Epigenetic regulation involves heritable changes in gene expression that are not caused by changes in DNA sequence, but rather, are associated with modifications superimposed onto DNA and core-histone proteins. Epigenetic modifications appear to be conserved across eukaryotes and include DNA (cytosine) methylation, post-translational histone modifications and nucleosome distribution. These modifications affect chromatin organization and transcription/gene expression. In humans, epigenetic pathways affect many diseases such as cancer, diabetes and mental illnesses.  Similarly in plants, epigenetic pathways affect plant growth and development and have far reaching effects on agricultural and breeding efforts, making genetic, genomic and biochemical characterization of epigenetic pathways in plants crucial.

In plants, RNA-dependent DNA methylation (RdDM) is one specific pathway that functions to direct changes in cytosine methylation, chromatin structure and gene expression at target loci. The RdDM pathway is reliant on the biogenesis and response to small RNAs (sRNAs) through the activity of two plant-specific DNA-dependent RNA polymerases (Pol IV and Pol V), an RNA-dependent RNA (RDR) polymerase, a Dicer-like protein, and an Argonaute-complex, in addition to other accessory proteins and chromatin remodelers (reviewed by Matzke MA and Mosher RA, 2014 Nature Reviews Genetics).

Maize is also an excellent model system for studying genetic and epigenetic regulation of gene expression; and a number of pioneering discoveries in epigenetics, such as paramutation and genomic imprinting, were first identified in this crop. Several genes required for epigenetic regulation in maize have been identified through forward genetics screens using loss of epigenetic silencing as phenotypes (Dorweiler, Carey et al. 2000; Hollick and Chandler 2001; Madzima, Mills et al. 2011), and provide useful genetic resources to dissect the mechanisms of epigenetic responses in maize.

Epigenetic Responses to the Environment: Epigenetic and chromatin-remodeling pathways play a critical role in plant response and acclimation to stress. While epigenetic regulatory mechanisms have far reaching effects on agricultural and breeding efforts (Madzima, Sloan et al. 2014), the extent and specific mechanisms of epigenetic responses to abiotic stress are as of yet poorly understood, particularly in crop plants. Understanding these mechanisms will be beneficial to molecular biologists and plant breeders alike. My research program incorporates molecular techniques, genetics, genomics and bioinformatics to determine how epigenetic mechanisms regulate transcription and facilitate plant responses to abiotic stress.