title: Genetic perturbation of the maize methylome.
abstract: 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.
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Qing
authors.initials: Q
authors.lastname: Li
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Steven R
authors.identifier: http://orcid.org/0000-0003-2268-395X
authors.initials: SR
authors.lastname: Eichten
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108.
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Hermanson
authors.affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Virginia M
authors.initials: VM
authors.lastname: Zaunbrecher
authors.affiliation: Texas Advanced Computing Center, University of Texas, Austin, Texas 78758.
authors.forename: Jawon
authors.initials: J
authors.lastname: Song
authors.affiliation: Roche NimbleGen, Madison, Wisconsin 53719.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Wendt
authors.affiliation: Roche NimbleGen, Madison, Wisconsin 53719.
authors.forename: Heidi
authors.initials: H
authors.lastname: Rosenbaum
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Thelma F
authors.initials: TF
authors.lastname: Madzima
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Amy E
authors.initials: AE
authors.lastname: Sloan
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Ji
authors.initials: J
authors.lastname: Huang
authors.affiliation: Roche NimbleGen, Madison, Wisconsin 53719.
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Burgess
authors.affiliation: Roche NimbleGen, Madison, Wisconsin 53719.
authors.forename: Todd A
authors.initials: TA
authors.lastname: Richmond
authors.affiliation: Department of Biological Science, Florida State University, Tallahassee, Florida 32306.
authors.forename: Karen M
authors.initials: KM
authors.lastname: McGinnis
authors.affiliation: DuPont Pioneer AgBiotech Research, Johnston, Iowa 50131.
authors.forename: Robert B
authors.initials: RB
authors.lastname: Meeley
authors.affiliation: DuPont Pioneer AgBiotech Research, Johnston, Iowa 50131.
authors.forename: Olga N
authors.initials: ON
authors.lastname: Danilevskaya
authors.affiliation: Texas Advanced Computing Center, University of Texas, Austin, Texas 78758.
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Vaughn
authors.affiliation: Department of Agronomy, University of Wisconsin, Madison, Wisconsin 53706.
authors.forename: Shawn M
authors.initials: SM
authors.lastname: Kaeppler
authors.affiliation: Roche NimbleGen, Madison, Wisconsin 53719.
authors.forename: Jeffrey A
authors.initials: JA
authors.lastname: Jeddeloh
authors.affiliation: Microbial and Plant Genomics Institute, Department of Plant Biology, University of Minnesota, Saint Paul, Minnesota 55108 springer@umn.edu.
authors.forename: Nathan M
authors.identifier: http://orcid.org/0000-0002-7301-4759
authors.initials: NM
authors.lastname: Springer
mesh_terms: D000483:Alleles; D003433:Crosses, Genetic; D004248:DNA (Cytosine-5-)-Methyltransferases / Q000235:genetics; D019175:DNA Methylation; D057890:Epigenomics; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D009154:Mutation; D003313:Zea mays / Q000235:genetics*
chemical_list: D004248:DNA (Cytosine-5-)-Methyltransferases; C112810:chromomethylase