Transcription regulation ultimately underlies cell differentiation, organism development and all cellular responses to environmental change. Yet, the molecular architecture and functional dynamics of the transcription initiation machinery are still incompletely understood. Here we synthesize available cryo-EM data to produce the most complete atomistic model of the human transcription pre-initiation complex (PIC) to date, including the ten-subunit general transcription factor TFIIH and its flexible kinase (CAK) module. The overall conformation of the assembly has been flexibly fitted into the EM density of the closed complex holo-PIC. The quality of our new models makes them suitable for molecular dynamics (MD) simulations on massively parallel computing platforms. Thus, we carried out extensive MD simulations to unveil the functional dynamics of Pol II holo- and core-PICs. To our knowledge, this is the first molecular simulation of the human transcription initiation machinery. Our analysis unveiled the hierarchical organization of the PIC machinery into dynamic communities and explained how its numerous structural elements function together to remodel the DNA substrate and facilitate promoter opening. The structure of the newly discovered allosteric modules and networks within TFIIH are in perfect correspondence with existing TFIIH mutational data from in vitro experiments and from disease-associated patient mutations.<br/>Thus, the present study provides a conceptual basis to rationalize a significant body of experimental evidence on the etiology of inherited genetic disorders such as xeroderma pigmentosum (XP) and trichothiodystrophy(TTD). In addition, our models provide a structural framework for future experiments aimed at unraveling the intricate molecular choreography of transcription initiation.

Molecular architecture and functional dynamics of the human transcription initiation machinery

2019 Spring National Meeting

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