|Title||An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.|
|Publication Type||Journal Article|
|Year of Publication||2020|
|Authors||Jehl, 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|
|Date Published||2020 Nov 24|
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.
|Alternate Journal||Sci Rep|
|PubMed Central ID||PMC7686352|