BPS2026 – CAG repeats reshape RNA polymerase II dynamics in the elongation complex

Trinucleotide CAG repeat expansions are central to the pathology of Huntington’s disease and other neurodegenerative disorders. It is known that transcription of expanded CAG-repeats has an increased dependency on the elongation factor DSIF compared to wild-type CAG-repeats, yet the impact of expanded repeats on the transcription machinery remains poorly understood. To explore their direct structural effects, we employed atomistic molecular dynamics (MD) simulations of the eukaryotic RNA Polymerase II (Pol II) elongation complex in the presence of varying CAG content. Using the Cryo-EM structure of the Pol II-DSIF complex bound to DNA and RNA (PDB: 5OIK), we constructed four systems: a wild-type control (no CAG repeat), a single CAG insertion in the upstream DNA and RNA, a system with six upstream CAG repeats and matching RNA, and a full-CAG model with repeats spanning the entire upstream and downstream DNA as well as the RNA. MD simulations revealed progressive increases in protein–nucleic acid contacts, especially for DSIF, and reduced flexibility in key structural regions as CAG content increased. Contact mapping highlighted enhanced interactions between repeat-rich RNA and residues near the RNA exit tunnel, while RMSF analysis showed dampened dynamics for DNA and RNA. These findings suggest that expanded CAG sequences can affect Pol II dynamics during elongation by modulating structural flexibility and altering the interactions between protein domains and upstream nucleic acids. This work provides a mechanistic foundation for how repeat expansions may directly impair transcription, offering insight into the molecular understanding of enhanced DSIF function on transcription of pathologically expanded CAG repeats.