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Nuclear compartmentalization as a mechanism of quantitative control of gene expression

Abstract

Gene regulation requires the dynamic coordination of hundreds of regulatory factors at precise genomic and RNA targets. Although many regulatory factors have specific affinity for their nucleic acid targets, molecular diffusion and affinity models alone cannot explain many of the quantitative features of gene regulation in the nucleus. One emerging explanation for these quantitative properties is that DNA, RNA and proteins organize within precise, 3D compartments in the nucleus to concentrate groups of functionally related molecules. Recently, nucleic acids and proteins involved in many important nuclear processes have been shown to engage in cooperative interactions, which lead to the formation of condensates that partition the nucleus. In this Review, we discuss an emerging perspective of gene regulation, which moves away from classic models of stoichiometric interactions towards an understanding of how spatial compartmentalization can lead to non-stoichiometric molecular interactions and non-linear regulatory behaviours. We describe key mechanisms of nuclear compartment formation, including emerging roles for non-coding RNAs in facilitating their formation, and discuss the functional role of nuclear compartments in transcription regulation, co-transcriptional and post-transcriptional RNA processing, and higher-order chromatin regulation. More generally, we discuss how compartmentalization may explain important quantitative aspects of gene regulation.

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Fig. 1: Mechanisms of nuclear compartments formation.
Fig. 2: Spatially constrained non-coding RNAs can drive compartmentalization in the nucleus.
Fig. 3: Enhancers, promoters and transcription factors can form condensates that may facilitate rapid target search in the genome.
Fig. 4: Compartmentalization and chromatin regulation.
Fig. 5: Spatial and kinetic coupling of RNA polymerase II transcription and mRNA splicing.
Fig. 6: Involvement of nuclear bodies in RNA processing.

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Acknowledgements

The authors thank members of the Guttman laboratory, especially M. Strehle, J. Jachowicz, S. Quinodoz and I. Goronzy for helpful comments and discussions, I.-M. Strazhnik for figures and S. Hiley for editing. P.B. is supported by the University of California, Los Angeles (UCLA)-Caltech Medical Scientist Training Program (MSTP), National Institutes of Health (NIH) F30CA247447 and a Chen Graduate Innovator Grant. M.G. is a New York Stem Cell Foundation Robertson Investigator and an investigator at the Heritage Medical Research Institute. Research in the Guttman laboratory is funded by the NIH 4DN programme, an NIH Director’s Transformative R01 Award, the Chan-Zuckerberg Initiative and funds from Caltech.

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Glossary

Affinity

The strength of a non-covalent biochemical interaction, defined as the ratio of the association and dissociation rates.

Diffusion and affinity models

Models describing how a molecule (such as a transcription factor) proceeding on a random walk through the nucleus samples many possible binding partners until it finds its high-affinity cognate target site.

Nuclear territories

A catch-all term for 3D regions contained within the nucleus.

Compartments

Nuclear territories enriched in specific DNA, RNA and/or protein molecules.

Mediator complex

A protein complex that facilitates enhancer–promoter interactions, RNA polymerase II (Pol II) loading and transcription initiation.

Stoichiometric interaction

Biochemical interaction that occurs with defined ratios of components, generally with high affinity and specificity, including in protein complexes or the binding of a transcription factor to its DNA motif.

Non-linear regulatory behaviours

Responses to alteration in the reaction rate or efficiency that exceed those expected under a linear model for the underlying changes in the amounts of reactants or catalysts.

Phase transitions

The biophysical process that leads to phase separation, referring to a discontinuous change in the thermodynamic equilibrium state of a system in response to a change in a parameter such as temperature, pressure or molecular concentration.

Multivalent interactions

Molecular associations between multiple binding sites on the interacting molecules; can result in variable stoichiometric ratios.

Intrinsically disordered regions

(IDRs). Protein regions that do not have a single preferred structural conformation.

Biomolecular condensates

Concentration-dependent assemblies of molecules of variable stoichiometry, usually driven by multivalent and cooperative interactions that can form with or without phase separation.

Avidity

(Also known as ‘functional affinity’). The collective strength of multiple non-covalent molecular interactions. Avidity represents the overall force conferred by multiple affinities in concert, which exceeds the sum of the strength of those interactions.

Phase separation

Thermodynamically driven partitioning of a homogeneous mixture into locally distinct chemical sub-mixtures (phases) with distinct properties.

Homotypic interactions

Interactions occurring between two or more copies of the same type of molecule.

Heterotypic interactions

Interactions occurring between at least two molecules of different types.

Valency

The number of non-covalent interactions with other molecules that a single molecule or domain can support.

Liquid–liquid phase separation

(LLPS). A specific form of phase separation defined by the formation of a liquid compartment within a larger liquid environment.

Granules

Small (<1 µm) condensates that generally have a simple composition compared with the larger nuclear bodies.

Diffusible

Refers to molecules that proceed on a random walk throughout the volume that contains them.

Constrained molecules

Molecules that proceed on a random walk preferentially within a sub-volume of their overall environment, often owing to having high affinity to other molecules in that sub-volume.

Bodies

In the nucleus, large (≥1 µm), functionally distinct territories, often involved in molecular biogenesis, such as the nucleolus (ribosome biogenesis) and Cajal bodies (biogenesis of small nuclear RNAs (snRNAs)).

Transcriptional condensates

Assemblies of general transcription factors and Mediator complexes around enhancers and promoters that facilitate transcription activation.

Facilitated diffusion

In the context of compartmentalization, the process by which compartments restrict the random walks of diffusible molecules to a smaller volume. For example, constraining the diffusion of a transcription factor to a small nuclear volume around its target.

Super-stoichiometric

Refers to interactions that occur without fixed ratios of components and can exceed the binding capacity of any individual molecule, often involving high-avidity, multivalent interactions.

X-inactivation centre

A region on the X chromosome containing X-inactive specific transcript (XIST) and its cis-regulators; necessary and sufficient for initiation of X-chromosome inactivation (XCI) and protected from it to allow continual expression of XIST.

Epigenetic memory

The set of DNA and histone modifications that are heritable either from parents to offspring or from a mother cell to daughter cells.

Splicing condensates

High concentrations of splicing factors localized around nascent RNA transcripts, often in proximity to (but distinct from) nuclear speckles.

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Bhat, P., Honson, D. & Guttman, M. Nuclear compartmentalization as a mechanism of quantitative control of gene expression. Nat Rev Mol Cell Biol 22, 653–670 (2021). https://doi.org/10.1038/s41580-021-00387-1

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