We have developed a single-molecule platform to visualize DNA transcription by individual RNA polymerases (RNAPs) over many kilobases. In the meantime, we have developed SEnd-seq, a sequencing method that simultaneously maps both 5’ and 3’ RNA ends in a transcriptome. These novel technologies enable us to gain unprecedented insights into the coordination between RNAPs and their regulatory factors on a crowded genome in both bacterial and eukaryotic systems.

We have established a longstanding collaboration with the O’Donnell Lab to study the eukaryotic replisome, a multi-component macromolecular machine responsible for genome replication. Our approach—single-molecule observation combined with in vitro reconstitution—offers the best opportunity to dissect the intricate dynamics of individual constituents within this extraordinarily sophisticated machinery.

Leveraging single-molecule manipulation and visualization, we have shown that nucleosomes are more than passive DNA packaging units of eukaryotic chromatin, but also potent hotspots to recruit DNA-binding proteins and DNA-processing machines and modulate their activities. As such, the physical parameters of the nucleosome constitute a rich layer of epigenetic regulation for genomic transactions.

Besides our main interests in the central dogma and epigenetics, we have also collaborated widely with groups within and outside Rockefeller and applied our expertise in single-molecule techniques to other areas of biology ranging from membrane proteins to cytoskeleton, CRISPR-Cas and SARS-CoV-2.

We have written several review articles to introduce the booming field of single-molecule biology, its mainstream methodology and latest applications, as well as our perspective on its future directions.