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

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.

Frequent translation of small open reading frames in evolutionary conserved lncRNA regions

“…The function of lncRNAs is a matter of intense debate. In general, lncRNAs display high evolutionary turnover (Kutter et al, 2012;Neme and Tautz, 2016), and show very weak sequence constraints according to single nucleotide polymorphism data (Wiberg et al, 2015). This is consistent with the idea that many lncRNAs are not functional but a result of the high transcriptional activity of the genome (Brosius, 2005;Struhl, 2007;Wang et al, 2004).…”

“…Previous studies found that lncRNAs conserved across different species were more constrained than species-specific lncRNAs (Kutter et al, 2012;Wiberg et al, 2015) or that sequences presumably evolving under no constraints (Marques and Ponting, 2009). It was also reported that putative low-accessibility nucleotides from secondary structure elements showed a depletion of polymorphisms when compared to other exonic and intronic sequences (Pegueroles and Gabaldón, 2016).…”

Biological function in the twilight zone of sequence conservation

“…In contrast to most mammalian protein-coding genes, which possess homologues that are identifiable across diverse animal phyla and beyond, 80% of human lncRNA families originated recently during primate evolution, and only 3% are conserved in more distantly related species such as chicken or frog [ 29 , 30 ]. Not only conservation, but also constraint and positive selection, are low or absent on intergenic lncRNAs among modern human or mouse populations [ 29 , 31 , 32 ].

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Translation of neutrally evolving peptides provides a basis for de novo gene evolution

“…A large fraction of the genome is transcribed; this includes functional genes but also thousands of transcripts that are not conserved across species and which show weak or no signatures of natural selection [1][2][3] . Many of the latter transcripts are annotated as long non-coding RNAs (lncRNAs) because they lack conserved long open reading frames (ORFs).…”