Genome-Wide Screening for Epigenome Modifications and Transcriptome Regulation during Rust Pathogen, Uromyces appendiculatus, Infection in Common Bean (Phaseolus vulgaris L.)

Epigenetic mechanisms appear to be prevalent in modulating plant development as well as physiological responses to environmental cues. There are several stress, disease-related,  histone binding, and chromatin remodeling proteins involved in such mechanisms. In addition, several plant-specific transcription factors have been known to play a significant role in pathogen defense, abiotic cues and phytohormone signaling. Fundamental knowledge gained from epigenetic research has not yet been fully exploited for the improvement of crop species. Considering that little is known in this important area, our continued interest is directed towards studying the interaction between abiotic and biotic stresses and the epigenome of common bean (Phaseolus vulgaris L.). The current state of the knowledge about the epigenome, and its interplay with the transcriptome during the common bean-bean rust interaction in the context of physiological stress, is very limited. In this study, we report on our work on the common bean-bean rust (Uromyces appendiculatus) race 53 interaction in relation to two histone modification marks, H3K9me2 and H4K12ac, which are suppressive and expressive marks, respectively.  Using a chromatin immunoprecipitation sequencing (ChIP-seq) protocol that we developed in common bean, we analyzed the binding of these histones on a global level, and its relationship to transcriptomics of biotic stress.  Our long-term goal is to develop efficient strategies and develop systems-level approaches to understand the interaction between crop plant genomes, transcriptomes, and epigenomes in order to better understand the effects of stress.