Differential Methylation and Gene Expression Between Leaf and Floral Tissues in Brachypodium

DNA methylation has been found to negatively correlate with gene expression in multiple plant systems. It remains unclear if this correlation could cause tissue differentiation. In this study we aim to determine if DNA is significantly differentiated between tissues, and whether these differences affect tissue-specific gene expression. To address these questions, we analyzed both bisulfite sequence (BSseq) and transcriptomic sequence data from three biological replicates of two tissues (leaf and floral bud) from the model grass species Brachypodium distachyon. First, we determined whether tissues were more differentiated in DNA methylation than explained by variation among biological replicates. Tissues were more differentiated than biological replicates in methylation, but the analysis of replicated data revealed high false positive rates in both differentially methylated sites and regions. Next, we compared methylation to gene expression and found that differential CG methylation consistently covaried negatively with gene expression, regardless as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expression and either CHG or CHH methylation was less consistent. In addition, DMRs were not significantly closer to differentially expressed genes and did not appear to have an affect on gene expression between tissues. In total, CG methylation in promoters explained 9% of the variation in tissue-specific expression across genes, suggesting that CG methylation is a minor but appreciable factor in tissue differentiation.