Ph.D., Department of Molecular Biophysics and Biochemistry, Yale University
Postdoctoral Associate, Yale University
The Rockefeller University
Our laboratory is interested in deciphering the functional and mechanistic role of homologous recombination in biology.
The Biology of Homologous Recombination
Homologous recombination (HR) governs genomic transactions. It represents a major chromosome repair tool that helps to eliminate deleterious lesions such as DNA double strand breaks (DSBs), mediate the restart of stalled or collapsed DNA replication forks, ensure proper meiotic chromosome segregation, as well as to maintain the length of telomeres in some circumstances (Fig. 1). As such, HR is indispensable for the maintenance of genome integrity. Studies in the past have provided compelling evidence for a tumor suppression role of HR. For instance, cell lines from familial breast cancer patients that harbor mutations in BRCA2 exhibit hypersensitivity to DNA damaging agents and a pronounced deficiency in HR. Aside from its genome maintenance and tumor suppression functions, HR also serves more specialized roles in various organisms, such as mating type switching in the budding yeast and V(D)J recombination in the immune system. In summary HR play an essential role in biology and dysregulation of HR causes severe disease such as cancer. Figure 1. Biological Roles of Homologous Recombination (HR)
Homologous Recombination Pathway
HR is often induced via the formation of DSBs, which leads to the nucleolytic processing of DSB ends to generate 3' single-stranded DNA (ssDNA) tails. Herein, the 3' single-stranded tail associates with recombinases to form a nucleoprotein filament, which is then activated to invade a homologous duplex DNA molecule to form a displacement loop or D-loop. The 3' invading strand is extended by DNA synthesis, followed by the pairing of the non-invading 3' single-stranded tail with the homologous ssDNA strand in the enlarging D-loop (second end capture). The now paired second 3' end is also extended by DNA synthesis and subsequent ligations generate a double Holliday Junction (dHJ) intermediate. Resolution of the dHJ intermediate can result in crossover or non-crossover recombinant products (Fig. 2). In summary, the HR pathway is constituted by a sequence of events that involve (1) DSBs formation; (2) end resection to create 3' overhang ssDNA; (3) assembly of recombinase onto ssDNA; (4) D-loop mediated DNA synthesis; and (5) formation & resolution of dHJ intermediate.
Figure 2. Homologous Recombination (HR) Pathway
The DNA double strand break (DSB) is resected to generate 3' ssDNA overhangs. Invasion of a homologous DNA molecule by one of these 3' ssDNA tails gives rise to a D-loop intermediate. After DNA synthesis, the second DNA end is captured to form an intermediate with two Holliday Junctions (HJ)s. Resolution of the Holliday Junctions yields either non-crossover or crossover products.
We are fascinated with sophisticated HR process and our desire is to focus on several related projects directed at understanding the action mechanisms of HR in accomplishing their biological mission. We hope the molecular insights garnered from our studies could potentially provide the basis for devising strategies to prevent and treat various cancers such as breast cancer.
Chang, H.Y., Liao, C.Y., Su, G.C., Lin, S.W., Wang, H.W., Chi, P. (2015) Functional Relationship of ATP Hydrolysis, Presynaptic Filament Stability, and Homologous DNA Pairing Activity of the Human Meiotic Recombinase DMC1. J Biol Chem., 290(32):19863-73.
Zhao, W., Saro, D., Hammel, M., Kwon, Y., Xu, Y., Rambo, R.P., Williams, G.J., Chi, P., Lu, L., Pezza, R.J., Camerini-Otero, R.D., Tainer, J.A., Wang, H.W., Sung, P. (2014) Mechanistic insights into the role of Hop2-Mnd1 in meiotic homologous DNA pairing. Nucleic Acids Res., 42(2):906-17.
Su, G.C., Chung, C.I., Liao, C.Y., Lin, S.W., Tsai, C.T., Huang, T., Li, H.W., Chi, P. (2014) Enhancement of ADP release from the RAD51 presynaptic filament by the SWI5-SFR1 complex. Nucleic Acids Res., 42(1):349-58.
Wilson, M.A., Kwon, Y., Xu, Y., Chung, W.H., Chi, P., Niu, H., Mayle, R., Chen, X., Malkova, A., Sung, P., Ira, G. (2013) Pif1 helicase and Polδ promote recombination-coupled DNA synthesis via bubble migration. Nature, 502(7471):393-6.
Busygina, V., Gaines, W.A., Xu, Y., Kwon, Y., Williams, G.J., Lin, S.W., Chang, H.Y., Chi, P., Wang, H.W., and Sung, P. (2013) Functional attributes of the Saccharomyces cerevisiae meiotic recombinase Dmc1. DNA Repair (Amst), 12(9):707-12.
Tsai, S.P., Su, G.C., Lin, S.W., Chung, C.I., Xue, X., Dunlop, M.H., Akamatsu, Y., Jasin, M., Sung, P., and Chi, P. (2012) Rad51 presynaptic filament stabilization function of the mouse Swi5-Sfr1 heterodimeric complex. Nucleic Acids Res., 40 (14):6558-69.
Chen, C.H., Chu, P.C., Lee, L., Lien, H.W., Lin, T.L., Fan, C.C., Chi, P., Huang, C.J., and Chang, M.S. (2012) Disruption of murine mp29/Syf2/Ntc31 gene results in embryonic lethality with aberrant checkpoint response. PLoS One, e33538.
Chi, P., Kwon, Y., Visnapuu, M.L., Lam, I., Santa Maria, S.R., Zheng, X., Epshtein, A., Greene, E.C., Sung, P., and Klein, H.L. (2011) Analyses of the yeast Rad51 recombinase A265V mutant reveal different in vivo roles of Swi2-like factors. Nucleic Acids Res., 1-12.
Niu, H., Chung, W.H., Zhu, Z., Kwon, Y., Zhao, W., Chi, P., Prakash, P., Seong, C., Liu, D., Lu, L., Ira, G., and Sung, P. (2010) Mechanism of the ATP-dependent DNA end-resection machinery from Saccharomyces cerevisiae. Nature, 467(7311):108-11.
Robertson, R.B., Moses, D.N., Kwon, Y., Chan, P., Chi, P., Klein, H., Sung, P., and Greene, E.C. (2009) Structural transitions within human Rad51 nucleoprotein filaments. PNAS, 106(31):12688-93.
Chi, P., Kwon, Y., Moses, D.N., Seong, C., Sehorn, M.G., Singh, A.K., Tsubouchi, H., Greene, E.C., Klein, H.L., and Sung, P. (2009) Functional interactions of meiotic recombination factors Rdh54 and Dmc1. DNA Repair (Amst), 8(2):279-84.
Robertson, R.B., Moses, D.N., Kwon, Y., Chan, P., Chi, P., Klein, H., Sung, P., and Greene, E.C., (2009) Visualizing the disassembly of S.cerevisiae Rad51 nucleoprotein filaments. J. Mol. Biol., 388(4):703-20.
Seong, C., Sehorn, M.G., Plate, I., Shi, I., Song, B., Chi, P., Mortensen, U., Sung, P., and Krejci, L. (2008) Molecular anatomy of the recombination mediator function of Saccharomyces cerevisiae Rad52. J. Biol. Chem., 283(18):12166-74.
Kwon, Y., Seong, C., Chi, P., Greene, E.C., Klein, H., and Sung, P. (2008) ATP-dependent chromatin remodeling by the Saccharomyces cerevisiae homologous recombination factor Rdh54/Tid1. J. Biol. Chem., 283(16):10445-52.
Hu, Y., Raynard, S., Sehorn, M.G., Lu, X., Bussen, W., Zheng, L., Stark, J.M., Barnes, E.L., Chi, P., Janscak, P., Jasin, M., Vogel, H., Sung, P., and Luo, G. (2007) RECQL5/Recql5 helicase regulates homologous recombination and suppresses tumor formation via disruption of Rad51 presynaptic filaments. Genes & Develop., 21(23):3078-84.
Chi, P., San Filippo, J., Sehorn, M.G., Petukhova, G.V., and Sung, P. (2007) Bipartite stimulatory action of the Hop2-Mnd1 complex on the Rad51 recombinase. Genes & Develop., 21(14):1747-57.
Kwon,Y., Chi, P., Roh, D. H., Klein, H., and Sung, P. (2007) Synergistic action of the Saccharomyces cerevisiae homologous recombination factors Rad54 and Rad51 in chromatin remodeling. DNA Repair (Amst), 6(10):1496-506.
Prasad, T.K., Robertson, R.B., Visnapuu, M.L., Chi, P., Sung, P., and Greene, E.C. (2007) A DNA-translocating Snf2 molecular motor: Saccharomyces cerevisiae Rdh54 displays processive translocation and extrudes DNA loops. J. Mol. Biol., 369(4):940-53.
Chi, P., Kwon, Y., Seong, C., Epshtein, A., Lam, I., Sung, P., and Klein, H. L. (2006) Yeast recombination factor Rdh54 functionally interacts with the Rad51 recombinase and catalyzes Rad51 removal from DNA. J. Biol. Chem., 281(36):26268-79.
Chi, P., Van Komen, S., Sehorn, M.G., Sigurdsson, S., and Sung, P. (2006) Roles of ATP binding and ATP hydrolysis in human Rad51 recombinase function. DNA Repair (Amst), 5(3): 381-91.
San Filippo, J., Chi, P., Sehorn, M.G., Etchin, J., Krejci, L., and Sung, P. (2006) Recombination mediator and Rad51 targeting activities of a human BRCA2 polypeptide. J. Biol. Chem., 281 (17):11649-57.
Raschle, M., Van Komen, S., Chi, P., Ellenberger, T., and Sung, P. (2004) Multiple interactions with the Rad51 recombinase govern the homologous recombination function of Rad54. J. Biol.Chem., 279(50):51973-80.
Chi, P., Doong, S.L., Lin-Shiau, S.Y., Boone, C. W., Kelloff, G. J., and Lin, J.K. (1998) Oltipraz, a novel inhibitor of hepatitis B virus transcription through elevation of p53 protein. Carcinogenesis,19(12):2133-2138. (Note: my name was Wei-Jie Chi in the publication)