Genome-wide Functional Annotation of Regulatory Elements in Livestock Species

The identification of regulatory elements is a key step in understanding how an organism’s genotype determines the phenotype. The technologies and assays developed in human and mouse ENCODE projects provide a solid foundation to functionally annotate chicken, pig and cattle genomes. They are major farm animals in providing the world’s food production. Robust functional annotations of their genomes could be leveraged to improve the production efficiency of these industries. We will present the current progress in generating and analyzing data from these three important species, including analysis of forty-eight RNA-seq libraries (sixteen per species) collected from two biological replicates across eight tissues: adipose, cerebellum, cortex, hypothalamus, liver, lung, muscle and spleen. Transcripts detected in these tissues show good coverage of the Ensembl gene sets for the three species, and an initial analysis has identified putative long non-coding RNAs, both tissue-specific and expressed across all tissues. For chicken, an analysis of eight DNase-seq libraries from liver and spleen (two replicates) and cerebellum, lung, muscle and adipose (one replicate) show that identified tissue-specific DNase hypersensitivity (DHS) sites are associated with genes that relate to unique biological functions of the organs or tissues. Integrative analysis of DHS sites, ChIP-seq (H3K4me3 and H3K27me3 histone modification marks), and RNA-seq allows the identification of genome-wide active and inactive promoter regions in chickens, which enables an in-depth comparison of the regulatory landscapes of multiple tissues within these species.