ArticleScientific reports2020
An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 28 citations in OpenAlex.
- Body-weight variation as a potential indirect indicator of abdominal fat weight with relevance to laying rate in 90-week-old laying hens.Poultry science · 2026Article
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- Genetic regulation of gene expression across multiple tissues in chickens.Nature genetics · 2025Article
- Transcriptomic Profiling Reveals Altered Expression of Genes Involved in Metabolic and Immune Processes in NDV-Infected Chicken Embryos.Metabolites · 2024Article
- The first chicken oocyte nucleus whole transcriptomic profile defines the spectrum of maternal mRNA and non-coding RNA genes transcribed by the lampbrush chromosomes.Nucleic acids research · 2024Article
- Comprehensive Annotation and Expression Profiling of C2H2 Zinc Finger Transcription Factors across Chicken Tissues.International journal of molecular sciences · 2024Article
- GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations.NAR genomics and bioinformatics · 2024Article
- Enriched atlas of lncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues.Scientific reports · 2024Article
- TAGADA: a scalable pipeline to improve genome annotations with RNA-seq data.NAR genomics and bioinformatics · 2023Article
- LncRNAs in domesticated animals: from dog to livestock species.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Genetic Basis of Sexual Maturation Heterosis: Insights From Ovary lncRNA and mRNA Repertoire in Chicken.Frontiers in endocrinology · 2022Article
- Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing.Frontiers in genetics · 2022Article
- Fourth Report on Chicken Genes and Chromosomes 2022.Cytogenetic and genome research · 2022Review
- Advances in Non-Coding RNA Sequencing.Non-coding RNA · 2021Review
- Tissue Resources for the Functional Annotation of Animal Genomes.Frontiers in genetics · 2021Article
- Watch Out for a Second SNP: Focus on Multi-Nucleotide Variants in Coding Regions and Rescued Stop-Gained.Frontiers in genetics · 2021Article
- Transcriptomes of an Array of Chicken Ovary, Intestinal, and Immune Cells and Tissues.Frontiers in genetics · 2021Article
- RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization andFrontiers in genetics · 2021Article
Corrections and comments
- Erratum issued
Authors and funding
17 authors at 8 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.