Seminars

Cell identity is determined by a set of genes that are expressed at a given time in a cell. Gene regulatory elements including cell type-specific transcription factors and enhancers regulate spatiotemporal expression of their target genes. There has been remarkable progress in our understanding of the mechanisms by which gene regulatory elements control transcription. However, it remains elusive how they function in time and space. To investigate how enhancer-bound transcription activators promote transcription initiation at unprecedented resolution, multi-wavelength single-molecule fluorescence microscopy was implemented. Our single-molecule experiments reveal several unexpected features of activator-dependent Pol II transcription activation and initiation.
Pol II and general transcription factors TFIIF and TFIIE preassemble on enhancer-bound activators with dwell times on the order of several seconds before loading into a preinitiation complex (PIC) at the core promoter. More interestingly, multiple Pol II complexes can simultaneously bind a single enhancer, creating a localized Pol II cluster.
This Pol II cluster suggests a plausible mechanism underlying transcription bursting that preassembled Pol II complexes at enhancer function as a Pol II reservoir and they are transferred to the core promoter when the core promoter is turned on. In contrast to other general transcription factors, TFIIH incorporation is dependent on the core promoter. In sum, our kinetic measurements lead to a new branched model for activator-dependent PIC assembly and suggest an importance of finely tuned spatial interactions between enhancer and the core promoter for gene expression at the right time.