Differentiating protein-coding and noncoding RNA: challenges and ambiguities.

The assumption that RNA can be readily classified into either protein-coding or non-protein-coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-...

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Autores principales:	Marcel E Dinger, Ken C Pang, Tim R Mercer, John S Mattick
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2008
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/93919d3375964c7b83ac10be8a57c50b
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spelling	oai:doaj.org-article:93919d3375964c7b83ac10be8a57c50b2021-11-25T05:41:57ZDifferentiating protein-coding and noncoding RNA: challenges and ambiguities.1553-734X1553-735810.1371/journal.pcbi.1000176https://doaj.org/article/93919d3375964c7b83ac10be8a57c50b2008-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/19043537/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358The assumption that RNA can be readily classified into either protein-coding or non-protein-coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein-coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as protein-coding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted.Marcel E DingerKen C PangTim R MercerJohn S MattickPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 4, Iss 11, p e1000176 (2008)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Marcel E Dinger Ken C Pang Tim R Mercer John S Mattick Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
description	The assumption that RNA can be readily classified into either protein-coding or non-protein-coding categories has pervaded biology for close to 50 years. Until recently, discrimination between these two categories was relatively straightforward: most transcripts were clearly identifiable as protein-coding messenger RNAs (mRNAs), and readily distinguished from the small number of well-characterized non-protein-coding RNAs (ncRNAs), such as transfer, ribosomal, and spliceosomal RNAs. Recent genome-wide studies have revealed the existence of thousands of noncoding transcripts, whose function and significance are unclear. The discovery of this hidden transcriptome and the implicit challenge it presents to our understanding of the expression and regulation of genetic information has made the need to distinguish between mRNAs and ncRNAs both more pressing and more complicated. In this Review, we consider the diverse strategies employed to discriminate between protein-coding and noncoding transcripts and the fundamental difficulties that are inherent in what may superficially appear to be a simple problem. Misannotations can also run in both directions: some ncRNAs may actually encode peptides, and some of those currently thought to do so may not. Moreover, recent studies have shown that some RNAs can function both as mRNAs and intrinsically as functional ncRNAs, which may be a relatively widespread phenomenon. We conclude that it is difficult to annotate an RNA unequivocally as protein-coding or noncoding, with overlapping protein-coding and noncoding transcripts further confounding this distinction. In addition, the finding that some transcripts can function both intrinsically at the RNA level and to encode proteins suggests a false dichotomy between mRNAs and ncRNAs. Therefore, the functionality of any transcript at the RNA level should not be discounted.
format	article
author	Marcel E Dinger Ken C Pang Tim R Mercer John S Mattick
author_facet	Marcel E Dinger Ken C Pang Tim R Mercer John S Mattick
author_sort	Marcel E Dinger
title	Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
title_short	Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
title_full	Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
title_fullStr	Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
title_full_unstemmed	Differentiating protein-coding and noncoding RNA: challenges and ambiguities.
title_sort	differentiating protein-coding and noncoding rna: challenges and ambiguities.
publisher	Public Library of Science (PLoS)
publishDate	2008
url	https://doaj.org/article/93919d3375964c7b83ac10be8a57c50b
work_keys_str_mv	AT marceledinger differentiatingproteincodingandnoncodingrnachallengesandambiguities AT kencpang differentiatingproteincodingandnoncodingrnachallengesandambiguities AT timrmercer differentiatingproteincodingandnoncodingrnachallengesandambiguities AT johnsmattick differentiatingproteincodingandnoncodingrnachallengesandambiguities
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Differentiating protein-coding and noncoding RNA: challenges and ambiguities.

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