Eukaryotic transcriptional dynamics: from single molecules to cell populations

Abstract

Transcriptional regulation is achieved through combinatorial interactions between regulatory elements in the human genome and a vast range of factors that modulate the recruitment and activity of RNA polymerase. Experimental approaches for studying transcription in vivo now extend from single-molecule techniques to genome-wide measurements. Parallel to these developments is the need for testable quantitative and predictive models for understanding gene regulation. These conceptual models must also provide insight into the dynamics of transcription and the variability that is observed at the single-cell level. In this Review, we discuss recent results on transcriptional regulation and also the models those results engender. We show how a non-equilibrium description informs our view of transcription by explicitly considering time-and energy-dependence at the molecular level.

Analyzing Fluctuating Asymmetry with Geometric Morphometrics: Concepts, Methods, and Applications

“…Because developmental processes are not completely deterministic, however, random fluctuations in developmental processes can cause deviations from the target phenotype. Such differences can occur because of the stochasticity of molecular processes due to the low number of copies of DNA and many other molecular species within cells and can translate to variability across developing tissues and organs [323][324][325][326][327]. Because the two copies of a structure on the left and right side (or different numbers and arrangements of copies for complex symmetries) develop separately from each other, the random fluctuations of developmental processes affect each copy separately and are thus likely to produce deviations from the target phenotype that are different from copy to copy.…”

Stochastic Dynamics of Genetic Broadcasting Networks

“…The kinetic experiments of Bosisio et al [38] conducted on living cells have shown that such a hyperdynamic scenario could be a possibility where the residence time of NFκB molecules is largely maintained by the high on rates while at the same time the dissociation is seen to happen at a faster time scale that would be inferred from in vitro measurements. There can be additional biological complexities behind the large residence times of transcription factors [7,39] such as presence of affinity enhancing cofactors, sliding, intersegmental transfer, and chromatin dynamics just to name a few. Regardless of the detailed molecular mechanism of transcription factor DNA interaction, however, we see that in the absence of stripping whenever there is a large number of decoys there will be a large residence time, therefore posing a fundamental challenge for the full clearance of transcription factors.…”

“…In vivo, however, eukaryotic networks are generally far from equilibrium, and the switching between states of a gene involves many elaborate kinetically controlled steps such as conformational changes of chromatin, assembly of various protein cofactors into larger transcription complexes, RNA polymerase attachment, etc. [7][8][9]. The apparently simple concept of a gene switching in response to equilibrium binding is therefore a high level idealization which may not be universally applicable.…”

“…Single molecule chase assay experiments which directly measure the dissociation rates of transcription factors are physically inconsistent with the naive equilibrium models for the genetic switch [11]. A number of possibilities have been proposed to account for the departures from thermodynamic models [7,11]. Some have argued that energy consuming kinetic proofreading schemes could be employed by eukaryotic cells for attaining greater sensitivity [13] and specificity [14] of transcription factor binding relative to binding in equilibrium.…”

The nuclear envelope as a mechanostat: a central cog in the machinery of cell and tissue regulation?

“…Nuclear stretch has been implicated in locally regulating the spatial organization of chromatin, 14 a fact that may have potentially important consequences for transcriptional regulation. 15 In this sense, a stretch-regulated stiffening of the nuclear envelope represents a potentially central mechanical 'switch' with a degree of physical and temporal stability. Such switches represent key elements in whole cell regulation, including state-dependent regulation of cell fate.…”