Nanoscale nuclear environments, fine-scale 3D genome organization and transcription regulation

Abstract

Decades of in vitro biochemical reconstitution, genetics and structural biology studies have established a vast knowledge base on the molecular mechanisms of chromatin regulation and transcription. A remaining challenge is to understand how these intricate biochemical systems operate in the context of the 3D genome organization and in the crowded and compartmentalized nuclear milieu. Here we review recent progress in this area based on high-resolution imaging approaches.

Figure 1.

Possible functional roles of focal RF accumulation at transcription sites. (A) RF clustering creates regions of high local concentration and by mass-action accelerates rate-limiting steps in the transcription cycle [17*]. (B) RF clustering modulates the target search processes of transcription factors and chromatin regulators, possibly by transient trapping in local zones [23**]. (C) Nano-scale environments of clustered RFs activate multiple embedded promoters [35**], facilitating gene co-regulation.

Figure 2.

Enhancer cluster “super-clusters” [35**]. Multiple distal enhancer clusters, from an extended genomic locus, are in the proximity (~100–200 nm) of a target gene. The multiple DNA and chromatin binding sites brought into close proximity for a scaffold for formation of RF clusters at active gene loci.

Figure 3.

Models for RF cluster formation at single gene loci (top row) and their predictions for recruitment of factors (bottom row). (A) Specific molecular recognition model. Clustering of RFs reflects multiple RF molecules recognizing multiple specific DNA and/or chromatin binding sites. Binding sites might be clustered in 1D and/or in 3D. Bottom panel in (A): molecules with IDR deletions can still incorporate into RF clusters but mutations or deletions of specific binding domains diminish cluster incorporation ability. (B and C) Models that depend on IDR-IDR interactions. (B) Sub-saturation clustering model. The system is globally below the saturating concentration, so droplet formation is thermodynamically unfavorable. However, binding of multiple RF molecules to multiple specific sites at the enhancer increases the local concentration above saturation, leading to clustering of additional RF molecules due to IDR-IDR interactions [15, 80]. (C) Droplet formation model [7, 11]. The system is above saturation and droplet formation is thermodynamically favorable. A large number of RF molecules accumulate at the enhancer, giving rise to a structure that exhibits properties of macroscopic droplets – interfacial tension and clear separation between bulk phases (inside and outside the droplet). Bottom panels in (B and C): RF molecules with mutations or deletions of specific binding domains are readily incorporated into RF clusters.