Dynamic regulation of histone lysine methylation

Histone lysine methylation is an important epigenetic mark for the regulation of chromatin structure and local transcription states. It had long been considered an enzymatically irreversible mark, however, the recent discovery of LSD1 (Lysine Specific Demethylase 1) unraveled the highly dynamic nature of this modification. At the time when I started my dissertation studies, several questions urgently needed to be addressed. These included the biological function of LSD1, the mechanism of the LSD1 protein complex, and the potential existence of more demethylases with additional substrate specificities. This dissertation has been organized into 4 chapters each focusing on a specific biological question mentioned above. Chapter 1 explores the biological significance of LSD1 in the model organism Schizosaccharomyces pombe . I find that the two LSD1 homologs, spLsd1 and spLsd2, form a stable complex and exhibit in vitro and in vivo demethylase activity toward H3K9me. They co-occupy a number of euchromatic promoters and activate transcription. My studies also reveal their roles in regulating heterochromatin boundaries and cell viability. Chapter 2 examines the working mechanism of LSD1 complex in vivo , focusing on one of its complex components, BHC80. I find that BHC80 binds histone H3 tails by recognizing unmethylated H3K4 residues through its PHD finger. In collaboration with Xiaodong Chen at Emory, we provide the structural basis for this interaction. I further demonstrate that BHC80 is required for LSD1-mediated transcription repression in vivo through maintaining LSD1 at target promoters, preventing H3K4 re-methylation. In an effort to search for more histone lysine demethylases, I have been involved in identifying two families of proteins possessing H3K4me3 and H3K27me3 demethylase activities. In chapter 3, I characterize SMCX/JARID1C as an H3K4 tri-methyl demethylase, and investigate its roles in neuronal development and dendritic growth. Finally, in chapter 4, I describe the finding of UTX and JMJD3 as histone H3K27me3 demethylases. Our data indicate that UTX occupies Hox gene promoters and regulates Hox gene activation, and inactivation of UTX in zebrafish results in a posterior defect in early development. Taken together, the work in this dissertation provides both mechanistic and biological insights into dynamic regulation of histone lysine methylation.