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 IncRNAs are functional or merely represent transcriptional noise. Although characterization of individual IncRNAs 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 IncRNAs are nonfunctional, the possibility remains that some represent recent evolutionary innovations. We examine recent selection pressures acting on IncRNAs in mouse populations. We compare patterns of within-species nucleotide variation at approximately 10,000 IncRNA 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 IncRNAs, and the associated flanking regions, show weak, but significantly lower levels of sequence diversity and divergence at IncRNAs compared with ARs. IncRNAs conserved deep in the vertebrate phylogeny show lower withinspecies sequence diversity than IncRNAs in general. A set of 74 functionally characterized IncRNAs show levels of diversity and divergence comparable to PC exons, suggesting that these IncRNAs are under substantial selective constraints. Our results suggest that, in mouse populations, most IncRNA loci evolve at rates similar to ARs, whereas older IncRNAs tend to show signals of selection similar to PC genes.