Whole-genome methylation reveals tissue-specific differences in non-CG methylation in bovine

DNA methylation at non-CG dinucleotides (mCH, H=A, C, T), has been shown to be widely present and play important roles in specific cell types such as pluripotent cells, brain, and germ cells. Currently, much is still unknown about the functions and mechanisms of mCH, particularly in species other than humans and mice. In this study, we analyzed the distribution of mCH across different tissues in bovine. In bovine embryonic stem cells (bESCs), brain, spleen, and ileum tissues, the mCH levels were significantly higher than in other tissues. There are significant differences in the pattern of mCH between somatic cells and bESCs, including different base preferences and differential expression of DNA methyltransferases. We also discovered methylation in exons in both CG and non-CG contexts, like those in plants associated with some genes. To identify differential CH methylation in various tissues, we developed a method for differential mCH analysis. Differential analysis results indicate that mCH is not randomly distributed but tends to be enriched in tissue-specific functional regions. Moreover, we demonstrated the positional correlation between CG methylation (mCG) and mCH through regression models. Studying the distribution and function of mCH in the somatic and stem cells of bovine can provide new insights into its roles in different species and tissues. This study not only advances our understanding of epigenetic mechanisms but also reveal potential roles of mCH in development and disease occurrence.