UMMS Affiliation
Program in Molecular Medicine; Program in Bioinformatics and Integrative Biology
Publication Date
4-1-2014
Document Type
Article
Subjects
Animals; Cattle; Conserved Sequence; *Evolution, Molecular; Exons; Humans; Mice; Organ Specificity; *Promoter Regions, Genetic; RNA, Long Noncoding; Rats
Disciplines
Comparative and Evolutionary Physiology | Computational Biology | Ecology and Evolutionary Biology | Evolution | Genetics and Genomics | Genomics | Molecular Genetics | Translational Medical Research
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. Of the 1898 human lincRNAs expressed in these tissues, we find orthologous transcripts for 80% in chimpanzee, 63% in rhesus, 39% in cow, 38% in mouse, and 35% in rat. Mammalian-expressed lincRNAs show remarkably strong conservation of tissue specificity, suggesting that it is selectively maintained. In contrast, abundant splice-site turnover suggests that exact splice sites are not critical. Relative to evolutionarily young lincRNAs, mammalian-expressed lincRNAs 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. Remarkably, we find that approximately 20% of human lincRNAs are not expressed beyond chimpanzee and are undetectable even in rhesus. These hominid-specific lincRNAs are more tissue specific, enriched for testis, and faster evolving within the human lineage.
Keywords
UMCCTS funding
Rights and Permissions
Copyright 2014 Washietl et al.; Published by Cold Spring Harbor Laboratory Press. This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see http://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 3.0 Unported), as described at http://creativecommons.org/licenses/by-nc/3.0/.
DOI of Published Version
10.1101/gr.165035.113
Source
Genome Res. 2014 Apr;24(4):616-28. doi: 10.1101/gr.165035.113. Epub 2014 Jan 15. Link to article on publisher's site
Journal/Book/Conference Title
Genome research
Related Resources
PubMed ID
24429298
Repository Citation
Washietl, Stefan; Kellis, Manolis; and Garber, Manuel, "Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals" (2014). UMass Center for Clinical and Translational Science Supported Publications. 32.
https://escholarship.umassmed.edu/umccts_pubs/32
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 3.0 License
Included in
Comparative and Evolutionary Physiology Commons, Computational Biology Commons, Evolution Commons, Genomics Commons, Molecular Genetics Commons, Translational Medical Research Commons