Mechanism of Cytoskeleton Modification by Histone Methyltransferase SETD2

In order for the busy and crowded cell to have a semblance of organization, it leverages a complex and dynamic network of polymers, the cytoskeleton, to provide structure and serve as molecular roads for cargo transport. Two main polymer systems, microtubules and actin filaments, provide long- and short-range transport, respectively. Additionally, microtubules form the mitotic spindle and primary cilia, while actin filaments are critical for cell migration and muscle contraction. How cytoskeletal elements have such diverse functional roles is in part due to post-translational modifications, where specific chemical modifications signal for protein interactions and particular motor protein motility. For example, tubulin methylation is only found on mitotic spindles, the microtubule-based bipolar structure that separates chromosomes during cell division and is enzymatically added by SETD2. SETD2 canonically modifies histones, specifically histone 3 at lysine 36, and is the only enzyme that can tri-methylate this residue. Knock-out of SETD2 results in histone- and/or microtubule-dependent genetic instability leading to cancer-driving mitotic defects like multipolar spindles and micronuclei formation. Mutations in SETD2 are implicated in cancer, most commonly in the kidney cancer clear cell renal cell carcinoma (ccRCC), with SETD2 mutations occurring in 10-15% of all ccRCC cases. Thus far, the role of SETD2 in cancer has only been studied in a histone methylation context, but the contribution of cytoskeletal methylation remains unclear. Studies using tumor cells from ccRCC patients demonstrated that when the level of the SETD2 gene product is less than normal (haploinsufficiency), there is a loss of tubulin methylation and genomic instability, whereas total SETD2 inactivation results in a loss of histone methylation. This stepwise model for the loss of SETD2 functionality describes histone and tubulin methylation at the gene level but does not describe the enzymatic regulation of SETD2 amongst its substrates biochemically. Moreover, specific ccRCC mutations have a differential impact on either histone or tubulin methylation in cells, where a R2510H mutation, found in a domain important for regulating protein-protein interactions of SETD2 (the Set2 Rpb1 Interacting SRI domain), retains histone methylation but not tubulin methylation. As such, there remains a significant realm of tubulin-dependent processes that drive ccRCC pathologies that remain unexplored. In this study, I used in vitro biochemical reconstitution with recombinant proteins to determine how SETD2 recognizes and methylates tubulin in addition to actin. By exploiting known tubulin-targeting agents, I found that SETD2 preferentially methylates the dimeric form of tubulin over microtubule polymers and, using recombinant single-isotype tubulin, I demonstrated that methylation is restricted to lysine 40 of alpha-tubulin. Moreover, by introducing pathogenic mutations into SETD2 to probe the recognition of histone and tubulin substrates, I found that particular mutations within the SRI domain tune histone and tubulin methylation by regulating protein-protein interactions with tubulin or RNA Polymerase II. Lastly, I found that tubulin substrate recognition requires the negatively-charged C-terminal tail of alpha-tubulin. Curiously, the SRI domain does not play a similar regulatory role with actin substrate suggesting an alternative recognition site, but our collaborative work found that actin methylation by SETD2 is necessary for cell motility and actin dynamics at the cell periphery. Future studies into tubulin and actin chemical modifications are required to understand the nuanced interactions and crosstalk amongst histone, tubulin, and actin chemical codes in cells and their implications for cancer and disease progression.PHDChemical BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/167990/1/skearns_1.pd