Join us for a talk on “Single-molecule studies of chromosome organization and transcription regulation by DNA supercoiling”

By Dr. Jie Xiao, Professor, Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD.

Abstract

Classic gene regulation dogma shows that transcription factor binding to specific DNA sequences regulates gene expression. In recent years, an increasing number of studies have shown that the supercoiling state of chromosomal DNA is a fundamental factor that impacts transcription. The topological organization of chromosomal DNA into individual domains, between which the diffusion of supercoiling is prohibited, thus plays an important role in gene regulation. In this talk, I will discuss our recent effort in developing in silico, in vivo, and in vitro single-molecule approaches to probe how DNA supercoiling impacts chromosome organization and transcription.  We have built a synthetic supercooling domain platform to control topological domain formation at will in single E. coli cells. We used single-molecule fluorescence in-situ hybridization (smFISH) to probe the expression and correlation of two genes enclosed in the domain and a third gene outside the domain under altered topoisomerase activities. We then developed a corresponding in vitro single-molecule transcription assay to probe how DNA’s supercoiling state affects transcription kinetics and the cooperation of neighboring RNA polymerase molecules. Finally, we combine these experimental studies to construct a quantitative computational model depicting the relationship between supercoiling and transcription regulation.

Sponsored by the Department of Chemistry, Biochemistry, and Biomolecular Sciences Institute.