RESEARCH-PGR: Determinants of Polycomb Recruitment in Monocot and Eudicot Crop Species

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The genomic era has provided a wealth of information about the composition of the genetic material in different organisms. How multicellular eukaryotes such as plants utilize the information content of their genomes to adjust their form and cellular function to a given environment is less well understood. Due to chromatin compaction, only certain portions of the genome are accessible for transcriptional activation; precisely which portions are accessible depends on the developmental stage, tissue type, or condition (biotic or abiotic stress, for example). Polycomb repression is a major epigenetic silencing and chromatin compaction mechanism for shutting off unnecessary or detrimental gene expression programs, and thus it is important for organismal form and function. A key question is how Polycomb Repressive Complexes, which lack inherent capability to bind specific DNA sequences, find their target loci in the genome. In Drosophila and mammals, different modes of Polycomb recruitment are employed – recruitment by sequence specific binding proteins to cis motifs in the former and genome scanning for dinucleotide repeats by Polycomb accessory proteins in the latter. Polycomb recruitment in Arabidopsis is very similar to that in Drosophila, yet, it is not known how Polycomb complexes are directed to the correct genomic locations in other plant species. The researchers hypothesize that the scanning mode of Polycomb recruitment may be better suited for organisms with a larger genome size and therefore aim to elucidate the mechanism for Polycomb Repressive Complex 2 recruitment in a plant crop species with a large genome size. This will test the hypothesis whether different modes of Polycomb recruitment also exist in the plant kingdom. New high school laboratory teaching modules focusing on plant epigenetics will be used to extend the impact of the research.The activity will develop and implement tools to test Polycomb repressive complex 2 (PRC2) recruitment by ChIPseq in several crops. Subsequent in-depth analysis will be conducted in a single crop species, which based on preliminary analysis, holds most promise for ability to test whether different modes of Polycomb recruitment also exist in the plant kingdom. These analyses will include PRC2, H3K27me3 and H3 ChIPseq as well as RNAseq to identify candidate Polycomb-recruiting DNA fragments linked to Polycomb regulated genes. Second, key features specifically enriched in the candidate Polycomb-recruiting DNA fragments, such as cis motifs or nucleotides, will be identified by computational approaches. The combined investigations will reveal commonalities or differences in the mode PRC2 recruitment in plants with different genome sizes. It will uncover critical regulatory DNA elements for genome annotation in crop species and set the groundwork for future epigenetic manipulation of crop genomes.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.