novel molecular technologies to study gene regulation
We invent high-throughput molecular tools to study how biology’s central dogma is regulated. We are particularly interested in devising ways to molecularly tag nucleic acids and proteins with unique genomic or proteomic identifiers. We then use these “barcodes” to quantify biological phenomena (e.g. chromatin accessibility, chromosomal structure, RNA abundance, protein synthesis rates) at the level of single cells and single molecules, using high-throughput sequencing and cutting-edge mass spectrometric techniques. Our ultimate goal is to combine these techniques with synthetic, metabolic, and genetic cellular perturbations, to understand how protein-nucleic acid interactions, transcriptional dynamics, and translational dynamics vary in the face of diverse cellular inputs, and how these phenomena ultimately encode cellular phenotype.
dissecting the circuitry connecting cellular metabolism and chromatin through single-cell sequencing
Cellular and organismal functions in the contexts of development and disease rely on the proper integration of extracellular signals into gene regulatory responses. We apply metabolic perturbation strategies to established cell culture systems, and then model these perturbations using a diverse array of genomic techniques. These methods include high-throughput single-cell sequencing techniques (e.g. sci-RNA-seq, sci-ATAC-seq), which allow us to characterize cellular state changes, and high-throughput protein-DNA interaction mapping techniques (e.g. ChIP-seq, CUT&RUN), which provide us with base-pair resolution maps of nucleosome-DNA and transcription factor-DNA interactions.
We are particularly interested in the role of the extended MYC network of transcription factors as transcriptional “integrators” of cellular metabolism. To this end, we collaborate with Bob Eisenman’s lab at the Fred Hutchinson Cancer Research Center, to apply our tools to diverse in vitro and in vivo models of MYC network dysregulation. Ultimately, we aim to define the processes by which cells normally relate metabolic state to specific transcriptional programs, and better understand how these programs go awry in diseases like cancer.
regulation of metazoan RNA polymerase III transcription
A fascinating consequence of deranging the extended MYC network is the ectopic expression of tRNA genes, which are not only critical to protein synthesis, but may also play unexpected “moonlighting” roles in other biological processes. We use synthetic genetic perturbation (i.e. CRISPR/CRISPRi/CRISPRa) in cell lines to characterize the molecular consequences of perturbing tRNAs and tRNA-associated genes.
In parallel, we employ high-resolution protein-DNA interaction mapping approaches to study redistribution of RNA polymerase III, its basal transcriptional machinery, and transcription factors in response to cellular perturbations. In this way, we hope to simultaneously decode the cis regulatory features responsible for regulating tRNA transcription, and the systems-level consequences of dysregulated tRNA transcription in cells.