PRJNA263520
Zea mays subsp. mays Epigenomics
DNA methylation is a chromatin modification that can be associated with altered levels of gene expression and plays an important role in the regulation of transposable elements. A collection of mutant alleles for 11 maize genes predicted to play roles in controlling DNA methylation were isolated through forward- or reverse-genetics approaches. Low-coverage whole genome bisulfite sequencing and high-coverage sequence-capture bisulfite sequencing were applied to mutant lines to determine context- and locus-specific effects of these mutations on DNA methylation profiles. Plants containing mutant alleles for components of the RNA-directed DNA methylation (RdDM) pathway exhibit loss of CHH methylation at many loci as well as CG and CHG methylation at a small number of loci. Those loci tend to have elevated CHH levels in wild-type plants relative to the average of genome-wide value, and are enriched for 21-nt to 24-nt small RNAs. Plants containing loss-of-function alleles for chromomethylase (CMT) genes exhibit strong genome-wide reductions in CHG methylation and some locus-specific loss of CHH methylation. There is evidence for two pathways mediating CHH methylation in maize with the RdDM pathway influencing CHH levels in regions near genes and in short length transposons, while an ortholog of the Arabidopsis CMT3 mediated pathway plays a role in CHH methylation present in long transposons, similar to the role played by CMT2 in Arabidopsis. In an attempt to identify stocks with stronger reductions in DNA methylation levels than provided by single gene mutations, we performed crosses to create double mutants for the maize CMT3 orthologs, Zmet2 and Zmet5, and for the maize DDM1 orthologs, Chr101 and Chr106. While loss-of-function alleles are viable as single gene mutants, the double mutants were not recovered, suggesting that severe perturbations of the maize methylome may have stronger deleterious phenotypic effects than in Arabidopsis.