Zea mays Epigenomics. Zea mays

Epigenetic marks such as DNA methylation can act as heritable marks on a genome leading to unique regulation of genomic sequences. As a transient mark, DNA methylation has been identified as a possible mechanism for reversible genetic regulation of cells derived through either mitotic or meiotic cellular division. Although variation between epigenetic states is known to exist between individuals, there is little known about the variability of DNA methylation patterns between different developmental stages of an individual. We have assessed genome-wide DNA methylation patterns in four tissues of two inbred maize lines: B73 and Mo17. Although hundreds of regions of differential methylation are present between the two genotypes, few examples of tissue-specific DNA methylation variation were observed. The lack of clear epigenetic variation between tissues indicates the limited impact of DNA methylation on developmental processes within maize. meDIP-chip analysis of four maize tissues identifed few tissue-specific DNA methylation variable regions (tDMRs), whereas hundreds of genotype-specific DMRs were identified that were conserved across tissues. Overall design: Methylation profiles for tassel, embryo, endosperm, and leaf of the maize inbred lines B73 and Mo17. Three biological replications for each tissue of each genotype were performed. A custom 2.1M NimbleGen array (GPL13499) was used for embryo, endosperm, and leaf, and a custom 3x1.4M NimbleGen array containing a subset of probes from the 2.1M NimbleGen array (GPL15621) was used for tassel. All of the processed data is based on the largest number of comparable probes (~1.4M) between the two arrays.