Li Qing, Eichten Steven R, Hermanson Peter J, Zaunbrecher Virginia M, Song Jawon, Wendt Jennifer, Rosenbaum Heidi, Madzima Thelma F, Sloan Amy E, Huang Ji, Burgess Daniel L, Richmond Todd A, McGinnis Karen M, Meeley Robert B, Danilevskaya Olga N, Vaughn Matthew W, Kaeppler Shawn M, Jeddeloh Jeffrey A, Springer Nathan M
Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706.
Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.
DNA methylation can play important roles in the regulation of transposable elements and genes. A collection of mutant alleles for 11 maize (Zea mays) genes predicted to play roles in controlling DNA methylation were isolated through forward- or reverse-genetic 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 pathway exhibit loss of CHH methylation at many loci as well as CG and CHG methylation at a small number of loci. 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. 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 thaliana.
DNA甲基化在转座元件和基因的调控中发挥重要作用。通过正向或反向遗传学方法，分离出了11个预计在控制DNA甲基化中起作用的玉米（Zea mays）基因的一系列突变等位基因。对突变系应用低覆盖度全基因组亚硫酸氢盐测序和高覆盖度序列捕获亚硫酸氢盐测序，以确定这些突变对DNA甲基化谱的上下文特异性和位点特异性影响。含有RNA指导的DNA甲基化途径组分突变等位基因的植物，在许多位点表现出CHH甲基化缺失，以及在少数位点表现出CG和CHG甲基化缺失。含有染色质甲基转移酶（CMT）基因功能缺失等位基因的植物，在全基因组范围内CHG甲基化显著降低，并且在一些位点特异性地出现CHH甲基化缺失。为了鉴定DNA甲基化水平降低程度比单基因突变更强的株系，我们进行杂交，创建了玉米CMT3直系同源基因Zmet2和Zmet5以及玉米DDM1直系同源基因Chr101和Chr106的双突变体。虽然功能缺失等位基因作为单基因突变体是可存活的，但双突变体未获得，这表明玉米甲基化组的严重扰动可能比拟南芥具有更强的有害表型效应。
