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Nature DOI:10.1038/nature12943

The evolution of lncRNA repertoires and expression patterns in tetrapods.

Publication TypeJournal Article
Year of Publication2014
AuthorsNecsulea, A, Soumillon, M, Warnefors, M, Liechti, A, Daish, T, Zeller, U, Baker, JC, Grützner, F, Kaessmann, H
Date Published2014 Jan 30
KeywordsAnimals, Anura, Chickens, Conserved Sequence, Evolution, Molecular, Gene Expression Regulation, Developmental, Genomics, Humans, Mice, MicroRNAs, Multigene Family, Primates, Proteins, RNA Precursors, RNA, Long Noncoding, Transcriptome

Only a very small fraction of long noncoding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but the absence of lncRNA annotations in non-model organisms has precluded comparative analyses. Here we present a large-scale evolutionary study of lncRNA repertoires and expression patterns, in 11 tetrapod species. We identify approximately 11,000 primate-specific lncRNAs and 2,500 highly conserved lncRNAs, including approximately 400 genes that are likely to have originated more than 300 million years ago. We find that lncRNAs, in particular ancient ones, are in general actively regulated and may function predominantly in embryonic development. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network suggests potential functions for lncRNAs in fundamental processes such as spermatogenesis and synaptic transmission, but also in more specific mechanisms such as placenta development through microRNA production.


Alternate JournalNature
PubMed ID24463510
Grant ListG0700089 / / Medical Research Council / United Kingdom
MC_PC_15004 / / Medical Research Council / United Kingdom
099175/Z/12/Z / / Wellcome Trust / United Kingdom
/ / Medical Research Council / United Kingdom