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Annotation of functional regulatory elements in livestock species
Genomics is playing an increasing role in improving animal production, health, and well-being. In order for a genome to be fully utilized, it needs to be well annotated. The goal of this project is to improve the annotation of regulatory regions for three of the most important farm animal genomes: chicken, cow, and pig. These genomes have been assembled, but there is very limited information on the enhancers, promoters, and insulators of the currently annotated genes. Recent work by the human and mouse ENCODE projects provide a blueprint for identifying the functional roles of regulatory elements in the human and mouse genomes, that can be implemented for similar efforts on animal genomes. Our specific goals are: 1) identify promoter, enhancer, and silencer regions using DNase-seq and ChIP-seq for specific chromatin marks, 2) determine functional roles of regulatory regions by integrating ChIP-seq, DNase-seq, and RNA-seq data, and 3) freely distribute all data to the public including the UCSC and Ensembl genome browsers. As a part of the Functional Annotation of ANimal Genomes (FAANG) initiative and supported by the NRSP8 Cattle, Chicken and Swine and commodity groups, we have ensured that the proposed tissues, assays and protocols are consistent with currently developing FAANG guidelines. This study will set a cornerstone for initiating farm animal ENCODE projects by providing a valuable resource for exploring the functional landscapes of the chicken, bovine, and swine genomes, and provide a valuable tool for a deeper and more meaningful understanding of complex biological systems.
Keywords: Farm animal, ENCODE, Regulatory elements, Annotation, FAANG