Non Technical Summary
The U.S. is one of the world's largest producers and exporters of poultry meat. The chicken genome assembly is at the stage where significant improvements in annotation would enable investigators to better utilize genomic information to improve production traits. This project is to efficiently generate a resource of epigenomic data for annotation of functional elements in the chicken genome and enhance our knowledge of regulation of genes associated with economically important traits such as immune function, feed efficiency, egg production, quality, disease resistance. The expected results will provide enhanced biological understanding of key genome elements that are potentially associated with important agronomic traits that will translate into significant improvements for U.S. poultry producers and industry.
Animal Health Component
Research Effort Categories
Goals / Objectives
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.
We plan to employ a variety of high-throughput genomic and epigenomic assays including RNA-seq, ATAC-seq, and ChIP-seq for four histone modifications and one insulator element (CTCF), lentiMPRA assay and, promoter capture Hi-C to identify targeted genes of enhancers and validate functions of the tissue-specific enhancers.