Biomolecular Condensates in the Nucleus

Abstract

Nuclear processes such as DNA replication, transcription, and RNA processing each depend on the concerted action of many different protein and RNA molecules. How biomolecules with shared functions find their way to specific locations has been assumed to occur largely by diffusion-mediated collisions. Recent studies have shown that many nuclear processes occur within condensates that compartmentalize and concentrate the protein and RNA molecules required for each process, typically at specific genomic loci. These condensates have common features and emergent properties that provide the cell with regulatory capabilities beyond canonical molecular regulatory mechanisms. We describe here the shared features of nuclear condensates, the components that produce locus-specific condensates, elements of specificity, and the emerging understanding of mechanisms regulating these compartments.

Keywords: biomolecular condensates; chromatin regulation; condensate dysregulation; condensate regulation; gene regulation; nuclear organization.

Figure 1.. Biomolecular Condensates in the Nucleus.

(A) Structured illumination microscopy images of immunofluorescence for the protein indicated in parentheses in murine embryonic stem cells. Immunofluorescence for indicated protein is colored green, and signal from Hoechst, a DNA stain, is colored dark blue (unpublished results AD and RAY). Condensates are denoted by their name (e.g., superenhancers), their function (e.g., gene activity), and the protein that provides the immunofluorescent signal (e.g., MED1). (B) Cartoon depiction of how various nuclear condensates organize and are organized by different chromatin substrates. The grey line represents the chromatin fiber, green arrow designates active transcription start site, and red squiggled lines represent RNA. For a more complete list of nuclear condensates see Table 1. Abbreviations: CBX2, chromobox protein homolog 2; CTCF, CCCTC-binding factor; HP1α, heterochromatin protein 1α.

Figure 2.. Types of Multivalent Interactions Thought to Contribute to Formation of Biomolecular Condensates.

These types and associated references are SH2-Yph [105] (PDB: 1SPS), SIM-SUMO [83] (PDB: 2ASQ), bromodomain-acetyl-lysine [16] (PDB: 3JVK), chromodomain-methyllysine [15,88] (PDB: 3FDT), SH3-PRM [83,106] (PDB: 5QU2), PTB1-RNA [83,106] (PDB: 2AD9), pi-pi interactions [78,81,82,107], pi-cation interactions [78,108], electrostatic nteractions [79,80,109,110], and labile structures [–113] (PDB: 5W3N and 6BZM). Abbreviations:

Figure 3.. Features Common to Condensates: Compartmentalization, Selective Partitioning, and Concentration.

(A) Condensates compartmentalize functionally related factors. A cartoon depiction of three functionally related factors (colored) depicted homogenously mixed (left) or compartmentalized within a condensate (right). (B) Functionally related factors can be compartmentalized by selective partitioning, where the condensate physicochemical environment may favor or disfavor interactions with such factors. (C) The search space for a molecule can be reduced in two ways. First, for factors which partition into the condensate the search space is reduced to the condensate. The factor can diffuse in and out of the condensate, but will spend more time within. Second, for factors disfavored to partition into condensates that collectively take up a large volume of the nucleoplasm the search space is reduced to the remaining volume of the nucleus. (D) The concentration of the compartmentalized factors is higher inside the condensate than outside, but the absolute concentration of total cellular protein may not be higher inside the condensate than outside.

Figure 4.. Bifunctional Proteins Promote Condensate Formation at Specific Genomic Loci.

A) representation of a protein that contains one domain that binds specifically and with high affinity to a DNA, RNA, or protein partner (tethering domain) and another domain that engages in multivalent interactions (condensate-promoting domain). These bifunctional proteins can promote condensate formation when crowded by binding a sufficient number and density of sites in DNA (e.g., regulatory element), RNA (e.g., nascent RNA or long noncoding RNA), or protein (e.g., modified nucleosomal histones). Condensate-promoting domains are depicted here as IDRs, but can be any domain capable of weak multivalent interactions (Box 1). (B) With increasing numbers of binding sites on a polymer substrate, the bifunctional protein will become more locally crowded and can cros a threshold where the multivalent interaction domains promote condensate formation. Abbreviations: IDR, intrinsically disordered region; LCD,; PTM, post-translational modifications.

Figure 5.. Sources of Compositional Specificity in Nuclear Condensates.

This model depicts four types of contributions to compositional specificity: (1) nuclear trafficking; (2) conventional high-affinity structured interactions among proteins; (3) the ability of bifunctional proteins with a condensate-promoting domain to be crowded by binding to multiple sites on a DNA, RNA, or protein substrate; and (4) the various weak multivalent interactions.

Figure 6.. Some Examples of Nuclear Condensate Regulation.

Biomolecular condensates can be regulated by modifying the underlying multivalent interactions. (A) Reversible covalent modifications of chromatin. Nucleosomal histones can be reversibly modified, leading to changes in chromatin state. A model is depicted where chromatin alone can form a condensate (center, gray) mediated by internucleosomal contacts (dotted lines). Methylation of histones at histone H3K9 can recruit HP1α via chromodomain binding and produce a condensate rich in HP1α and other heterochromatin factors (left). In contrast, acetylation of histones at multiple lysine residues can reduce internucleosomal interactions, exposing TF-binding sites on DNA and recruit bromodomain-containing factors, leading to a condensate rich in components of the transcriptional machinery (right). B) Local RNA synthesis. A nascent transcript tethered to the elongating polymerase can be bound by many RNA processing enzymes, leading to a condensate rich in RNA processing machinery. Abbreviations: HP1α, heterochromatin protein 1α; TF, transcription factor.