The initiation and maintenance of CHH methylation and its effects on gene expression are unique in maize.

Trans -chromosomal interactions resulting in changes in DNA methylation during hybridization have been observed in several plant species. However, very little is known about the causes or consequences of these interactions, many of which result in changes in methylation of transposable elements. Here, we compared DNA methylomes of F1 hybrids that are mutant for two small RNA biogenesis genes, Mop1 ( mediator of paramutation1 ) and Lbl1 ( leafbladeless1 ) with that of their parents, wild type siblings, and backcrossed progeny in maize. Our data show that hybridization triggers global changes in both trans -chromosomal methylation (TCM) and trans -chromosomal demethylation (TCdM). Despite changes in CHH methylation in F1 hybrids, no significant changes in the quantity or distribution of small RNAs were observed. The methylation at the CHH TCM differentially methylated regions (DMRs) was largely removed in the mop1 mutant, although the effects of this mutant vary depending on the location of the CHH sites. Interestingly, an increase in CHH at TCM DMRs was associated with enhanced expression of a subset of highly expressed genes and suppressed expression of a small number of lowly expressed genes. Examination of the methylation levels in backcrossed plants demonstrates that the newly triggered methylation can be maintained to the subsequent generation, but that TCdM is maintained more stable than is TCM. Surprisingly, although increase CHH methylation in F1 plants did require Mop1 , heritability of TCM or TCdMs did not require a functional copy of this gene, suggesting that initiation of these heritable changes in epigenetic state are not dependent on RdDM.