Tissue-Specific Transcriptome Regulation through Histone Modifications in Chickens

The chicken is an invaluable agricultural asset in addition to being a great model organism for studying reproductive development, growth, metabolism, and disease resistance. Published works from the human Encyclopedia of DNA Elements (ENCODE) have begun to highlight the importance of identifying regulatory elements in order to completely understand the regulation of the genome. The objective of this study was to identify tissue specific expression patterns under epigenetic regulation. Transcripts of three different tissues (liver, spleen, and breast muscle) from 3 different individuals of a highly inbred chicken line (UCD003) were sequenced. In addition, two of the most informative histone modifications, H3K4me3 and H3K27me3, were sequenced from these same tissues and individuals. Regions associated with tissue-specific epigenetic gene regulation through either H3K27me3 or H3K4me3 were identified using MACS and SICER analysis programs. Across all 3 individuals, we identified approximately 12,000, 23,000, and 5,000 peaks associated with H3K27me3 in the liver, spleen, and breast muscle respectively. For histone mark H3K4me3, we found approximately 5,000, 7,000, and 4,000 gene regions up-regulated in expression in liver, spleen, and breast muscle. Our ongoing analysis has also identified 2,023 spleen-specific genes, 407 liver-specific genes, and 366 muscle-specific genes that were also associated with tissue specific histone modification regulation. The functional roles of these regulatory elements such as promoters and enhancers through this integrative approach has laid a solid foundation towards functionally annotating the chicken genome, as a part of international farm animal ENCODE initiative.