FUNCTIONAL ANNOTATION AND VALIDATION OF REGULATORY ELEMENTS IN THE CHICKEN GENOME

The advent of the FAANG Consortium signified the critical need for annotating the chicken genome. Specifically, regulatory elements have not been functionally characterized, and more importantly, target genes of distal regulatory elements remains largely unknown, which is essential to understand spatio-temporal transcriptional regulation. Building on our current efforts, we propose to extend annotation to other biologically important tissues, and address the critical gaps of validating functional enhancers and assigning them to their target genes. Our specific aims are: (1) Identify and annotate regulatory elements in chicken gut and reproductive tissues by integrating information from RNA-seq, ATAC-seq, and ChIP-seq; (2) Use lentiMPRA in a model cell line to functionally validate a set of enhancers; (3) Employ promoter capture Hi-C to identify target genes of enhancers.