Differential Expression of DNA Methylation Regulating Factors and Dynamic Methylation Patterns of Alternanthera philoxeroides under Different Water Treatments

DNA methylation functions as an important epigenetic mechanism involved in various biological processes. Different enzymes participate in the dynamic regulation of DNA methylation status. Changes in DNA methylation can be induced by environmental factors and can result in phenotypic variations by altering gene expression and eventually ontogenetic trajectory. Alternanthera philoxeroides is an invasive species that grows in a variety of habitats, showing high phenotypic plasticity. To investigate the effects of epigenetic modulation on phenotypically variation of A.philoxeroides, the gene expression patterns of 16 DNA methylation regulating factors were measured at different time points of water treatment using quantitative RT-PCR. Thirteen genes responsible for DNA and histone methylation were differentially expressed under different water treatments, with most up-regulated in the early stages of water treatment. Bisulfite sequencing was employed to detect the methylation status of CpG islands within the promoter regions of two genes, Contig942 and Contig23336, which were differentially expressed in response to different water treatments. Some cytosines, especially at asymmetric CHH sites, experienced fast and reversible changes in methylation status during water treatment. These changes in promoter methylation were probably responsible for the altered expression of these genes in different environments.