28 The functional annotation of the sheep genome project

摘要

Reference genomes for some agricultural animals have been available for almost a decade; however, the annotation of these genomes remain an ongoing process. As a result, a detailed understanding of gene and gene product regulation that impart biological traits and physiological systems remains elusive. Through the Functional Annotation of ANimal Genomes (FAANG) consortium, coordinated efforts of the international scientific community are addressing this deficiency. The overarching goal of the Ovine FAANG project is to generate comprehensive transcriptome and chromatin state data sets from a large variety of adult tissues to accurately map functional elements of the ovine genome. In total, 100 tissues were collected (snap & slow frozen) from Benz 2616, the new reference genome, Oar_rambouillet_v1.0. Three methods of RNA sequencing have been utilized to fully understand tissue specific gene expression profiles. Transcript sequencing using poly-A+ messenger RNA has been completed for 60 tissues, whereas small microRNA as well as long read Iso-Sequencing data have been generated in a subset of these tissues. To further complement the gene expression data and to identify active promoters and confirm transcription start sites, Cap Analysis of Gene Expression (CAGE) has been completed. Histone modifications are being examined through Chromatin Immuno-precipitation (ChIP) sequencing to define different regulatory features. We are capitalizing on the knowledge that H3K4me3 and H3K27ac are enriched at transcription start sites and H3K4me1 at enhancer sites of actively transcribed genes, whereas H3K27me3 represses gene transcription. To determine chromatin accessibility, ATAC-seq is being performed for the 60 highest priority tissues. DNA methylation assays, specifically whole genome bisulfite and reduced representation bisulfite sequencing, are being performed on these tissues. This project will provide the first detailed understanding of tissue-specific gene regulatory signals and gene products, imparting a greater understanding of the mechanisms for genome to functional phenotype variation within sheep.