However, analysis of these multi-copy, mobile elements is considerably more difficult than analysis of single-copy genes located in stable regions of the genome. Plants are an excellent system for studying the mechanisms of LTR retrotransposon inhibition such as DNA methylation and small RNA-mediated degradation of retrotransposon transcripts. To prevent retrotransposon activity, eukaryotic cells have evolved overlapping mechanisms to repress transposition. Although often viewed as molecular parasites, retrotransposons have been shown to influence neighboring gene expression and play a structural and potential regulatory role in the centromere. These retrotransposons can comprise a large fraction of the genome (75 % in maize). In contrast to mammalian genomes, in which non-LTR retrotransposons have proliferated, plant genomes show evolutionary evidence of an explosion in LTR retrotransposon copy number.

Retrotransposons can be divided into two major classes based on their mechanism of transposition and the presence or absence of long terminal repeats (LTRs). Retrotransposons are transposable elements that duplicate themselves by converting their transcribed RNA genome into cDNA, which is then integrated back into the genome.

Touchdown pcr bisulfite sequencing