Exchange dynamics and kinetic control of gene regulation complexes.

Modulation of noisy gene expression by general sequestration mechanisms

Sequestration of gene products through diverse mechanisms forms a fundamental layer of regulation in intracellular biochemical processes, including post-translational modification, promiscuous binding to genomic decoy sites, and partitioning into membraneless compartments formed through phase separation. Here, we develop a unified stochastic framework to quantify how such sequestration-type processes, when coupled to noisy gene expression, modulate cell-to-cell variation in protein levels. In this model, protein molecules reversibly switch between active (free) and inactive (sequestered) states, whose switching rates are arbitrary functions of the molecular counts. Using exact analytical calculations and the linear noise approximation, we derive expressions for the Fano factor of the active-protein level and identify fluctuation attenuation regimes in terms of the logarithmic sensitivities of the switching rates to protein abundances. We show that inactive-protein-dependent switching, of which genomic decoy binding is a natural example, can preserve Poisson-level fluctuations in the active-protein level under appropriate conditions. Enzymatic inactivation, a type of post-translational modification, emerges as a special case of active-protein-dependent sequestration, where greater responsiveness of the inactivation propensity attenuates active-protein fluctuations. In both decoy binding and enzymatic inactivation, protecting the inactive protein from decay lowers active-protein fluctuations. Finally, a noise-buffering regime associated with intracellular phase separation is recovered when the inactive-to-active switching rate depends inversely on the inactive-protein level. Together, the examples of genomic decoy binding, enzymatic inactivation, and intracellular phase separation suggest that noise buffering observed across diverse intracellular processes is rooted in a broader class of reversible sequestration mechanisms that attenuate protein-level fluctuations.

Characterization of RNA Structure Dynamics with Trans-Factors Using Single-Molecule Optical Tweezers.

Quantitative Model of Transcriptional Noise Regulation by mRNA Condensates

A fundamental biological process of transcription occurs in the cell nucleus, which is a complex medium that also contains multiple heterogeneous structures known as biomolecular condensates. Interestingly, some of these condensates contain mRNA molecules in addition to proteins, suggesting an important cellular role in transcription that is not yet well understood. In this work, we develop a minimal theoretical framework for quantitative investigation of the role of reversible mRNA condensation in transcription. Our discrete-state stochastic approach accounts for the most relevant processes, allowing us to explicitly evaluate the properties of the system and clarify the effects of condensation. Analytical calculations supported by computer simulations suggest that reversible mRNA condensation influences the transcription processes by maintaining a constant level of free mRNA in the nucleoplasm while lowering the degree of stochastic noise and increasing the robustness against external perturbations. Physicochemical arguments are presented to explain these observations. The proposed theoretical framework elucidates important microscopic aspects of transcription, providing a convenient quantitative tool for investigating complex biological phenomena. TOC Graphic

Integrative structural biology of protein-RNA interactions in four dimensions.

Recent developments in integrative modeling of protein-RNA complexes are reviewed, highlighting advances in in-cell, 4D and condensate structural biology, and how these approaches shape the understanding of RNP assembly, regulation, and function in physiologically relevant environments are discussed.

Current Challenges of Transcription Compartmentalization Research

Transcription is spatially organized in the nucleus, concentrating transcription factors, coactivators, and RNA polymerase II into dynamic, membraneless compartments. Such assemblies have been described in many ways, from small complexes of defined stoichiometry to membraneless biomolecular condensates. We argue that these are not competing descriptions but positions along a single continuum, and propose “transcriptional compartment” as an umbrella term for it. We then turn to the functional literature and ask what these compartments have been shown to do, and what they have not. The clearest evidence for a functional role of condensation may emerge in contexts where transcription must generate switch‐like responses, such as cell‐fate decisions, stress responses, environmental sensing, and disease. Much of the remaining biology, however, sits in the small, transient assemblies between the two extremes. These are the hardest to study, in part because they fall below the diffraction limit of light microscopy and because the interactions that drive their formation usually also carry out their function, so the two cannot be perturbed independently. We survey the experimental and computational toolkit available for this problem and outline the open methodological challenges that remain.

High-throughput methods for studying protein self-assembly.

Emerging high-throughput strategies to study protein condensation and aggregation at scale are reviewed, emphasizing what they truly measure, their limitations, and how the cross-talk among these complementary approaches can provide a more accurate and mechanistic mapping of sequence-to-assembly relationships.