Modeling DNA Opening in the Eukaryotic Transcription Initiation Complexes via Coarse-Grained Models

Area of Science:

• Molecular Biology
• Structural Biology
• Biophysics

Background:

• Transcription initiation is crucial for gene regulation.
• Cryo-electron microscopy has provided static structural insights into eukaryotic transcription initiation.
• The dynamic process of promoter DNA opening remains poorly understood.

Purpose of the Study:

• To elucidate the dynamic mechanisms of promoter DNA opening during transcription initiation.
• To model the structural transitions between closed, open, and initially transcribing complexes.
• To identify intermediate states and key molecular players in DNA opening.

Main Methods:

• Multiscale molecular dynamics (MD) simulations combining coarse-grained and all-atom approaches.
• Utilized three cryo-electron microscopic yeast structures (closed, open, initially transcribing complexes).
• Back-mapping all-atom models for detailed interaction analysis.

Main Results:

• Developed an atomic model for the DNA bubble in open complexes.
• Discovered a previously unidentified intermediate state in the transition from open to initially transcribing complexes.
• Identified the fork loop 1 of RNA Polymerase II (Pol II) as a bottleneck and gatekeeper for DNA opening.
• Characterized interactions between the non-template DNA strand and conserved residues in the Rpb2 subunit of Pol II within the initially transcribing complex.

Conclusions:

• The fork loop 1 of Pol II acts as a critical gatekeeper regulating promoter DNA opening.
• Specific interactions within the Rpb2 subunit are vital for stabilizing the non-template DNA strand during transcription.
• The study provides atomistic insights into the dynamic process of transcription initiation, paving the way for further simulation studies.