Role of histone modifying enzymes in regulating alternate active versus silent gene expression in plants

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This project addresses a poorly studied, yet fundamental, question of how enzymes that chemically modify chromosome-associated proteins can elicit opposing effects on gene expression, i.e., activating or silencing the gene. A combination of genetic and genomic approaches will be applied in the model plant, Arabidopsis thaliana, to test the idea that these alternate outcomes arise from coordinating the action of distinct enzymes. The research is integrated into educational activities including: research experiences for undergraduate students from two predominantly undergraduate and minority-serving institutions--Hunter College and Lehman College--in New York City; training for high school teachers through a series of seminars and summer workshops offered through Stony Brook's Center for Science and Mathematics Education; and mentoring of a postdoctoral researcher for an independent career in academia, industry, or the Federal government. Post-translational histone modifications are central to gene regulation in all eukaryotic organisms, determining the active or inactive state of the chromatin. These modifications are dynamic, effected by writers and erasers, i.e., histone modifying enzymes that add or remove specific functional groups. Moreover, one histone modification often promotes generation of another, a process termed histone crosstalk, that shapes the histone modification landscape and its transcriptional outcomes. In plants, one major class of important, yet poorly characterized, erasers are histone deubiquitinases, implicated in diverse aspects of the plant life cycle. The study focuses on histone deubiquitinase OTLD1, which is known to deubiquitylate histone H2B, associate with the chromatin mainly by binding to histone H3, and directly interact with another histone modifying enzyme, the histone lysine demethylase KDM1C. OTLD1 is found at the promoter regions of target genes and, fascinatingly, OTLD1 can both repress and activate its direct targets. These findings identify a gap in our understanding: how does deubiquitylation of the same type of histone by the same histone deubiquitinase elicit two opposing effects on transcription of the direct target genes and what is the biological significance of this ability? This question will be addressed by two specific aims: (i) define how association of OTLD1 and KDM1C with different histones variants affects the resulting histone modifications and transcriptional regulation of the target genes, and (ii) discover whether KDM1C and/or OTLD1 are down-regulated via the ubiquitin/proteasome system and study the effects of this regulation on OTLD1/KDM1C-mediated histone modifications and their transcriptional outcomes. The results are expected to advance understanding of new junction in chromatin-level processes leading to transcriptional repression or activation.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.