Speaker
Description
RNAPolII transcription is a stochastic process where efficiency and fidelity emerge from nonequilibrium dynamics. We present a methodology to quantify the transcriptional efficiency of RNAPII using time series obtained from dual-bead optical tweezers experiments.
Our approach combines stochastic thermodynamics and graph-based time-series analysis. Probability fluxes along the inferred transcriptional states are estimated and used to quantify the breaking of detailed balance associated with transcriptional progression. To characterize the dynamics of RNAPII motion along the DNA template, the experimental TS are mapped into Horizontal Visibility Graphs, allowing the evaluation of the efficiency–precision trade-off in terms of the structural properties of the corresponding graphs.
Special attention is devoted to transcriptional pauses, which appear as dynamical regimes where entropy production increases significantly, suggesting enhanced nonequilibrium dissipation during these events. Finally, we incorporate hydrodynamic coupling between the two beads of the optical tweezers setup as a potential mechanism of energy transfer within the experimental system, and assess its influence on the inferred thermodynamic and graph-theoretic observables.
This framework provides a quantitative link between transcription dynamics, nonequilibrium thermodynamics, and graph-theoretical descriptors of experimental time series.
