Michael Boddy, PhD - Scripps Research

Research Focus

Every time a cell divides, it must copy billions of base pairs of DNA with near-perfect fidelity and do so under constant chemical and environmental assault. Our laboratory studies the biological molecular machines that detect DNA damage, coordinate its repair, and suppress the genome instability that drives cancer and premature aging. We also study the "moonlighting roles” of these DNA repair factors in the innate immune response to episomal circular DNAs, which include pathogenic viruses and key gene therapy vehicles. To address these critical areas of research, we integrate cell biology, proteomics, genetics and protein structural biology techniques.

Scripps News on some of our key studies:

The STUbL Discovery: Our laboratory discovered a novel family of proteins we named STUbLs (SUMO-targeted ubiquitin ligases). This discovery revealed an unanticipated crosstalk between the SUMO and ubiquitin post-translational modifiers, providing critical insight into how cells handle DNA damage and how a leukemia therapy works.

See: https://www.scripps.edu/newsandviews/e_20070910/protein.html

Related Scholar Award: https://www.scripps.edu/newsandviews/e_20090209/etc.html

Molecular Mimicry of SUMO in Genome Integrity: Our discovery that a DNA repair protein exploits structural mimicry to parasitize the SUMO conjugation cascade — rather than being a passive SUMO substrate — fundamentally changed how the field thinks about SUMO pathway regulation. It opened the question of how many other proteins use SUMO-like domain mimicry to modulate SUMO signaling without being SUMOylated themselves, a question directly relevant to cancer and antiviral biology, given the central role of the SUMO pathway in SMC5/6-mediated genome stability and viral silencing.

See: https://www.scripps.edu/newsandviews/e_20090420/sumo.html

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Boddy, Michael; Howe, K.; Etkin, L. D.; Solomon, E.; Freemont, P. S. PIC 1, a novel ubiquitin-like protein which interacts with the PML component of a multiprotein complex that is disrupted in acute promyelocytic leukaemia. Oncogene 1996, 13, 971-982.
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Boddy, Michael N.; McGowan, Clare H.; Tainer, John A.; Perry, J. J.; Slavin, Daniela A.; Raffa, Grazia D.; Pebernard, Stephanie; Prudden, John SUMO-targeted ubiquitin ligases in genome stability. The EMBO Journal 2007.
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Boddy, Michael N.; Tainer, John A.; Arvai, Andrew S.; Perry, J. J.; Prudden, John Molecular mimicry of SUMO promotes DNA repair. Nature Structural & Molecular Biology 2009.
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Oravcová, Martina; Nie, Minghua; Zilio, Nicola; Maeda, Shintaro; Jami-Alahmadi, Yasaman; Lazzerini-Denchi, Eros; Wohlschlegel, James A.; Ulrich, Helle D.; Otomo, Takanori; Boddy, Michael N. The Nse5/6-like SIMC1-SLF2 complex localizes SMC5/6 to viral replication centers. eLife 2022, 11.
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Oravcová, Martina; Nie, Minghua; Otomo, Takanori; Boddy, Michael N. SMC5/6-mediated plasmid silencing is directed by SIMC1-SLF2 and antagonized by the SV40 large T antigen. eLife 2025, 14.
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Wu, Tong; Li, Youhang; Zhao, Yuqin; Bournique, Elodie; Ortega, Pedro; Nie, Minghua; Wang, Yiqing; Wang, Hailong; Buisson, Rémi; Hickson, Ian D.; Boddy, Michael N.; Wu, Xiaohua The SMC5/SMC6 complex is critical for resolving R-loop-induced transcription-replication conflicts. Nucleic Acids Research 2026, 54.
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