A Complex Interplay Between Genes and Transposons within the Maize Genome

Transposons are a major component of the genome of many crop plants.  The simplified expectation is that transposons are the target for epigenetic silencing via DNA methylation or other repressive chromatin marks such as H3K9me2 while genes are expected to lack these repressive modifications.  Several different types of analyses have been performed to better understand the interaction between transposons and genes within the maize genome.  The analysis of DNA methylation and H3K9me2 levels within maize transposons and in flanking regions reveals that while nearly all maize transposons are associated with these marks there is variation among transposon families for their ability to spread these repressive chromatin modifications to surrounding low copy sequences.  The maize genome includes a several thousand genes that contain transposon insertions within introns.  These transposons are generally associated with high levels of DNA methylation even through the gene is actively transcribed suggesting that plants can tolerate blocks of heterochromatin within transcribed genes.    On-going research is focused on comparing the level of DNA methylation of maize transposons in different maize genotypes or mutant strains to understand the processes of transposon regulation in maize.