSN:0027-8424<br />ISSN:1091-6490
- Subjects :
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 10916490 and 00278424
- Volume :
- 114
- Issue :
- 46
- Database :
- OpenAIRE
- Journal :
- Proceedings of the National Academy of Sciences of the United States of America
- Accession number :
- edsair.doi.dedup.....968841e1022b10a3013227ff807c53c7