Back to Search
Start Over
Long noncoding RNA repertoire in chicken liver and adipose tissue
- Source :
- Genetics Selection Evolution, Genetics Selection Evolution, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩, Genetics Selection Evolution, BioMed Central, 2017, 49 (1), pp.6. ⟨10.1186/s12711-016-0275-0⟩, Genetics Selection Evolution 1 (49), . (2017), Genetics, Selection, Evolution : GSE
- Publication Year :
- 2017
- Publisher :
- Springer Science and Business Media LLC, 2017.
-
Abstract
- Background 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. Results 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. Conclusions 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. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0275-0) contains supplementary material, which is available to authorized users.
- Subjects :
- 0301 basic medicine
Genotype
[SDV]Life Sciences [q-bio]
Quantitative Trait Loci
poulet
génomique fonctionnelle
tissu adipeux
Adipose tissue
Biology
Genome
Evolution, Molecular
Transcriptome
Open Reading Frames
analyse de génome
03 medical and health sciences
Genetics
Animals
Humans
RNA, Antisense
Genetics(clinical)
RNA, Messenger
Gene
Conserved Sequence
Ecology, Evolution, Behavior and Systematics
Synteny
030102 biochemistry & molecular biology
Gene Expression Profiling
General Medicine
Lipid Metabolism
foie
Phenotype
Long non-coding RNA
[SDV] Life Sciences [q-bio]
Gene expression profiling
030104 developmental biology
Adipose Tissue
Gene Expression Regulation
Liver
Organ Specificity
RNA, Long Noncoding
Animal Science and Zoology
Chickens
annotation fonctionnelle
Research Article
Subjects
Details
- ISSN :
- 12979686 and 0999193X
- Volume :
- 49
- Database :
- OpenAIRE
- Journal :
- Genetics Selection Evolution
- Accession number :
- edsair.doi.dedup.....4d65bc800750cc05fa0b9fbce0e95783