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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.

TitleAn integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.
Publication TypeJournal Article
Year of Publication2020
AuthorsJehl, F, Muret, K, Bernard, M, Boutin, M, Lagoutte, L, Désert, C, Dehais, P, Esquerré, D, Acloque, H, Giuffra, E, Djebali, S, Foissac, S, Derrien, T, Pitel, F, Zerjal, T, Klopp, C, Lagarrigue, S
JournalSci Rep
Volume10
Issue1
Pagination20457
Date Published2020 Nov 24
ISSN2045-2322
Abstract

Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC ( http://www.fragencode.org/ ), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.

DOI10.1038/s41598-020-77586-x
Alternate JournalSci Rep
PubMed ID33235280
PubMed Central IDPMC7686352