Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II

Abstract

The precise, sequence-specific regulation of RNA synthesis is the primary mechanism underlying differential gene expression. This general statement applies to both prokaryotic and eukaryotic organisms, as well as to their viral pathogens. Thus, it is not surprising that genomes use a substantial portion of their protein-coding content to regulate the process of RNA synthesis. Transcriptional regulation in bacterial systems is particularly well understood. In this essay, we build on this knowledge and propose two opposing models to describe promoter opening and transcription initiation in the eukaryotic RNA polymerase II system. Promoter opening in the "twisting by cranking" model is based on changes in the trajectory of DNA. In contrast, invasion of single-stranded DNA-binding proteins between the DNA strands drives the reaction in the "peeling by binding" model.