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

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...

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Autores principales:	Frédéric Jehl, Kévin Muret, Maria Bernard, Morgane Boutin, Laetitia Lagoutte, Colette Désert, Patrice Dehais, Diane Esquerré, Hervé Acloque, Elisabetta Giuffra, Sarah Djebali, Sylvain Foissac, Thomas Derrien, Frédérique Pitel, Tatiana Zerjal, Christophe Klopp, Sandrine Lagarrigue
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2020
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/f7ec168bb4cf424d887e2d8f110bd830
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spelling	oai:doaj.org-article:f7ec168bb4cf424d887e2d8f110bd8302021-12-02T16:08:47ZAn integrative atlas of chicken long non-coding genes and their annotations across 25 tissues10.1038/s41598-020-77586-x2045-2322https://doaj.org/article/f7ec168bb4cf424d887e2d8f110bd8302020-11-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-77586-xhttps://doaj.org/toc/2045-2322Abstract 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.Frédéric JehlKévin MuretMaria BernardMorgane BoutinLaetitia LagoutteColette DésertPatrice DehaisDiane EsquerréHervé AcloqueElisabetta GiuffraSarah DjebaliSylvain FoissacThomas DerrienFrédérique PitelTatiana ZerjalChristophe KloppSandrine LagarrigueNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-17 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Frédéric Jehl Kévin Muret Maria Bernard Morgane Boutin Laetitia Lagoutte Colette Désert Patrice Dehais Diane Esquerré Hervé Acloque Elisabetta Giuffra Sarah Djebali Sylvain Foissac Thomas Derrien Frédérique Pitel Tatiana Zerjal Christophe Klopp Sandrine Lagarrigue An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
description	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.
format	article
author	Frédéric Jehl Kévin Muret Maria Bernard Morgane Boutin Laetitia Lagoutte Colette Désert Patrice Dehais Diane Esquerré Hervé Acloque Elisabetta Giuffra Sarah Djebali Sylvain Foissac Thomas Derrien Frédérique Pitel Tatiana Zerjal Christophe Klopp Sandrine Lagarrigue
author_facet	Frédéric Jehl Kévin Muret Maria Bernard Morgane Boutin Laetitia Lagoutte Colette Désert Patrice Dehais Diane Esquerré Hervé Acloque Elisabetta Giuffra Sarah Djebali Sylvain Foissac Thomas Derrien Frédérique Pitel Tatiana Zerjal Christophe Klopp Sandrine Lagarrigue
author_sort	Frédéric Jehl
title	An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
title_short	An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
title_full	An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
title_fullStr	An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
title_full_unstemmed	An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
title_sort	integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/f7ec168bb4cf424d887e2d8f110bd830
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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues

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