UC Berkeley

Biological systems provide a rich environment for studying non-equilibrium phenomena, an exciting new frontier in physics. Of particular interest is the study of transcriptional regulation---the process by which transcription factors regulate the activity of mRNA production. Recent evidence suggests that in eukaryotes, organisms whose cells possess nuclei, transcription involves non-equilibrium effects such as energy expenditure. In this work, we undergo a systematic dissection of transcriptional regulation in eukaryotes and demonstrate the necessity for non-equilibrium models in the case of the developing fruit fly. We then investigate some theoretical ramifications of non-equilibrium models of chromatin accessibility that incorporate transient dynamics. Finally, we describe a novel experimental and computational framework for studying the entire transcription cycle---consisting of mRNA initiation, elongation, and cleavage---in order to investigate transcriptional regulation beyond that of simple regulation of initiation.