Overview

Our research program focused on developing mass spectrometry (MS)–based proteomic and bioinformatic approaches to elucidate protein–protein and protein–nucleic acid interactions involved in R-loop biology, RNA metabolism, and epigenetic regulation of gene expression in human cells. Our long-term goal is to define the molecular mechanisms by which RNA-centered structures and modifications interface with chromatin to regulate gene expression and maintain genome integrity.

Research Vision and Approach

R-loops and RNA modifications, particularly N6-methyladenosine (m6A), play central roles in transcriptional regulation, RNA processing, and chromatin organization. However, the protein networks that recognize and regulate these RNA-centered features remain incompletely understood. My laboratory addresses this gap by integrating quantitative LC–MS/MS proteomics, computational prediction, and functional genomics to systematically identify interacting proteins and define their mechanistic roles.

Our interdisciplinary approach combines MS-based proteomics, bioinformatics, recombinant protein expression and purification, CRISPR/Cas9-mediated genome editing, fluorescence microscopy, and next-generation sequencing. This integrated framework enables unbiased discovery of interaction partners followed by rigorous functional validation, allowing us to link molecular interactions to biological outcomes in transcription, RNA metabolism, and genome stability.

Research Infrastructure

Our laboratory have built robust experimental platforms to support sustained independent research. These include bacterial and mammalian cell culture systems, gene perturbation strategies for overexpression and knockdown, and a curated collection of engineered human cell lines generated using stable expression and CRISPR/Cas9-based genome editing. These resources provide a strong foundation for both discovery-driven research and student training.

Research Directions

1. Proteomic mapping of RNA- and R-loop–associated protein networks.
   We develop and apply affinity purification and proximity labeling quantitative proteomic strategies to identify proteins that interact with R-loops and R-loop regulatory proteins.

2. Crosstalk between RNA modifications and chromatin regulation.
   Another major focus of my lab is understanding how RNA modifications, particularly m6A, influence chromatin-associated processes such as histone modification, transcriptional regulation, and genome stability through protein-mediated mechanisms.

3. Functional consequences for transcription and genome integrity.
   By integrating proteomics with genome editing and sequencing-based assays, we define how RNA–protein interactions affect transcriptional output, co-transcriptional splicing, and susceptibility to genome instability.

These directions position our laboratory at the interface of RNA biology, chromatin regulation, and proteomics, with broad relevance to fundamental biology and disease mechanisms.