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

Frédéric Jehl 1 Kévin Muret 1 Maria Bernard 2 Morgane Boutin 1 Laetitia Lagoutte 1 Colette Désert 1 Patrice Dehais 2 Diane Esquerré 3 Hervé Acloque 4 Elisabetta Giuffra 5 Sarah Djebali 6 Sylvain Foissac 4 Thomas Derrien 7 Frederique Pitel 4 Tatiana Zerjal 5 Christophe Klopp 2, * Sandrine Lagarrigue 1, *
* Corresponding author
1 PEGASE - Physiologie, Environnement et Génétique pour l'Animal et les Systèmes d'Elevage [Rennes]
2 SIGENAE - Système d'Information des GENomes des Animaux d'Elevage
3 GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique
4 GenPhySE - Génétique Physiologie et Systèmes d'Elevage
5 GABI - Génétique Animale et Biologie Intégrative
6 IRSD - Institut de Recherche en Santé Digestive
7 IGDR - Institut de Génétique et Développement de Rennes
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.frage ncode .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.
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https://hal.inrae.fr/hal-03039897
Contributor : Hervé Acloque <>
Submitted on : Friday, December 4, 2020 - 9:48:14 AM
Last modification on : Thursday, May 6, 2021 - 10:49:49 AM

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INRAE | CNRS | AGROCAMPUS-OUEST-UMR-PEGASE | AGROCAMPUS-OUEST | INSERM | IRSD | UNIV-RENNES | AGROPARISTECH | UR1-UFR-SVE | BIOSIT | UNIV-TLSE3 | UNAM | IGDR | UNIV-RENNES1 | GS-BIOSPHERA

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Frédéric Jehl, Kévin Muret, Maria Bernard, Morgane Boutin, Laetitia Lagoutte, et al.. An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩. ⟨hal-03039897⟩

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