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

R Axel W Wiberg1, Daniel L Halligan2, Rob W Ness2

  • 1Institute of Evolutionary Biology, University of Edinburgh, United Kingdom Present address: Centre for Biological Diversity, School of Biology, University of St. Andrews, United Kingdom raww@st-andrews.ac.uk.

Genome Biology and Evolution
|August 15, 2015
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Summary

Most long noncoding RNAs (lncRNAs) in mice evolve neutrally, similar to ancestral repeats. However, functionally characterized lncRNAs and those conserved deeply in vertebrates show evolutionary constraints, suggesting they are under selection.

Keywords:
functionalitygenomicslong noncoding RNAsselection

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Molecular Biology

Background:

  • Long noncoding RNAs (lncRNAs) are a significant class of noncoding RNA, but their functionality versus transcriptional noise remains debated.
  • Limited evidence of long-term evolutionary conservation for most lncRNAs suggests they may be nonfunctional or recent innovations.

Purpose of the Study:

  • To investigate recent selection pressures on long noncoding RNAs (lncRNAs) in mouse populations.
  • To compare evolutionary conservation patterns of lncRNAs with protein-coding exons and ancestral repeats.

Main Methods:

  • Comparative genomics analysis of nucleotide variation within Mus musculus castaneus and divergence from Rattus norvegicus.
  • Examination of sequence diversity and divergence at approximately 10,000 lncRNA loci, protein-coding exons, and ancestral repeats.

Main Results:

  • Most lncRNA loci exhibit limited sequence conservation, evolving at rates similar to ancestral repeats.
  • lncRNAs conserved deeply in vertebrate phylogeny show reduced within-species sequence diversity.
  • Functionally characterized lncRNAs display diversity and divergence levels comparable to protein-coding exons, indicating selective constraint.

Conclusions:

  • The majority of lncRNA loci in mouse populations appear to evolve under neutral or near-neutral conditions.
  • Older and functionally validated lncRNAs exhibit evolutionary signatures consistent with functional importance and selective pressure.
  • These findings suggest a subset of lncRNAs are under selection, potentially representing functional elements or evolutionary innovations.