GSE61936
Genome-wide H3K4me3 analysis in Angus cattle with divergent tenderness
Tenderness is one of the most important properties of meat quality, which is influenced by genetic and environmental factors. As an intensively studied epigenetic marker, histone methylation, occurring on arginine and lysine residues, has pivotal regulatory functions on gene expression. To examine whether histone methylation involves in beef tenderness variation, we analyzed the transcriptome and H3K4me3 enrichment profiles of muscle strips obtained from the longissimus dorsi (LD) of Angus steers previously classify to the tender or tough group. We first plotted a global bovine H3K4me3 map on chromosomes and called peak-enriched regions and genes. We found that majorities of H3K4me3 on genes were occupying the first intron and intergenic regions and its maps displayed similar patterns in tender and tough groups, with high H3K4me3 enrichment surrounding the transcription start site (TSS). We also explored the relationship of H3K4me3 and gene expression. The results showed that H3K4me3 enrichment is highly positively correlated with gene expression across the whole genome. Cluster analysis results confirmed the relationship of H3K4me3 enrichment and gene expression. By using a pathway-based approach in genes with H3K4me3 enrichment in promoter regions from the tender cluster, we revealed that those genes involved in the development of different tissues–connective tissue, skeletal and muscular system and functional tissues–; while in tough group those genes engaged in cell death, lipid metabolism and  small molecule biochemistry. The results from this study provide a deep insight into understanding of the mechanisms of epigenetic regulations in meat quality and beef tenderness. Overall design: Nineteen purebred Angus steers were obtained from the Wye Farm. At approximately 12 months of age, the animals were serially harvested. Immediately after harvest, samples of longissimus dorsi (LD) from the right side of the carcass were obtained and placed in RNAlater solution at -80°C. The carcass were stored at 4°C for a total of 14 days. After this period, steaks were obtained from the LD at the level of the 12th intercostal space and then frozen. For measurement of the WBSF, steaks were thawed at room temperature to an internal temperature of 4°C. Then, the steaks were cooked to a core temperature of 70°C using a George Foreman Lean Mean Fat Grilling Machine. The cooked steaks were then cooled down to room temperature. Using a sharp cylinder, especially designed for muscle, six cores (1.27 cm in diameter) were sampled parallel to the muscle fiber orientation. The Warner-Bratzler shear forces (WBSF) of the cores were obtained. The average WBSF of the six cores was calculated and used as the WBSF for the samples. From these 19 steers, 4 with the lowest WBSF values (6.77±0.56 kg) were identified as tender and 5 samples with the largest WBSF values (19.93±0.39 kg) labeled as tough. Then both groups underwent further analysis..