The Complex Role of the 3D Chromatin Architecture in Gene Regulation
The Complex Role of the 3D Chromatin Architecture in Gene Regulation
The dynamic orchestration of gene expression requires the activity of cis-regulatory elements such as gene proximal promoters, distal enhancers, insulator elements, and silencer elements. Multiple studies have suggested that the extrusion of DNA loops, supported by a set of factors that include the CCCTC-binding factor (CTCF) protein and the cohesin complex, promotes the physical interaction of enhancers and promoters to induce gene expression. Importantly, these two factors also support the formation of topologically associating domains (TADs), which function as insulating elements that limit interactions between enhancers and constrain the regulatory influence of cis-regulatory elements within a single domain to ensure tight control over gene expression.
Fascinatingly, recent studies have revealed i) that the loss of CTCF or cohesin does not significantly influence gene expression even though the local chromatin landscape undergoes significant disruption (Hsieh et al.) and ii) that TADs do not completely constrain enhancer elements from regulating gene expression in other TADs (Gabriele et al. and Bintu et al.). Overall, these data provide evidence that the 3D chromatin architecture of the genome may play a much more complex role in transcriptional regulation than previously assumed.
In a recent preprint article, researchers from the laboratory of Bing Ren (University of California San Diego) sought to comprehensively investigate transcriptional regulation by distal enhancers after the disruption of the 3D chromatin architecture by the depletion of cohesin (Rad21)/CTCF in mouse embryonic stem cells (mESCs) under maintenance and differentiation-inducing conditions (Tastemel and Jussila et al.). The Epigenome Technologies blog now reports on how these fascinating results help to fill a knowledge gap and reveal how the interplay between the loop extrusion machinery and a histone-modifying complex underpins the context-dependent, gene-specific regulatory role of the 3D chromatin architecture.
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How Loop-extrusion Machinery and Histone Modifiers Mediate the Role of Chromatin Architecture
Tastemel and Jussila et al. first focused their single-molecule chromatin tracing experiments (Bintu et al.) and epigenome profiling on the Sox2 Huang et al.). Here, the acute depletion of cohesin/CTCF and the associated disruption of TAD formation helped to reveal the context-dependent role of 3D chromatin architecture in the enhancer-mediated regulation of Sox2 Sox2
As the context- and gene-specific nature of loop extrusion machinery and 3D chromatin architecture suggested the involvement of additional regulators of transcriptional insulators, the team next employed a genome-wide CRISPR knockout screen in mESCs to identify the underlying mechanisms that modulated the context-dependent, gene-specific effects of DNA loop extrusion controlled by cohesin/CTCF on enhancer-driven gene transcription; this approach highlighted factors that modulated the transcriptional insulation of TAD boundaries. Overall, they demonstrated that i) the MOZ/MORF histone acetyltransferase complex (comprising the Kat6b histone acetyltransferase, the PHD-finger protein Ing5, and the multivalent chromatin regulator Brpf1) antagonized the transcriptional insulation mediated by DNA loop-extrusion by cohesin/CTCF and ii) that the localization of MORF to the active and bivalent transcriptional start site-proximal regions of developmentally-associated genes facilitated the formation of long-range enhancer-promoter loops in mESCs. The MORF complex plays essential roles in many biological processes (Zu et al.), with mutations in the associated genes linked to multiple human developmental disorders and cancers. Interestingly, Kat6b depletion in mESCs prompted the loss of enhancer-promoter contacts at developmentally-associated genes and rescued the insulator/gene transcription defects observed in cells lacking Nipbl (a cohesin loader protein linked to Cornelia de Lange syndrome), an observation that may have clinical relevance.
Exploring the Context-Dependent, Gene-Specific Regulatory Role of 3D Chromatin Architecture: A Summary
Overall, the findings from this exciting preprint article describe how the complex interplay between DNA loop extrusion machinery and a histone-modifying complex underpins the context-dependent and gene-specific role of 3D chromatin architecture of the genome in establishing gene expression profiles during development and pathogenesis.
The profiling of multiple histone modifications combined with simultaneous RNA sequencing at the single-cell level may provide an even finer level of understanding in this case. Paired-Tag from Epigenome Technologies generates joint epigenetic and gene expression profiles at the single-cell resolution and detects histone modifications and RNA transcripts in individual nuclei with an efficiency comparable to single-nucleus RNA-seq/ChIP-seq assays. As such, applying Paired-Tag technology may enable giant leaps forward in understanding gene regulation and its implications for various diseases/disorders. This advance was first developed by a team guided by Bing Ren; now, Epigenome Technologies offers optimized Paired-Tag kits and services (and more!) to researchers in the epigenetics field under an exclusive license from the Ludwig Institute for Cancer Research.
For even more details regarding the context-dependent, gene-specific regulatory role of the 3D chromatin architecture, see bioRxiv, February 2025.