Project description
Nucleosome structure and chromatin transcription
The nucleosome represents the fundamental part of chromatin, helping to compact DNA to fit within the cell nucleus. The structure of a nucleosome consists of DNA wrapped around histone proteins. The molecular mechanisms underlying chromatin transcription remain poorly understood as the most important studies were conducted on naked DNA and not on chromatin. The EU-funded CHROMATRANS project proposes to take the next step towards an understanding of the transcription mechanism and investigate the structural basis for polymerase II (pol II) transcription of chromatin templates. The main objectives are to determine structures of initiation factors bound to nucleosomes, the structure of the pol II pre-initiation complex on the nucleosome at the beginning of transcription and structures of mammalian pol II elongation complexes.
Objective
Transcription of protein-coding genes by RNA polymerase II (Pol II) governs cell identity and fate. We previously provided the structural basis of Pol II transcription initiation (ERC Advanced Grant TRANSIT: Sainsbury, Nature 2012; Lariviere, Nature 2012, Plaschka, Nature 2015) and of Pol II elongation regulation (ERC Advanced Grant TRANSREGULON: Vos, Nature 2018; Vos & Farnung, Nature 2018). These studies elucidated the mechanisms of transcription regulation. However, they were conducted on naked DNA, and not on chromatin, which is the natural template in cells and regulates transcription in many ways. As a consequence, the molecular mechanism underlying chromatin transcription and the regulatory interplay between chromatin and the transcription machinery remain poorly understood. Here I propose to take the next big step towards an understanding of the transcription mechanism and investigate the structural basis for Pol II transcription of chromatin templates. Integrated structural biology will provide structures of the transcription machinery on nucleosomal DNA. Nucleosomes are the building blocks of chromatin and regulate transcription in many ways. In particular, we will solve structures of pioneer factors bound to nucleosomes, to investigate how chromatin is opened locally for transcription (aim 1). We will solve the structure of the Pol II pre-initiation complex on the ‘+1’ nucleosome at the beginning of a gene, to understand how initiation is regulated by this specialized nucleosome (aim 2). Finally, we will determine structures of mammalian Pol II elongation complexes with many factors during nucleosome passage, to elucidate how Pol II transcribes chromatin (aim 3). Together with functional analysis in vitro and in vivo, these ground-breaking efforts will take the structural biology of transcription regulation to the chromatin level. The proposed research will also advance methods for the reconstitution and analysis of transient, higher-order complexes.
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Funding Scheme
ERC-ADG - Advanced GrantHost institution
80539 Munchen
Germany