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 ENCODE projects have made significant progress in this area for human and mouse, and the FAANG project aims to utilize information learned from ENCODE and leverage technology and assays available for the FAANG project to functionally annotate chicken, pig and cattle. Tissues will be collected from eight tissues: adipose, cerebellum, cortex, hypothalamus, liver, lung, muscle, and spleen. To ensure data integrity, two biological replicates will be used to validate consistency. Seven libraries will be prepared per tissue sample: RNA-seq, DNase-seq, and five ChIP-seq (H3K4me3, H3K27me3, H3K4me1, H3K27ac, CTCF). To integrate all the data and generate comprehensive functional annotations, ChromHMM will be used.