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

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 u...

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Detalles Bibliográficos
Autores principales: Jehl, Frédéric, Muret, Kévin, Bernard, Maria, Boutin, Morgane, Lagoutte, Laetitia, Désert, Colette, Dehais, Patrice, Esquerré, Diane, Acloque, Hervé, Giuffra, Elisabetta, Djebali, Sarah, Foissac, Sylvain, Derrien, Thomas, Pitel, Frédérique, Zerjal, Tatiana, Klopp, Christophe, Lagarrigue, Sandrine
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7686352/
https://www.ncbi.nlm.nih.gov/pubmed/33235280
http://dx.doi.org/10.1038/s41598-020-77586-x
Descripción
Sumario: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.