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Genetic regulation of gene expression across multiple tissues in chickens
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Edité par CCSD ; Nature Publishing Group -
All raw data analyzed in this study are publicly available for download without restrictions from SRA (https://www.ncbi.nlm.nih.gov/sra/) and NGDC BioProject(https://bigd.big.ac.cn/bioproject/) databases. Details of RNA-Seq, WGS, ChIP-Seq peaks and single-cell RNA-Seq can be found in Supplementary Tables,respectively. The GRCg6a chicken reference genome (v102) is available at Ensembl (https://www.ensembl.org). All processed data and the full summary statistics ofmolQTL mapping and genotype imputation reference panel are available at http://chicken.farmgtex.org.. International audience. The chicken is a valuable model for understanding fundamental biology and vertebrate evolution and is a major global source of nutrient-dense and lean protein. Despite being the first non-mammalian amniote to have its genome sequenced, a systematic characterization of functional variation on the chicken genome remains lacking. Here, we integrated bulk RNA sequencing (RNA-seq) data from 7,015 samples, single-cell RNA-seq data from 127,598 cells and 2,869 whole-genome sequences to present a pilot atlas of regulatory variants across 28 chicken tissues. This atlas reveals millions of regulatory effects on primary expression (protein-coding genes, long non-coding RNA and exons) and post-transcriptional modifications (alternative splicing and 3 '-untranslated region alternative polyadenylation). We highlighted distinct molecular mechanisms underlying these regulatory variants, their context-dependent behavior and their utility in interpreting genome-wide associations for 39 chicken complex traits. Finally, our comparative analyses of gene regulation between chickens and mammals demonstrate how this resource can facilitate cross-species gene mapping of complex traits.
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