In this research area, our laboratory has been using a multi-pronged approach, encompassing mass spectrometry-based analytical chemistry, synthetic organic chemistry, biochemistry, molecular biology, and genetic tools to achieve a comprehensive understanding about the occurrene, repair and biological endpoints of DNA damage products. We aim to understand, at the molecular level, how structurally defined DNA lesions perturb the efficiency and fidelity of flow of genetic information during DNA replication and transcription. The types of DNA damage that we have been working with include DNA lesions induced by reactive oxygen species and alkylating agents. Students and postdocs working in this area are exposed to highly interdisciplinary training at the interface of chemistry and biology.
Our laboratory is equipped with five state-of-the-art mass spectrometers, including two Orbitraps (a Q Exactive Plus and an LTQ Orbitrap Velos). We also have access to an Orbitrap Fusion in the Institute for Integrated Genome biology and a TSQ Vantage triple-quadrupole in the Analytical Chemistry Instrumentation Facility. By taking advantage of these instruments, our research program in proteomics encompasses several different areas. In one area, we develop targeted quantitative proteomic methods, relying on multiple-reaction monitoring and parallel-reaction monitoring, for interrogating the human kinome, small GTPase proteome as well as other nucleotide- and metabolite-binding proteomes. We also empoly SILAC-based interaction screening for uncovering novel nucleic acid recognition proteins. Moreover, we are interested in uncovering novel protein players involved in the post-translational modifications of proteins and post-transcriptional regulations of RNA and in unraveling the mechanisms underlying the antineoplastic effects of the drugs and the cytotoxic effects of the environmental agents.
In this area, we are interested in all aspects of epigenetic regulation of gene expression, including DNA methylation, post-translational modifications of histone proteins, and post-transcriptional modifications of RNA. In the latter aspect, we develop high-throughput LC-MS/MS-based method to quantify the global levels of modified ribonucleosides in RNA. We also employ proteomic tools, along with genetic manipulations (siRNA, shRNA, and genomic editing using CRISPR-Cas9), to uncover novel proteins involved in deposition, removal and recongition of modified nucleosides in RNA.