Eukaryotic transcriptional dynamics: from single molecules to cell populations

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Abstract
Single-molecule and genome-wide studies of transcription reveal the importance of dynamics for understanding the mechanisms of gene regulation. A single gene can be regulated by dozens of factors interacting in a combinatorial manner. Observing all such interactions experimentally is still a daunting task, but computational models of transcription dynamics can provide insight into the underlying mechanisms. Molecular models of transcription often emphasize sequential, ordered recruitment, for example in the formation of a pre-initiation complex at a promoter. These sequential processes are best-described by non-equilibrium thermodynamics, in which kinetics and energy dependence are treated explicitly. Models based on non-equilibrium thermodynamics provide insight into a range of transcription phenomena, including nucleosome positioning, transcriptional bursting, and refractory periods during transcription.

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