Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.

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Serval ID
serval:BIB_F5DB36DCCBD8
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Assessing Recent Selection and Functionality at Long Noncoding RNA Loci in the Mouse Genome.
Journal
Genome Biology and Evolution
Author(s)
Wiberg R.A., Halligan D.L., Ness R.W., Necsulea A., Kaessmann H., Keightley P.D.
ISSN
1759-6653 (Electronic)
ISSN-L
1759-6653
Publication state
Published
Issued date
2015
Peer-reviewed
Oui
Volume
7
Number
8
Pages
2432-2444
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: epublish
Abstract
Long noncoding RNAs (lncRNAs) are one of the most intensively studied groups of noncoding elements. Debate continues over what proportion of lncRNAs are functional or merely represent transcriptional noise. Although characterization of individual lncRNAs has identified approximately 200 functional loci across the Eukarya, general surveys have found only modest or no evidence of long-term evolutionary conservation. Although this lack of conservation suggests that most lncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on lncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 lncRNA loci in a cohort of the wild house mouse, Mus musculus castaneus, with between-species nucleotide divergence from the rat (Rattus norvegicus). Loci under selective constraint are expected to show reduced nucleotide diversity and divergence. We find limited evidence of sequence conservation compared with putatively neutrally evolving ancestral repeats (ARs). Comparisons of sequence diversity and divergence between ARs, protein-coding (PC) exons and lncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at lncRNAs compared with ARs. lncRNAs conserved deep in the vertebrate phylogeny show lower within-species sequence diversity than lncRNAs in general. A set of 74 functionally characterized lncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these lncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most lncRNA loci evolve at rates similar to ARs, whereas older lncRNAs tend to show signals of selection similar to PC genes.
Keywords
Animals, Evolution, Molecular, Genetic Loci, Genetic Variation, Genome, Mice/genetics, RNA, Long Noncoding/genetics, Rats, Selection, Genetic
Pubmed
Web of science
Open Access
Yes
Create date
29/09/2015 16:37
Last modification date
20/08/2019 16:22
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