On the Origin and Evolutionary Consequences of Gene Body DNA Methylation

In plants, CG DNA methylation is prevalent in the transcribed regions of constitutively expressed genes (“gene body methylation; gbM”), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum, has lost gbM from its genome, the first known instance for a flowering plant. Of all known DNA methyltransferases, only CHROMOMETHYLTRANSFERASE 3 (CMT3) is missing from E. salsugineum, indicating that CMT3 may be required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z and various histone modifications in E. salsugineum and Arabidopsis thaliana epiRILs turned up no evidence in support of any role for gbM in regulating transcription or affecting the composition and modifications of chromatin over evolutionary time scales. Examination of DNA methylation, gene expression, and histone variant H2A.Z between Eutrema salsugineum, A. thaliana and methylation/histone modification mutants.