Our lab works on three interrelated subjects: (1) DNA Repair Enzymology and Genomics; (2) Mammalian Circadian Clock; (3) Control of DNA Repair by the Circadian Clock.
DNA Repair Enzymology and Genomics
DNA damage by exogenous physical and chemical agents is the most common cause of cancer. Conversely, some of the most commonly used anticancer drugs kill malignant cells by damaging their DNA. DNA Repair is the ensemble of molecular mechanisms that eliminate DNA damage from the genome, and it plays crucial roles in carcinogenesis and in cancer therapy. Our lab works on Nucleotide Excision Repair which is the sole pathway for repairing cyclobutane pyrimidine dimers (CPDs) and cisplatin 1,2-d(GpG) adducts that cause cancer and cure cancer, respectively. We discovered that these lesions are removed from DNA by dual incisions that generate 24-32 nucleotide-long oligomers (“nominal 30-mer”). We identified and purified the 6 repair factors, RPA, XPA, XPC, TFIIH, XPG, XPF-ERCC1, that are essential for dual incisions. Using these purified factors, we reconstituted human excision repair in vitro and defined the molecular mechanism of excision repair. The in vitro work was complemented by in vivo studies which enabled us to generate a repair map of the entire genome. We discovered that the nominal 30-mer is released in a tight complex with TFIIH, and this finding enabled us to isolate the nominal 30-mers from irradiated cells and subject them to deep sequencing (Fig. 1). By using normal human fibroblasts and mutant cell lines we created repair maps for general repair and transcription-coupled repair of UV damage for the entire human genome through this method which we have named XR-seq (eXcision Repair-Sequencing). Our future work will exploit XR-seq to uncover novel genomic regulators of excision repair of DNA damage by anti-cancer drugs with the ultimate goal of developing improved chemotherapy regimens. In addition, we plan to investigate the effect of the excised nominal 30-mer on cellular physiology and the processing and ultimate fates of the excised oligonucleotides.