SRA

The maize genome is relatively large (~2.3Gb) and has a complex organization of interspersed genes and transposable elements which necessities frequent boundaries between different types of chromatin. The examination of maize genes and conserved non-coding sequences reveals that many of these are flanked by regions of elevated asymmetric CHH (where H is any base except G) methylation. These mCHH islands are quite short (~100bp) and are enriched near active genes. The analysis of DNA methylation in other sequence contexts and several chromatin modifications reveal that the mCHH island marks the transition from heterochromatin associated modifications to euchromatin associated modifications. The mCHH island often occurs at the edge of the transposon that is located nearest to the gene. The presence of a mCHH island is fairly consistent in several distinct tissues that were surveyed but shows some variation among different haplotypes. The presence of InDels in promoters often influences the presence and position of the mCHH island. The mCHH islands are dependent upon RNA-directed DNA methylation activities. The mCHH islands are lost in the mop1 and mop3 mutants but the nearby genes do not necessarily exhibit altered expression levels. Instead, the loss of the mCHH island often results in the erosion of heterochromatic marks into the nearby transposon. This suggests that mCHH islands and RNA-directed DNA methylation near maize genes may act to preserve the silencing of transposons from activity of the genes.