TRANSIT · Mechanism of Regulated Transcription Initiation

The regulation of gene transcription governs eukaryotic cell growth and differentiation. Despite its importance, transcription regulation is not understood at a mechanistic level. Regulation occurs mainly during initiation, when the enzyme RNA polymerase II (Pol II) assembles with ~50 polypeptides on promoter DNA. Regulatory signals are transmitted by the 25-subunit Mediator, and convert the initiation complex into a productive elongation complex. Ten years after the solution of the Pol II structure (Cramer et al., Science 2000, 2001), elongation is understood, but the structure and regulatory control of the initiation complex remain largely unknown. Here I propose to solve this central problem of molecular genetics and obtain a movie that shows how a gene is activated. Our recent structure of Pol II with initiation factor TFIIB (Kostrewa et al. Nature 2009) provides the starting point for the proposed risky and challenging structure-function analysis of regulated initiation. First, we will determine structures of Pol II in the initiating state. Second, we will solve the structure of the essential, gene-regulatory 7-subunit head module of the Mediator core. Third, we will establish ¿nascent transcriptome analysis¿ as a novel technique that measures mRNA synthesis rates globally, and will use it to probe the mechanisms of regulated initiation by structure-based mutagenesis in vivo. Expected results will open new horizons for investigating the function of eukaryotic genomes, and will have a strong impact on biomedicine, since deregulated transcription underlies many diseases, including cancers and certain metabolic dysfunctions. This ground-breaking research requires the long-term, flexible commitment of the ERC, to successfully compete with teams in the US and Japan.