Epigenetic Regulation of Duplicated Genes Involving Spreading of DNA Methylation in Legumes

DNA methylation is a chromatin mark that plays an important role in the regulation of genes and transposable elements (TEs). While methylation of genes at CG sites is generally associated with gene transcription, the methylation of TEs occurs in three cytosine contexts (CG, CHG, and CHH, where H = A, C, or T), which leads to their transcriptional silencing. Recent studies have shown that DNA methylation can spread from TEs to nearby genes and repress their expression. To understand the extent of this phenomenon and its impact on duplicated genes, we sequenced the methylomes of soybean (both wild and cultivated) and common bean using whole-genome bisulfite sequencing. Between duplicated genes, diverged methylation patterns were found in non-CG contexts, due mostly to TEs in or near genes. Thousands of soybean genes were determined to have methylation marks spread from nearby TEs, including genes that were differentially methylated compared with their duplicated copies. We found evidence of gene silencing mediated by the methylation spreading from a TE, which was inserted after WGD event. Moreover, some shared methylation-spreading events between wild and cultivated soybeans were lost in one species, leading to the reversal of gene silencing. Together, our results suggest a possible role for TE insertions and spreading of non-CG methylation in regulating gene expression, post polyploidy.