Structure Maintenance of Chromosome (SMC) complexes are central to chromosome segregation, compaction and DNA repair, thereby impacting on gene expression and regulation. SMC family members that control chromosome topology during the cell cycle, range in eukaryotes from cohesion, condensin and Smc5/6 exhibiting ATPase-mediated hydrolysis activities to the MRN/MRX complex with both ATPase and nuclease activities. Recent efforts in our lab have focused on complexes mediating DNA double strand break (DSB) repair. These range from the Structure Maintenance of Chromosome Smc5/6 complex involved in rescue of stalled replication forks to the MRE11-Rad50 (MR) complex involved in preservation of genomic integrity and suppression of tumorigenesis. Our group is also interested in understanding the mechanism and regulation of homologous recombination during meiosis initiated by DNA DSBs mediated by the Spo11 protein together with a suite of accessory factors.
Smc5/6 Complex
While cohesin and condensin contribute to sister chromatid cohesion and DNA packaging respectively through loop extrusion, Smc5/6 mediates resolution of recombination intermediates during mitosis, meiosis or as a consequence of replication stress, as well as a viral restriction factor restraining disease-causing viruses. Notably, Smc5/6 plays a critical role in mediating homologous recombination (HR)-mediated rescue of stalled or collapsed replication forks, thereby preventing DNA entanglements, breakages and translocations associated with DNA damage syndromes caused by Smc5/6 mutations. This is a new project in collaboration with the Xiaolan Zhao lab (MSKKC) with that involve recent cross-linking mass spectrometry data on apo-Smc5/6 (Yu et al. 2021) and our recent cryo-EM structure determination of the dsDNA-bound S. cerevisiae Smc5/6 complex (composed of Smc5, Smc6, Nse1, Nse3 and Nse4 kleisin) that reveals DNA clamping enabled by multi-subunit conformational changes (Yu et al. 2022). In future studies, we plan to investigate the role of Nse5 and Nse6 subunits, SUMOylation and ubiquitination, as well as the interaction of partner proteins, in mediating Smc5/6 function.
Yu, Y., Li, S., Ser, Z., Sanyal, T., Choi, K., Sali, A., Kentsis, A., Patel, D. J. & Zhao, X. (2021). Integrative analysis reveals unique structure and functional features of the Smc5/6 complex. Proc. Natl. Acad. Scis. USA. 118, e2026844118.
Yu, Y., Li, S., Ser, Z., Kuang, H., Than, T., Guan, D., Zhao, X. & Patel, D. J. (2022). Cryo-EM structure of dsDNA-bound S. cerevisiae Smc5/6 complex reveals DNA clamping enabled by multi-subunit conformational changes. Proc. Natl. Acad. Scis. USA.
MRX Complex
The DNA damage response (DDR) comprises multiple functions that collectively preserve genomic integrity and suppress tumorigenesis. The MRN complex in humans (MRX in yeast) and ATM govern a major axis of the DDR and several lines of evidence implicate that axis in tumor suppression. Components of the MRN complex are mutated in approximately five percent of human cancers. Inherited mutations of complex members cause severe chromosome instability syndromes, such as Nijmegen Breakage Syndrome, which is associated with strong predisposition to malignancy (Hohl et al. 2020). This is a new project in collaboration with the John Petrini (MSKKC) lab, with our recent result being the cryo-EM structure determination of the dsDNA-bound S. cerevisiae MR complex (composed of a dimer of MRE11 and Rad50) that establishes DNA encapsulation within the Rad50 scaffold.
Hohl, M., et al., Patel, D. J., Burgers, P. M., Cobb, J. A. & Petrini, J. H. (2020). Modeling cancer genomic data in yeast reveals selection against ATM function during tumorigenesis. PLOS Genetics 16:e1008422.
DSB Formation and Repair During Meiosis
Human reproductive success and the development of healthy offspring depend on accurate transmission of genetic material. Homologous recombination during meiosis plays a central role in this genetic transmission by ensuring accurate chromosome segregation. Understanding the mechanism and regulation of recombination is thus critical for understanding how meiotic errors affect human fertility and child development. Meiotic recombination initiates with DNA double-strand breaks (DSBs) made by the Spo11 protein together with a suite of accessory factors. In collaboration with the Scott Keeney lab (MSKKC), we are interested in the structural and functional characterization of the Saccharomyces cerevisiae DSB core Spo11-Rec102–Rec104–Ski8 complex, as well as the Rec114-Mei4-Mer2 complex that forms nucleoprotein condensates on DNA that are critical for regulating DSB timing, number and location (Boekhout et al. 2019; Bouuaert et al.2021). The ongoing structural efforts which have recently resulted in the cryo-EM structure determination of the Spo11-Rec102–Rec104–Ski8 complex, will be complemented by single molecule biophysical approaches in vitro together with functional experiments in vivo undertaken in the Keeney lab.
Boekhout, M. et al., Patel, D. J. & Keeney, S. (2019). REC114 partner ANKRD31controls number, timing and location of meiotic DNA breaks. Mol. Cell 74, 1053-1068.
Bouuaert, C. C., Pu, S., Wang, J., Oger, C., Daccache, D., Xie, W., Patel, D. J. & Keeney, S. (2021). DNA-driven condensation assembles the meiotic break machinery. Nature 592, 144-149.