Research Description

Epigenetics is the term used to described patterns of inheritance that involve changes in gene expression that do not result from classical mutation. For example, when genes are introduced into plants by genetic engineering, the genes become part of the genome by inserting at random into one of the plant chromosomes. Expression of the inserted gene depends, in part, on where the gene inserts. In some chromosomal sites, the gene may be expressed very well, but in other sites the gene may be expressed poorly or not at all. Because this differential expression is based on chromosomal context rather than DNA mutation, it can be considered to be under epigenetic control. Trying to understand epigenetic mechanisms of gene regulation is one of the goals of research in our lab. We are taking both genetics and genomics approaches.

Our genetic approach takes advantage of natural variants (mutants) in a regulatory gene, called Purple, that controls purple anthocyanin pigment synthesis in maize. Plants carrying a normal allele of Purple develop intense purple pigmentation in virtually all of the vegetative tissues of the plant, but do not have pigmented kernels. By contrast, plants carrying the Blotched allele of Purple display a variegated pattern of pigmentation in all tissues of the plant, including the kernel. Molecular and genetic analyses indicate that Blotched is an "epimutation", that is, a variant with altered gene expression but no substantive mutation at the DNA level. However, there are striking differences between the alleles in the level of genomic DNA methylation and in chromatin structure. To understand how these differences arise, we have isolated mutants that increase or decrease pigmentation in Blotched plants and also change epigenetic patterns of methylation and/or chromatin structure. We are trying to isolate the genes responsible for altering Pl-Blotched as a way to dissect the mechanisms of epigenetic regulation.

In a genomics approach, we have joined forces with several colleagues across the country to identify and functionally analyze a large number of genes in maize that contribute to chromatin-based control of gene expression. Our strategy is to identify genes by their homology to known chromatin regulators, use genetic engineering to make mutations in these genes, and then ask what effect the mutations have on gene expression. One set of assays for the mutants involves crossing to Pl-Blotched to ask if any of the mutations cause Pl-Blotched to become more pigmented or less pigmented. Preliminary results indicate that several of the chromatin-gene mutations lead to altered levels of pigmentation in Pl-Blotched plants. This implicates these genes as players in the epigenetic regulation of the Pl-Blotched gene. Status of this genomics project can be seen at http://www.chromatin-consortium.org/.