title: Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.
abstract: DNA methylation is a stable modification of chromatin that can contribute to epigenetic variation through the regulation of genes or transposons. Profiling of DNA methylation in five maize (Zea mays) inbred lines found that while DNA methylation levels for more than 99% of the analyzed genomic regions are similar, there are still 5,000 to 20,000 context-specific differentially methylated regions (DMRs) between any two genotypes. The analysis of identical-by-state genomic regions that have limited genetic variation provided evidence that DMRs can occur without local sequence variation, but they are less common than in regions with genetic variation. Characterization of the sequence specificity of DMRs, location of DMRs relative to genes and transposons, and patterns of DNA methylation in regions flanking DMRs reveals a distinct subset of DMRs. Transcriptome profiling of the same tissue revealed that only approximately 20% of genes with qualitative (on-off) differences in gene expression are associated with DMRs, and there is little evidence for association of DMRs with genes that show quantitative differences in gene expression. We also identify a set of genes that may represent cryptic information that is silenced by DNA methylation in the reference B73 genome. Many of these genes exhibit natural variation in other genotypes, suggesting the potential for selection to act upon existing epigenetic natural variation. This study provides insights into the origin and influences of DMRs in a crop species with a complex genome organization.
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Qing
authors: Q
authors: Li
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Jawon
authors: J
authors: Song
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Patrick T
authors: http://orcid.org/0000-0001-8039-7535
authors: PT
authors: West
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Greg
authors: http://orcid.org/0000-0003-4992-9614
authors: G
authors: Zynda
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Steven R
authors: http://orcid.org/0000-0003-2268-395X
authors: SR
authors: Eichten
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.).
authors: Matthew W
authors: http://orcid.org/0000-0002-1384-4283
authors: MW
authors: Vaughn
authors: Department of Plant Biology, Microbial and Plant Genomics Institute, University of Minnesota, Saint Paul, Minnesota 55108 (Q.L., P.T.W., S.R.E., N.M.S.); andTexas Advanced Computing Center, University of Texas, Austin, Texas 78758 (J.S., G.Z., M.W.V.) springer@umn.edu.
authors: Nathan M
authors: http://orcid.org/0000-0002-7301-4759
authors: NM
authors: Springer
mesh_terms: D001947:Breeding; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D005838:Genotype; D003313:Zea mays / Q000235:genetics*