title: Long noncoding RNA repertoire in chicken liver and adipose tissue.
abstract: Improving 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.
  
  
  
  We 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.
  
  
  
  We 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.
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Kévin
authors.initials: K
authors.lastname: Muret
authors.affiliation: SIGENAE, INRA, 31326, Castanet-Tolosan, France.
authors.forename: Christophe
authors.initials: C
authors.lastname: Klopp
authors.affiliation: UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France.
authors.forename: Valentin
authors.initials: V
authors.lastname: Wucher
authors.affiliation: Plateforme GENOTOUL, INRA, 31326, Castanet-Tolosan, France.|GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France.
authors.forename: Diane
authors.initials: D
authors.lastname: Esquerré
authors.affiliation: UMR IGEPP, INRA, 35042, Rennes, France.|UMR IGEPP, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Legeai
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Lecerf
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Colette
authors.initials: C
authors.lastname: Désert
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Boutin
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Jehl
authors.affiliation: GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Acloque
authors.affiliation: GABI, AgroParisTech, INRA, Université Paris Saclay, 78350, Jouy-en-Josas, France.
authors.forename: Elisabetta
authors.initials: E
authors.lastname: Giuffra
authors.affiliation: GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France.
authors.forename: Sarah
authors.initials: S
authors.lastname: Djebali
authors.affiliation: GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France.
authors.forename: Sylvain
authors.initials: S
authors.lastname: Foissac
authors.affiliation: UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France. tderrien@univ-rennes1.fr.
authors.forename: Thomas
authors.initials: T
authors.lastname: Derrien
authors.affiliation: UMR PEGASE, INRA, 35042, Rennes, France. sandrine.lagarrigue@agrocampus-ouest.fr.|UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France. sandrine.lagarrigue@agrocampus-ouest.fr.
authors.forename: Sandrine
authors.initials: S
authors.lastname: Lagarrigue
mesh_terms: D000273:Adipose Tissue / Q000378:metabolism*; D000818:Animals; D002645:Chickens / Q000235:genetics* / Q000378:metabolism; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D016678:Genome; D005838:Genotype; D006801:Humans; D050356:Lipid Metabolism / Q000235:genetics; D008099:Liver / Q000378:metabolism*; D016366:Open Reading Frames; D009928:Organ Specificity; D010641:Phenotype; D040641:Quantitative Trait Loci; D016372:RNA, Antisense; D062085:RNA, Long Noncoding / Q000737:chemistry / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics; D059467:Transcriptome
chemical_list: D016372:RNA, Antisense; D062085:RNA, Long Noncoding; D012333:RNA, Messenger