Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals
- ↵* Corresponding author; email: manuel.garber{at}umassmed.edu
Abstract
Long intergenic noncoding RNAs (lincRNAs) play diverse regulatory roles in human development and disease, but little is known about their evolutionary history and constraint. Here, we characterize human lincRNA expression patterns in nine tissues across six mammalian species and multiple individuals. We find that at least 35% of human lincRNAs show orthologous transcripts across mammals, and 20% are not conserved beyond chimp and undetectable even in rhesus. Mammalian-conserved lincRNAs show remarkably strong conservation of tissue specificity, suggesting it is essential and selectively maintained, but abundant splice site turnover, suggesting that exact splice sites are not critical. Relative to evolutionarily-young lincRNAs, they show higher primary sequence conservation in their promoters and exons, increased proximity to protein-coding genes enriched for tissue specific functions, fewer repeat elements, and more frequent single-exon transcripts. Hominid-specific lincRNAs are more tissue-specific, enriched for testis, and faster-evolving within the human lineage.
- Received August 10, 2013.
- Accepted January 14, 2014.
- Published by Cold Spring Harbor Laboratory Press
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