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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues
- Source :
- Scientific Reports, Scientific Reports, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩, Scientific Reports, Nature Publishing Group, 2020, 10 (1), pp.1-17. ⟨10.1038/s41598-020-77586-x⟩, Scientific Reports, Vol 10, Iss 1, Pp 1-17 (2020)
- Publication Year :
- 2020
- Publisher :
- Nature Publishing Group UK, 2020.
-
Abstract
- International audience; 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.
- Subjects :
- animal structures
Science
[SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy
[SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics
[SDV.BBM.BM] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology
Article
Avian Proteins
Atlases as Topic
Genetics
Animals
Gene Regulatory Networks
Tissue Distribution
Author Correction
[SDV.SA.AGRO] Life Sciences [q-bio]/Agricultural sciences/Agronomy
Genome
Sequence Analysis, RNA
Gene Expression Profiling
Computational Biology
[SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology
Molecular Sequence Annotation
Functional genomics
Genomics
Gene regulation
[SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics
MicroRNAs
Gene Expression Regulation
Organ Specificity
Medicine
RNA, Long Noncoding
Gene expression
Chickens
Subjects
Details
- Language :
- English
- ISSN :
- 20452322
- Volume :
- 10
- Database :
- OpenAIRE
- Journal :
- Scientific Reports
- Accession number :
- edsair.pmid.dedup....06fb00ff0d754089df0cc26b0a88da09