In a groundbreaking study recently published in Nature, researchers have unveiled intricate connections between the spatial organization of the human genome and its regulation of gene expression, offering unprecedented insight into how enhancer-promoter interactions shape transcriptional dynamics. This work meticulously integrates chromatin looping patterns with functional genomic data to decode the complex relationship between genome structure and cellular function across different cell types.
Fundamental to the study is the examination of chromatin loops linking distal enhancers to gene promoters within two human cell lines: H1 embryonic stem cells and HFFc6 fibroblasts. The research identified over fourteen thousand protein-coding genes in H1 cells and approximately twelve thousand in HFFc6 cells with detectable enhancer interactions. Crucially, the median distance of these enhancer-promoter interactions averaged around 173 kb, significantly shorter than loops mediated by the architectural protein CTCF, suggesting distinct mechanisms at play in enhancer-promoter communication.
A compelling correlation emerged between the number of enhancers interacting with a gene and its transcriptional activity level. Genes with more extensive enhancer contacts demonstrated higher expression levels, illustrating that enhancer connectivity serves as a critical determinant of transcriptional output. Furthermore, this connectivity closely mirrored transcriptional differences between the two cell types, indicating a dynamic rewiring of enhancer-promoter loops corresponding with cellular identity.
Expanding beyond transcriptional magnitude, the study probed gene expression breadth across diverse tissues, revealing that genes engaging numerous enhancers tended to be ubiquitously expressed across many tissues. Conversely, genes lacking such interactions displayed more tissue-specific expression profiles. Notably, a majority of housekeeping genes—genes fundamental to basic cellular functions and ubiquitously active—exhibited at least one enhancer interaction in both cell types. This finding challenges prior assumptions that housekeeping genes rely minimally on distal enhancers due to their strong promoters.
Delving deeper into housekeeping gene regulation, the researchers distinguished two classes based on their nuclear positioning relative to speckles, nuclear substructures implicated in RNA processing. Genes associated with speckles possessed more enhancer interactions, corroborating the notion that proximity to nuclear speckles facilitates complex enhancer-promoter communication. Intriguingly, enhancer-promoter loops involving housekeeping genes displayed remarkable cell-type specificity, with over 80% of loops being unique to either H1 or HFFc6 cells, underscoring the dynamism and plasticity of genome folding even among broadly expressed genes.
These observations stand in nuanced contrast with previous reports suggesting fewer functional enhancer links for housekeeping genes. The authors extended their analysis to encompass thirty-two additional human cell types, rigorously accounting for variable sequencing depth and loop detection sensitivity. This extensive survey reinforced the initial findings, showing genes with more numerous enhancer interactions tend to be expressed across multiple tissues and are enriched for housekeeping functions, highlighting the importance of considering high-confidence physical interactions.
Notably, the study emphasizes that detected enhancer-promoter loops represent physical contact events rather than guaranteed regulatory functions. The inherent redundancy among multiple enhancers complicates functional deconstruction, as perturbation experiments targeting single enhancers may underestimate the collective regulatory impact. Future investigations will be essential to unravel the coordination mechanisms enabling multiple enhancers to collaboratively modulate gene expression robustness in diverse cellular contexts.
Turning attention to genome architecture within repressive nuclear compartments, the research probed lamina-associated domains (LADs), regions traditionally regarded as transcriptionally silenced. Remarkably, genes located in LADs can still establish contacts with distal enhancers, correlating with active gene expression despite the repressive milieu. Detailed examination using lamin B1 DamID-seq showed that both promoters and their associated enhancers in these regions reside in localized domains enriched for active chromatin marks but depleted of lamina association, suggesting that chromatin looping enables targeted escape from nuclear lamina repression to permit gene activation.
The integration of various hierarchical structural features of the genome—including A/B compartments, chromatin interaction neighborhoods (SPIN states), topologically associating domains (TADs), subTADs, and loops—illuminated the nuanced interplay between genome folding and functional domains. The analysis demonstrated that SPIN states and A/B compartments form large structural scaffolds of hundreds of kilobases to megabases, encompassing distinct replication timing profiles and transcriptional activity patterns.
SPIN states embedded within the larger compartments specify more refined functional neighborhoods, with nuclear speckle-associated and interior active states enriched for highly transcribed genes and early DNA replication, while lamina-proximal states correlate with late replication and transcriptional repression. This multi-scale chromatin folding hierarchy illustrates that while compartments set the broad functional landscape, SPIN states demarcate localized chromatin environments with specific gene regulatory consequences.
Further stratifying TADs and subTADs by their structural features revealed that these domains typically reside entirely within a single SPIN state or compartment, indicating hierarchical nesting of spatial organization. However, unlike compartments or SPIN states, TADs largely reflect the replication timing characteristics of their encompassing environment without creating distinct replication domains intrinsically. Intriguingly, dot-shaped TAD boundaries are enriched for early replication initiation zones, linking cohesin-mediated chromatin folding to replication timing regulation and emphasizing the functional diversity within TAD architecture.
Collectively, these findings affirm that different scales of genome folding play specialized roles in coordinating replication and transcription. Large compartments and SPIN states mirror broad replication timing and transcription patterns, while finer structures like TADs localize gene expression regulation, especially at domain boundaries enriched for active transcriptional units. The study propels our understanding of the 4D nucleome, elucidating how the dynamic three-dimensional chromatin landscape integrates gene regulation, nuclear architecture, and DNA replication timing.
This comprehensive exploration into the human 4D nucleome bridges functional genomics with spatial genome organization, offering a fundamental framework for future studies investigating gene regulation mechanisms and their perturbations in development and disease. By elucidating how enhancer-promoter looping varies between cell types and modulates housekeeping gene expression, the work challenges existing paradigms and deepens appreciation of genome complexity in cellular identity. Understanding these architectural principles may pave the way to targeted genomic interventions and novel therapeutics that exploit chromatin folding dynamics.
Subject of Research:
Spatial organization of the human genome, enhancer-promoter interactions, chromatin loops, gene regulation, and nuclear architecture.
Article Title:
An integrated view of the structure and function of the human 4D nucleome.
Article References:
Dekker, J., Oksuz, B.A., Zhang, Y. et al. An integrated view of the structure and function of the human 4D nucleome. Nature (2025). https://doi.org/10.1038/s41586-025-09890-3
Image Credits: AI Generated
DOI: https://doi.org/10.1038/s41586-025-09890-3
Keywords:
4D nucleome, enhancer-promoter loops, chromatin structure, gene regulation, housekeeping genes, nuclear speckles, lamina-associated domains, TADs, SPIN states, replication timing, genome architecture
Tags: chromatin looping patternsdynamic rewiring of gene regulationenhancer connectivity and transcriptionenhancer-promoter interactionsgene expression regulationH1 embryonic stem cellsHFFc6 fibroblastshuman genome structureNature study on nucleomeprotein-coding genes in humansspatial organization of the genometranscriptional dynamics
