CHEMICAL GENOMICS
Our group harnesses next-generation genome editing tools for chemical genetic approaches. In one major direction, we have advanced CRISPR mutational scanning approaches to interrogate protein structure-function and small molecule mechanism of action. These approaches enable the broad and systematic identification of functional mutations across endogenous proteins of interest. We study key mutations in deeper mechanistic studies using any method at our disposal, enabling us to deconvolute small molecule mechanism, uncover sites of protein functionality and allosteric regulation, and identify new cancer dependencies. We have expanded these approaches to investigate multi-subunit complexes and pathways, employ new forms of precision genome-editing and single-cell technologies, and explore the mechanisms of diverse small molecule modalities. To enable these and other efforts, we pursue the chemical synthesis of small molecules and their functional derivatives. Ongoing projects are focused on exploring chromatin complexes, transcription factors, signaling molecules, and E3 ubiquitin ligases. Our long-term goal is to leverage large-scale chemical-genomic maps with mechanistic insight for the development of therapeutic approaches.
Selected Publications:
- UM171 glues asymmetric CRL3-HDAC1/2 assembly to degrade CoREST corepressors. Yeo* et al. Nature 2025.
- Converging mechanism of UM171 and KBTBD4 nomorphic cancer mutations. Xie* et al. Nature 2025.
- Base editor scanning charts the DNMT3A activity landscape. Lue et al. Nature Chemical Biology 2022.
- CRISPR-suppressor scanning reveals a nonenzymatic role of LSD1 in AML. Vinyard* et al. Nature Chemical Biology 2019.
Reviews:
- Base editor screens for in situ mutational scanning at scale. Lue & Liau, Molecular Cell 2023.
- Discovering new biology with drug-resistance alleles. Freedy & Liau, Nature Chemical Biology 2021.
MECHANISMS OF GENE CONTROL
We investigate the mechanisms that control transcription and broader genome function. One major research focus is understanding chromatin complexes and transcription factors, with the long-term goal of defining and targeting functional sites, mechanisms, and dependencies for small molecule development.
Selected Publications:
- Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase. Roh*, Shen*, Hu* et al. Nature Methods 2025.
- An autoinhibitory switch of the LSD1 disordered region controls enhancer silencing. Waterbury*, Kwok*, Lee* et al. Molecular Cell 2024.
- Drug addiction unveils a repressive methylation ceiling in EZH2-mutant lymphoma. Kwok*, Freedy* et al. Nature Chemical Biology 2023.
- Polycomb-lamina antagonism partitions heterochromatin at the nuclear periphery. Siegenfeld*, Roseman* et al. Nature Communications 2022.