Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences.
Keywords: Epigenetic effects; Methyl-sensitive transposon display; Plants; Transposable elements; Transposons.