Eukaryotic RNA synthesis is catalyzed by three classes of RNA Polymerases (Pol I-III). The key regulatory step in the initiation of transcription by all eukaryotic Pols is the formation of a pre-initiation complex (PIC). After PIC assembly, the initial closed promoter complex (CC) transitions into an open complex (OC), in which the melted template DNA is inserted into the Pol active site. This transient OC is then converted into an initial transcribing complex (ITC), competent to synthesize RNA. Until recently this complex transcription apparatus had proven refractory to experimental structural determination. Advances in cryo-electron microscopy and novel computational modeling methods allowed us, in collaboration with the groups of Prof. Eva Nogales and Prof. Yuan He, to visualize the human Pol II PIC during all significant steps of transcription promoter opening. Subsequently, we visualized eukaryotic Pol I PIC at near-atomic resolution allowing us to contrast the ATP-dependent Pol II initiation mechanism to the ATP-independent promoter opening by Pol I. Finally, new cryo-EM maps of Pol III PIC allowed us to model the Pol III system at the atomistic level. Having multiple structural snapshots of all three classes of PIC (Pol I - III) offers an unprecedented opportunity to connect the experimentally observed states and delineate the overall mechanism for DNA remodeling during the early stages of transcription. To this end, we have carried out path optimization and extensive MD modeling of the Pol I and Pol II systems, providing insight into the global dynamics of these complexes, which are crucial for gene expression.

Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling

256th National Meeting (2018)

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