Grant: Discovery Grants Program - Individual

In higher organisms including plants, DNAs are highly folded into DNA-protein (mainly histones) complexes called chromatins. Gene expression regulation at chromatin level, often referred to as epigenetic regulation, is mediated by the joint activities of two enzymatic complexes that catalyze covalent histone modifications and alter chromatin structure. The Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved proteins that mediate epigenetic gene repression and activation, respectively. PcG proteins form multimeric protein complexes including the Polycomb Repressive Complex 2 (PRC2) that catalyzes the repressive trimethylation of lysine 27 of histone 3 (H3K27me3). TrxG proteins are biochemically heterogeneous, including the chromatin-remodeller BRM and the H3K27me3 demethylase (eraser) REF6 in the model plant Arabidopsis, but all function to antagonize Polycomb activities. It is of great interest to decipher how these two groups of proteins antagonize genome-wide, and how they are targeted to specific genomic sites. Using cutting edge genomics techniques such as Chromatin Immuno-Precipitation followed by high throughput sequencing (ChIP-seq), we have recently investigated the genome-wide functional interplay between BRM, REF6 and PRC2. We first examined the interaction between BRM and PRC2 in regulating H3K27me3 levels and identified a key role of the two proteins in controlling flowering time. We then examined the interaction between BRM and REF6 and found that REF6 targets directly to genomic loci by recognizing a specific DNA motif (CTCTGYTY, Y representing C or T) and then facilitate the recruitment of BRM. This work provides a new paradigm in the field of plant epigenetics. Here, we propose to continue our work on the functional interplay between BRM/REF6 and PcG proteins. First, we will expand our previous work on BRM-PRC2 interaction by examining the role of BRMs close homolog SYD in regulating PRC2 function. We will also profile the genome-wide occupancy of SYD and identify the unique and shared targets of BRM and SYD. Second, we propose to further investigate the genomic targeting mechanism of REF6. We will conduct a series of experiments to identify the chromatin context and/or other factors that determine the accessibility of the REF6 binding motif across the Arabidopsis genome. The work proposed is critical for understanding the functional interplay between the key epigenetic regulators that affect the expression of genes involved in important developmental pathways and biotic and abiotic stress responses. We believe that this knowledge can be applied to genetic improvement of Canadian crops. The projects will be very beneficial to students and postdocs, allowing them to obtain training in several disciplines, including genetics, epigenetics, epigenomics, bioinformatics, molecular biology, and others.