Maize is not Arabidopsis

Unlike Arabidopsis, the maize genome has a complex organization of interspersed repetitive elements and genes.  The genome-wide profiling of DNA methylation patterns in maize reveals high levels of CG and CHG methylation, particulary in transposons, and quite low levels of CHH methylation as compared to Arabidopsis.  Nearly 10% of maize genes contain transposable element insertions within intron sequences and these elements have high levels of DNA methylation and H3K9me2.  However, the presence of these sequences marked with heterochromatin do not appear to influence the ability for transcription of these genes.  DNA methylation patterns were analyzed in a panel of maize mutants that might be expected to influence DNA methylation levels.  The lethality of double mutants for paralogous genes suggests that DNA methylation is required normal embryogenesis in maize.  There is also evidence for two distinct pathways for CHH methylation in maize; one dependent upon RNA-directed DNA methylation and the other dependent upon chromomethylase enzymes.  While there are many similarities in the patterns and mechanisms for DNA methylation in maize and Arabidopsis, there are also a number of differences between these species.