Long noncoding RNA repertoire in chicken liver and adipose tissue

Genetics Selection Evolution

Research Article

Elisabetta Giuffra¹  Sarah Djebali²  Sylvain Foissac²  Hervé Acloque²  Diane Esquerré³  Christophe Klopp⁴  Fabrice Legeai⁵  Frédéric Jehl⁶  Kévin Muret⁶  Frédéric Lecerf⁶  Colette Désert⁶  Morgane Boutin⁶  Sandrine Lagarrigue⁶  Thomas Derrien⁷  Valentin Wucher⁷ 

[1] GABI, AgroParisTech, INRA, Université Paris Saclay, 78350, Jouy-en-Josas, France;GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France;Plateforme GENOTOUL, INRA, 31326, Castanet-Tolosan, France;GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France;SIGENAE, INRA, 31326, Castanet-Tolosan, France;UMR IGEPP, INRA, 35042, Rennes, France;UMR IGEPP, AGROCAMPUS OUEST, 35042, Rennes, France;UMR PEGASE, INRA, 35042, Rennes, France;UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France;UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France;

关键词: Noncoding RNAs;    Chicken Genome;    Abdominal Adipose Tissue;    lncRNA Gene;    lncRNA Transcript;   

DOI  :  10.1186/s12711-016-0275-0

 received in 2016-07-03, accepted in 2016-11-29,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundImproving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling.ResultsWe predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis.ConclusionsWe provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken.

【 授权许可】

CC BY   
© The Author(s) 2017