Contribution of Epigenetic Variation to Expression Changes Among Tissues and Genotypes

Epigenetic variation describes heritable differences that are not attributable to changes in DNA sequence. In particular, epigenetic information can affect the transcription level for genes and thereby influence phenotype.  Methylation of cytosine residues provides one mechanism for the inheritance of epigenetic information. Genome-wide methylation patterns were profiled in several tissues of the maize inbreds B73 and Mo17 using methylated DNA immunoprecipitation followed by hybridization to custom designed microarrays (meDIP-chip).  The gene expression levels in the same tissues were assessed using RNAseq. There are numerous examples of differential methylation between the two genotypes including a subset that correlate with altered expression of nearby genes.  However, with the exception of endosperm tissue there are relatively few differences of altered DNA methylation patterns in maize tissues.  An expansion of this work will integrate large-scale sequence-based analysis of epigenetic and transcriptional variation across a wide number of diverse maize lines to assess the role of epigenetics in natural phenotypic variation.