Towards Understanding Gene Expression in Red Jungle Fowl

As the de facto model bird genome, the chicken occupies a unique and important evolutionary niche and plays a central role in comparative and evolutionary genomics. However, the chicken genome’s coding sequences, intron/exon structures, and potential protein products from each gene in different tissues are not conclusively identified experimentally. We are experimentally annotating the chicken genome by measuring mRNA, protein and miRNA expression from multiple Red Jungle Fowl tissues (male and female). Analysis of multiple tissues from the same individuals also provides insights about gene expression in these birds. We compare our experimental expression data to current annotations for public resources and investigate the source of novel transcripts identified from RNASeq experiments. We also quantitatively compare mRNA and proteins expression across multiple tissues and use this information to improve miRNA target prediction. We will also present a review of allelic imbalance between male and female Red Jungle Fowl and describe how this allele specific expression contributes to functional differences. All data generated by this project is submitted to SRA and PRIDE archives and gene expression results are freely and publicly available for viewing or download at the Chickspress (http://geneatlas.arl.arizona.edu/) website.