Epiallele biogenesis in maize

We have correlated cytosine methylation of two epialleles, P1-rr and P1-pr, with variation in gene expression and therefore phenotype. The p1 gene in maize encodes a transcription factor that controls phlobaphene pigment accumulation in floral tissues. While cytosine methylation was assayed in various regions spanning 17 kb, the only difference in DNA methylation pattern between the expressed P1-rr allele and the silenced P1-pr allele was detected in a region that consists of a complex arrangement of transposons and adjacent repeats. This region, which comprises the distal enhancer element of P1-rr, is hypermethylated in P1-pr compared to P1-rr. Based on other precedents, we hypothesize that DNA methylation spreads from the transposable elements into the flanking P1-rr enhancer, thereby transcriptionally silencing the gene. Interestingly, P1-pr is reactivated in mutants of the dominant epigenetic modifier Ufo1. DNA methylation in the distal enhancer sequence is significantly reduced, which inversely correlates with increased transcript levels and pigmentation in P1-pr Ufo1 plants. If in general DNA methylation spreads from transposons into adjacent sequences containing regulatory elements for neighboring genes, the corresponding genes could be silenced by chance. Given the large amount of transposable elements in the maize genome, epialleles may be far more frequent than previously estimated.