Cited by 1,000Cancer-related molecular mechanisms researchChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

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The evolution of lncRNA repertoires and expression patterns in tetrapods

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Necsulea, Anamaria, Soumillon, Magali, Warnefors, Maria, Liechti, Angélica, Daish, Tasman, Zeller, Ulrich, Baker, Julie C., Grützner, Frank, Kaessmann, Henrik·2014·Nature

DOI 10.1038/nature12943

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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.

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Authors: Necsulea, A., Soumillon, M., Warnefors, M., Liechti, A., Daish, T., Zeller, U., Baker, J. C., Grützner, F., & Kaessmann, H.
Affiliations: Broad Institute (US)
SIB Swiss Institute of Bioinformatics (CH)
The University of Adelaide (AU)
Humboldt-Universität zu Berlin (DE)
Stanford Medicine (US)
Corresponding author: Kaessmann, Henrik
ORCID: Liechti, Angélica
Baker, Julie C.
Grützner, Frank
Kaessmann, Henrik
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2014-01-19
Volume: 505
Issue: 7485
Pages: 635-640
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature12943
OpenAlex: W2088069070
Cited by: 984
References: 58
Citations by year: 2026: 30 · 2025: 26 · 2024: 62 · 2023: 55 · 2022: 70 · 2021: 85 · 2020: 116 · 2019: 107 · 2018: 87 · 2017: 106 · 2016: 104 · 2015: 91 · 2014: 44
FWCI: 36.87
Type: journal article
Language: en
Open access: green
cnrs.hal.science
Licence: other-oa
www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
HAL (submittedVersion, other-oa)
RePEc: Research Papers in Economics (submittedVersion)
Adelaide Research & Scholarship (AR&S) (University of Adelaide) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion)
Infoscience (Ecole Polytechnique Fédérale de Lausanne) (submittedVersion, cc-by-nc-nd)
IRIS (submittedVersion)
SERVAL (Université de Lausanne) (submittedVersion)
Funders: Wellcome Trust (099175/Z/12/Z)
Medical Research Council (MC_PC_15004)
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords: long non-coding RNA, lncRNA evolution, tetrapods, embryonic development, tissue-specific gene expression, co-expression network, spermatogenesis, synaptic transmission, placental development, non-model organisms
MeSH terms: Animals, Anura, Chickens, Multigene Family, Humans, Primates, Proteins, RNA Precursors, Conserved Sequence, Gene Expression Regulation, Developmental, Evolution, Molecular, Genomics, MicroRNAs, Mice, Transcriptome, RNA, Long Noncoding

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The evolution of lncRNA repertoires and expression patterns in tetrapods

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