CG methylation covaries with differential gene expreion between leaf and floral bud tiues of brachypodium distachyon

Abstract

DNA methylation has the potential to influence plant growth and development through its influence on gene expreion. To date, however, the evidence from plant systems is mixed as to whether patterns of DNA methylation vary significantly among tiues and, if so, whether these differences affect tiue-specific gene expreion. To addre these questions, we analyzed both bisulfite sequence (Beq) and transcriptomic sequence data from three biological replicates of two tiues (leaf and floral bud) from the model gra species Brachypodium distachyon. Our first goal was to determine whether tiues were more differentiated in DNA methylation than explained by variation among biological replicates. Tiues were more differentiated than biological replicates, but the analysis of replicated data revealed high (>50%) false positive rates for the inference of differentially methylated sites (DM) and differentially methylated regions (DMRs). Comparing methylation to gene expreion, we found that differential CG methylation consistently covaried negatively with gene expreion, regardle as to whether methylation was within genes, within their promoters or even within their closest transposable element. The relationship between gene expreion and either CHG or CHH methylation was le consistent. In total, CG methylation in promoters explained 9% of the variation in tiue-specific expreion acro genes, suggesting that CG methylation is a minor but appreciable factor in tiue differentiation.