Talk:Molecular Development - Ribonucleic acid
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Cite this page: Hill, M.A. (2020, September 21) Embryology Molecular Development - Ribonucleic acid. Retrieved from https://embryology.med.unsw.edu.au/embryology/index.php/Talk:Molecular_Development_-_Ribonucleic_acid
Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes
Cell Rep. 2014 Sep 11;8(5):1365-79. doi: 10.1016/j.celrep.2014.07.045. Epub 2014 Aug 21.
Ingolia NT1, Brar GA2, Stern-Ginossar N2, Harris MS3, Talhouarne GJ3, Jackson SE4, Wills MR4, Weissman JS2.
Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be noncoding, including 5' UTRs and long noncoding RNAs (lncRNAs). Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here, we show hallmarks of translation in these footprints: copurification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including the induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts at understanding how cells manage and exploit its consequences. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.
Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs
Development. 2013 Jul;140(13):2828-34. doi: 10.1242/dev.098343. Epub 2013 May 22.
Chew GL1, Pauli A, Rinn JL, Regev A, Schier AF, Valen E.
Large-scale genomics and computational approaches have identified thousands of putative long non-coding RNAs (lncRNAs). It has been controversial, however, as to what fraction of these RNAs is truly non-coding. Here, we combine ribosome profiling with a machine-learning approach to validate lncRNAs during zebrafish development in a high throughput manner. We find that dozens of proposed lncRNAs are protein-coding contaminants and that many lncRNAs have ribosome profiles that resemble the 5' leaders of coding RNAs. Analysis of ribosome profiling data from embryonic stem cells reveals similar properties for mammalian lncRNAs. These results clarify the annotation of developmental lncRNAs and suggest a potential role for translation in lncRNA regulation. In addition, our computational pipeline and ribosome profiling data provide a powerful resource for the identification of translated open reading frames during zebrafish development. KEYWORDS: ES cells; Embryogenesis; Long non-coding RNAs; Ribosome profiling; Zebrafish