Variation in methylation patterns between maize mop1 mutants
In maize, the balance between gene expression and transposon silencing is maintained largely by the RNA-directed DNA methylation (RdDM) pathway. Loss of RdDM through knockout of the mediator of paramutation 1 (mop1) gene has been demonstrated to cause widespread, nonlethal changes to the maize epigenome, but little is known about whether and how RdDM activity is affected by genotype. Bisulfite sequencing data from three inbred lines in both wild-type and mop1-defective mutant states were analyzed to refine our understanding of mop1 targets and to examine whether methylation patterns differ across genomes suffering loss of RdDM. Genotypes showed an unexpectedly high amount of variability in their relative methylation change across genes and transposable element subfamilies. Additionally, the set of genes under direct mop1-mediated regulation were characterized, and a novel set of RdDM-associated epialleles were discovered. This research suggests that RdDM has previously unreported genotype-specific effects, both globally and at particular loci.