PSVII-1 - Widespread Allele-specific expression across tissues and cells of the chicken genome.

Abstract: Chickens are a valuable livestock species, providing an affordable and nutritious food source worldwide through eggs and meat. Additionally, chickens are extensively used in scientific research as model organisms in virology, immunology, epigenetics, development, and conservation biology. Considering this, there are increasing efforts to deepen our understanding of their genome complexity, such as efforts by the Functional Annotation of Animal Genomes (FAANG) Consortium. Toward this goal, we are working to contribute to the annotation of the chicken transcriptome. Allele-specific expression (ASE) is an imbalance of allelic gene expression often driven by genetic and epigenetic changes in cis-regulatory regions. We, therefore, aimed to determine allelic imbalances in gene expression across 20 tissues and cells to shed light on mechanisms regulating gene expression. Using replicate paired-end (PE) RNA-seq samples, we identified around 7 million variants across 20 tissues and cells (e.g., reproductive tissues, intestine tissues, muscle, and immune tissues and cells). We applied quality control measures and filtered out monoallelic and homozygous variants. After that, we calculated read counts per allele to determine allelic expression. We found 365,894 significant ASE SNPs and 11,530 ASE genes in at least one tissue or cell type (FDR ≤ 0.05). We discovered that ASE SNPs are widely distributed throughout the chicken genome, and ASE SNPs and ASE genes showed a varied distribution across tissues and cells. Primary macrophage exhibited the most abundant, while the pectoralis major (breast muscle) had the lowest ASE genes and ASE SNPs, ranging from 7,592 to 32,505 ASE SNPs and 773 to 2,387 ASE genes. Our findings reveal several important pathways affected by allelic imbalance of expression. These pathways included fatty acid biosynthesis and regulation, cell proliferation and differentiation, cell metabolism, adipocytokine signaling, proteolysis and autophagy, and focal adhesion. In summary, our study provides insight into relevant biological processes critical to chickens and can contribute to improving genome annotation, helping to expand the transcriptomic reference source.