Single-molecule studies of transcription regulation by DNA topology

The classic bacterial gene regulation dogma depicts that a gene’s transcription activity is regulated by protein transcription factors. In recent years, an increasing number of studies have shown that the supercoiling state of chromosomal DNA is a fundamental factor impacting chromosome organization and transcription regulation. The topological organization of chromosomal DNA into individual domains, within which supercoiling diffusion is prohibited, thus plays an important role in gene regulation. In this talk, I will discuss our investigations of how DNA topology impacts transcription using single-molecule imaging approaches in vivo and in vitro and computational modeling in silico. We show that DNA topology has a profound impact on transcription independent of any protein factors. Specifically, chromosomal topological domain formation represses transcription and gene orientation–dependent effects, reshapes the supercoiling sensitivity of genes, and modulates intrinsic coupling between adjacent genes in a context-dependent, non-monotonic manner. These effects are likely mediated by altered transcription initiation and elongation kinetics of multiple RNA polymerases in response to the local supercoiling environment. Our work suggests that the DNA mechanics-based transcription regulation is possibly a more fundamental, universal mechanism for gene regulation, predating the more intricate, protein-based gene regulation that evolved.