Home LiteratureArticle Details
PMID: 24463510 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

The evolution of lncRNA repertoires and expression patterns in tetrapods.

Nature ·Vol. 505 ·No. 7485 ·2014-01-30 ·Pages 635-40

Necsulea A, Soumillon M, Warnefors M, Liechti A, Daish T, Zeller U, Baker JC, Grützner F, Kaessmann H

Abstract

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.

MeSH Terms
Animals Anura/genetics Chickens/genetics Conserved Sequence/genetics Evolution, Molecular Gene Expression Regulation, Developmental/genetics Genomics Humans Mice MicroRNAs/genetics Multigene Family Primates/genetics Proteins/genetics RNA Precursors/genetics RNA, Long Noncoding/genetics Transcriptome
Chemicals
H19 long non-coding RNA MicroRNAs Proteins RNA Precursors RNA, Long Noncoding
Authors & Affiliations
9 authors, click to expand affiliations / ORCID
Necsulea Anamaria
1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.).
Soumillon Magali
1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland [3] Laboratory of Developmental Genomics, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland (A.N.); Harvard Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA, and Broad Institute, Cambridge, Massachusetts 02142, USA (M.S.).
Warnefors Maria
1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Liechti Angélica
1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
Daish Tasman
The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
Zeller Ulrich
Department of Systematic Zoology, Faculty of Agriculture and Horticulture, Humboldt University Berlin, 10099 Berlin, Germany.
Baker Julie C
Department of Genetics, Stanford University School of Medicine, Stanford University, Stanford, California 94305, USA.
Grützner Frank
The Robinson Institute, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia 5005, Australia.
Kaessmann Henrik
1] Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland [2] Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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Article Info
Journal
Nature
Abbr.
Nature
ISSN
1476-4687
DOI
10.1038/nature12943
Published
2014-01-30
Epub
2014-00-19
Pages
635-40
Language
English
Region
England
NLM ID
0410462
Subset
IM
Grants
Medical Research Council · G0700089 · United Kingdom
Medical Research Council · MC_PC_15004 · United Kingdom
Wellcome Trust · 099175/Z/12/Z · United Kingdom
Databases
GEO
GSE43520
External Links
PubMed source DOI: 10.1038/nature12943 View journal details
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