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Topologically associating domain

A topologically associating domain (TAD) is a megabase-scale genomic region characterized by frequent chromatin interactions within its boundaries and reduced interactions with adjacent regions, serving as a fundamental unit of three-dimensional genome organization in eukaryotic cells.^[1] These domains, first identified in mammalian genomes through high-throughput chromosome conformation capture methods like Hi-C, typically range from hundreds of kilobases to several megabases in size and are conserved across cell types and species, with boundaries often enriched for architectural proteins such as CTCF and active chromatin marks.^[1] TADs play a critical role in gene regulation by confining enhancer-promoter interactions, thereby insulating regulatory elements and preventing ectopic gene activation that could lead to developmental abnormalities or diseases.^[2] TADs were discovered in 2012 using Hi-C data from human and mouse embryonic stem cells, revealing their stability across differentiation states and evolutionary conservation from fruit flies to mammals.^[1] In mammals, TAD formation is primarily driven by the loop extrusion model, where cohesin complexes extrude chromatin loops until halted by convergent CTCF binding sites at domain boundaries, creating insulated compartments that maintain proper spatial proximity of cis-regulatory elements.^[2] This organization contrasts with mechanisms in other species, such as Drosophila, where boundaries are associated with insulator proteins like BEAF-32 and promoter-proximal active genes rather than CTCF.^[2] Disruptions to TAD structure, such as boundary deletions or mutations in boundary-associated factors, can cause enhancer hijacking and misregulated gene expression, contributing to congenital disorders like limb malformations and cancers.^[3] Despite their importance, TADs exhibit hierarchical nesting and variability in resolution depending on experimental techniques, with sub-TADs representing finer-scale loops within larger domains.^[4] Ongoing research continues to elucidate how TADs integrate with broader chromatin compartments and respond to dynamic cellular processes like replication and transcription.^[5]

Definition and Background

Core Definition

A topologically associating domain (TAD) is a self-interacting chromatin region within the genome, characterized by significantly higher frequencies of chromatin interactions among loci within the domain compared to those between the domain and adjacent regions.^[1] These domains typically span 100 kilobases (kb) to 1 megabase (Mb) in size, with a median length of approximately 880 kb in mammals, forming fundamental units of higher-order chromatin organization.^[2] TADs are identified through methods like Hi-C, which capture pairwise chromatin contacts genome-wide.^[1] TADs play a crucial role in the three-dimensional (3D) folding of the genome by compartmentalizing chromatin into insulated neighborhoods, thereby restricting long-range regulatory interactions to within domain boundaries and preventing inappropriate cross-talk between adjacent regions.^[2] This insulation helps maintain stable and cell-type-invariant gene expression patterns by ensuring that enhancers and promoters interact preferentially within their local TAD environment.^[1] Such organization is evolutionarily conserved across species, underscoring TADs as an inherent feature of eukaryotic genome architecture.^[2] The edges of TADs are defined by boundary elements that act as barriers to chromatin looping, prominently featuring binding sites for the insulator protein CTCF and the structural maintenance of chromosomes protein complex cohesin.^[2] In mammals, 75-95% of TAD boundaries are enriched with CTCF motifs, often oriented convergently to facilitate loop anchoring, while cohesin mediates the extrusion process that shapes these domains.^[2] These proteins collectively enforce domain integrity, with disruptions leading to altered regulatory landscapes.^[1] In Hi-C contact maps, TADs are visualized as square-like blocks of elevated interaction signals along the diagonal, reflecting the enriched intra-domain contacts and sharp drops at boundaries, sometimes accompanied by "corner peaks" indicative of anchored loops.^[2]

Historical Discovery

The concept of topologically associating domains (TADs) emerged from early analyses of chromatin conformation data, with initial evidence from Hi-C datasets generated in Drosophila melanogaster in 2012, which revealed patterns of local chromatin clustering that resembled self-interacting domains, though not yet formally identified as TADs. This observation laid the groundwork for subsequent formalization in mammalian systems.^[6] The definitive identification of TADs occurred in 2012 through two landmark studies that applied Hi-C to human and mouse genomes. In one study, Dixon et al. analyzed Hi-C data from multiple mouse cell types and identified discrete, megabase-scale domains where chromatin interactions were enriched within the domain and insulated from neighboring regions, terming them "topological domains" or TADs; these structures were highly conserved between human and mouse genomes.^[1] Concurrently, another group examined the mouse X chromosome inactivation center using Hi-C and observed similar self-interacting domains, confirming their presence and stability across different cell types and developmental stages.^[1] These findings established TADs as a fundamental unit of 3D genome organization in mammals. Building on these discoveries, studies from 2015 to 2017 extended TAD-like structures to non-metazoan species, highlighting their evolutionary breadth but also revealing structural diversity. In budding yeast (Saccharomyces cerevisiae), Hi-C and chromatin interaction analyses identified TAD-like domains associated with specific histone modifications and replication timing, though smaller and more variable than in mammals.^[7] Similarly, in the plant Arabidopsis thaliana, genome-wide Hi-C mapping uncovered TAD-like regions characterized by insulated interactions, but these were less prominent and lacked the sharp boundaries seen in animals, suggesting species-specific adaptations.^[8] Early post-discovery research sparked debates on the universality of TADs, particularly whether they represented invariant genome features or varied by cell type and species. Initial mammalian studies suggested broad conservation, but emerging data from diverse organisms raised questions about their presence and stability across contexts. These debates were largely resolved by 2015 through multi-species comparisons and high-resolution Hi-C profiling across cell lineages, which demonstrated that TAD boundaries are predominantly cell-type invariant in mammals while exhibiting nuanced variations in other species, affirming TADs as a conserved yet flexible architectural principle.^[9]

Methods for Identification

Experimental Techniques

The primary experimental technique for identifying topologically associating domains (TADs) is Hi-C, a genome-wide chromatin conformation capture method that quantifies pairwise chromatin interactions by generating contact frequency matrices.^[10] In the Hi-C protocol, cells are first fixed with formaldehyde to cross-link interacting chromatin regions, followed by chromatin fragmentation via restriction enzyme digestion, typically using enzymes like HindIII or DpnII that produce compatible overhangs.^[10] The digested ends are then filled in with biotinylated nucleotides, proximity-ligated to join interacting fragments, purified, and subjected to high-throughput sequencing, yielding millions of read pairs that map to interaction frequencies across the genome.^[10] These data are normalized and visualized as heatmaps, where TADs appear as square-like regions of elevated intra-domain contacts separated by boundaries, often enriched for CTCF binding sites.^[11] To reduce noise from random ligations and improve resolution, the in situ Hi-C variant performs proximity ligation directly within intact nuclei, minimizing uninformative inter-molecular joins and enabling kilobase-scale mapping of chromatin loops and domains.^[11] This approach, which requires 10-100 million cells, has been optimized in protocols like the improved Hi-C method described in 2021, incorporating enhanced biotinylation efficiency and multiplexed sequencing to achieve higher signal-to-noise ratios for TAD boundary detection.^[12] Single-cell Hi-C extends these methods to individual cells, revealing cell-to-cell variability in TAD structures that is averaged out in bulk assays; it was first introduced in 2013 using combinatorial indexing to barcode and pool single-cell libraries, though early versions yielded sparse data with only thousands of contacts per cell.^[13] Advances from 2023 to 2025 have boosted resolution through droplet-based encapsulation and improved ligation efficiencies, enabling the capture of over 10,000 contacts per cell and the identification of cell-type-specific TADs in heterogeneous populations like developing tissues.^[14] For instance, single-nucleus Hi-C adaptations now facilitate tissue-specific TAD mapping by isolating nuclei from frozen samples, preserving architecture in non-dissociable tissues such as brain or tumors.^[15] Complementary techniques like ChIA-PET provide targeted insights into protein-mediated chromatin interactions relevant to TADs by immunocapturing specific factors (e.g., RNA polymerase II or CTCF) before paired-end tag sequencing, identifying enhancer-promoter loops within domains at base-pair resolution. For validation of candidate TAD boundaries or interactions, 4C (circular chromosome conformation capture) focuses on genome-wide contacts from a single viewpoint via inverse PCR, while 5C (carbon copy) scales this to multiplexed ligation-mediated amplification for hundreds of predefined anchors, offering higher throughput for confirming domain insulation in specific loci.

Computational Tools and Databases

The identification of topologically associating domains (TADs) from Hi-C data relies on computational algorithms that detect regions of enriched intra-domain interactions and depleted inter-domain contacts within contact frequency matrices. One seminal method is the Arrowhead algorithm, introduced in 2014 as part of the Juicer software suite, which transforms Hi-C matrices to highlight diagonal "arrowhead" patterns indicative of TAD boundaries through a kernel-based filtering approach that emphasizes corner-like features in the interaction matrix.^[11] This algorithm efficiently processes high-resolution Hi-C data to call TADs by identifying sharp transitions in contact frequencies, enabling the annotation of thousands of domains across the genome. A key metric underlying many TAD callers, including Arrowhead and subsequent tools, is the insulation score, which quantifies boundary strength by computing the inverse of the interaction frequency crossing a potential boundary within a sliding window along the matrix diagonal. Specifically, for a genomic position i and window size w, the insulation score IS(i) is defined as:

IS(i) = \left( \sum_{u=1}^{w} \sum_{d=1}^{w} M(i - u, i + d) \right)^{-1}

where M represents the normalized Hi-C contact matrix; lower scores indicate stronger insulation and thus likely TAD boundaries.^[16] This score provides a robust, resolution-agnostic measure that has been integrated into various pipelines for hierarchical TAD detection. Recent advancements incorporate artificial intelligence to enhance TAD prediction accuracy, particularly for sparse or noisy Hi-C datasets. The deepTAD tool, released in 2025, employs a hybrid convolutional neural network (CNN) and transformer architecture to extract spatial features from Hi-C submatrices, predicting TAD boundaries with improved sensitivity over traditional methods by capturing long-range dependencies in interaction patterns.^[17] Similarly, HTAD, developed in 2024, integrates human-in-the-loop labeling with supervised machine learning, allowing iterative refinement of TAD calls through expert annotation of ambiguous regions, which boosts precision in complex genomic contexts like nested domains.^[18] Public databases facilitate access to precomputed TAD annotations and Hi-C datasets for comparative analyses. The 3D Genome Browser serves as an interactive platform hosting integrated Hi-C data from multiple species and cell types, enabling users to visualize TAD structures alongside epigenetic tracks and download boundary coordinates for custom analyses.^[19] TADKB, a dedicated knowledge base, curates TAD annotations from diverse studies, classifying domains by family and providing 2D/3D visualizations enriched with functional metadata such as gene content and regulatory elements.^[20] Benchmarking efforts in 2024 have evaluated hierarchical TAD detection tools across varied Hi-C resolutions and species, revealing that methods like SuperTAD and TADbit excel in capturing nested structures while maintaining low false positive rates, with operational guidelines emphasizing preprocessing steps like matrix normalization for optimal performance.^[21]

Mechanisms of Formation

Molecular Mechanisms

Topologically associating domains (TADs) are primarily formed through the loop extrusion model, in which the cohesin complex actively reels in DNA to generate loops that grow until they encounter architectural barriers, such as CTCF-bound sites. In this process, cohesin, a ring-shaped ATPase, loads onto chromatin and extrudes loops by translocating along the DNA in an ATP-dependent manner, effectively pulling distant genomic regions closer together. Extrusion continues bidirectionally until the growing loop is halted by convergent CTCF motifs at domain boundaries, where CTCF's zinc-finger domains interact with cohesin to anchor and stabilize the structure, thereby defining TAD insulation. This model, supported by polymer simulations and Hi-C data, explains the observed enrichment of convergent CTCF sites at TAD borders and the loss of domain organization upon cohesin or CTCF depletion.^[22] Alternative hypotheses invoke liquid-liquid phase separation (LLPS) to contribute to TAD organization, particularly at interfaces between TADs and larger chromatin compartments. In this framework, heterochromatic proteins like HP1 bind to H3K9me3-marked nucleosomes, promoting multivalent interactions that drive phase-separated condensates, which compact B compartments and enhance their segregation from euchromatic A compartments. Similarly, Polycomb-group proteins, through their PRC1 and PRC2 complexes, undergo LLPS via intrinsically disordered regions, forming dense foci that reinforce H3K27me3-rich domains and potentially delineate TAD edges by modulating chromatin solubility and interactions. These phase-separated states are thought to complement loop extrusion by providing biophysical stability to compartment-TAD transitions, as evidenced by imaging and biochemical assays showing condensate formation correlates with reduced inter-compartment contacts.^[23]^[24] TAD architecture undergoes dynamic remodeling across the cell cycle, driven by regulated cohesin loading and unloading. Cohesin primarily loads onto chromatin during S-phase, facilitated by the loader complex NIPBL-MAU2, which establishes initial loops and supports replication fork progression while promoting sister chromatid cohesion. As cells progress through G2 and mitosis, cohesin is progressively released via the WAPL and PDS5 regulators, leading to TAD dissolution and global chromatin decompaction, only to be reloaded in the subsequent S-phase for interphase reorganization. This cyclic process ensures TADs are re-established post-mitosis, with Hi-C profiles revealing heightened loop dynamics in G1 and S phases compared to mitotic states.^[25]^[26] Recent studies from 2023 to 2025 have elucidated how CTCF motif orientation and binding affinity modulate boundary strength, influencing TAD insulation robustness. Convergent CTCF motifs, where upstream and downstream sites face each other, exhibit stronger boundary activity by more effectively arresting cohesin extrusion, as quantified by increased insulation scores in Hi-C maps upon motif inversion or weakening. Multi-feature clustering of CTCF sites—integrating binding strength, spacing, and orientation—further enhances boundary resilience, with clustered, high-affinity convergent pairs resisting disruption better than isolated sites, as demonstrated in genome editing experiments. Additionally, boundary width emerges as a key determinant, with extended CTCF clusters forming broader, more stable insulators that maintain TAD separation even under cohesin perturbations. These findings underscore the tunable nature of TAD boundaries, where motif properties dictate extrusion arrest efficiency and overall domain integrity.^[27]00126-6)^[28]

Key Regulatory Elements

CTCF (CCCTC-binding factor) is a multifunctional zinc-finger transcription factor containing 11 zinc-finger motifs that recognizes specific DNA sequences, predominantly at TAD boundaries where it binds in a convergent, orientation-specific manner to anchor chromatin loops and enforce insulation. This binding pattern, characterized by motifs facing each other across interacting regions, stabilizes TAD structures by blocking inappropriate cross-domain contacts. The cohesin complex, composed of core subunits SMC1, SMC3, RAD21 (also known as SCC1), and the kleisin subunit, plays a central role in TAD formation through its loop extrusion activity, where it reels in DNA to create loops that are halted at CTCF-bound boundaries.^[22] Cohesin loading and processive extrusion dynamically shape TAD interiors, with its depletion leading to TAD dissolution and loss of domain-specific interactions. Additional factors contribute to boundary reinforcement and enhancer-mediated stability within TADs. YY1, a ubiquitously expressed zinc-finger transcription factor, co-localizes with CTCF at many TAD borders, facilitating enhancer-promoter looping and boundary strength independently of CTCF in some contexts.^[29] Similarly, ZNF143 (zinc-finger protein 143) binds near CTCF sites to mediate promoter-enhancer loops essential for gene activation and reinforces TAD insulation by stabilizing chromatin architecture.^[30] Architectural proteins such as LDB1 (LIM domain-binding protein 1) operate within TADs to organize multi-enhancer networks, promoting spatial connectivity at enhancers without direct DNA binding but through interactions with tissue-specific transcription factors.^[31] Experimental deletions of TAD boundaries, particularly those involving CTCF sites, have demonstrated their critical role in preventing ectopic interactions. In 2023 and 2024 studies using genome editing in mice, removal of boundary elements at loci such as Kit led to TAD fusion, ectopic activation of neighboring genes like Kdr in mast cells and melanocytes, and tissue-specific misregulation due to loss of insulation.^[32] These findings underscore how boundary disruption compromises TAD integrity, allowing aberrant long-range contacts that alter chromatin folding.^[3]

Structural Properties

Evolutionary Conservation

Topologically associating domains (TADs) exhibit high evolutionary conservation within mammals, with studies showing substantial overlap in their positions and boundaries across species. For instance, comparisons between human and mouse genomes reveal that approximately 54% of human TAD boundaries are shared, reflecting preserved synteny and structural integrity over ~80 million years of divergence.^[33] This conservation extends to other mammals, where TAD structures maintain functional regulatory landscapes despite sequence variations.^[3] Recent analyses in 2025 have further elucidated TAD evolution across vertebrates by integrating Hi-C data from multiple species. One study examining 12 vertebrate genomes found that TAD boundaries are frequently anchored to conserved genes, suggesting stabilizing selection preserves these domains for regulatory consistency.^[34] In contrast, TAD conservation diminishes in invertebrates, where domain structures are less prevalent and more variable compared to vertebrates. TADs are notably absent in yeast, a unicellular eukaryote lacking complex chromatin looping, but they emerge prominently in metazoans, coinciding with the evolution of multicellularity and sophisticated gene regulation.^[2] In organisms like Drosophila, TAD-like domains exist but show reduced boundary fidelity relative to mammals, indicating a progressive refinement along the metazoan lineage. TADs also contribute to evolutionary innovation through structural variants that generate neo-TADs, novel domains formed by rearrangements such as inversions or duplications. These neo-TADs can rewire enhancer-promoter interactions, fostering adaptive regulatory changes without disrupting broader genomic stability, as observed in comparative analyses of mammalian lineages.^[35] Such mechanisms underscore how TAD plasticity enables evolutionary diversification while conserving essential boundaries, often involving factors like CTCF for anchoring.^[36]

Interactions with Gene Regulation

Topologically associating domains (TADs) play a crucial role in insulating gene regulatory elements, thereby preventing inappropriate enhancer-promoter interactions across domain boundaries. This insulation mechanism restricts enhancers from hijacking promoters in adjacent TADs, which helps maintain tissue-specific gene expression patterns by limiting ectopic activation. For instance, disruptions to TAD boundaries, such as those observed in chromosomal rearrangements, can lead to enhancer hijacking, where enhancers from one TAD aberrantly activate genes in another, resulting in misregulated expression. Within TADs, chromatin looping facilitates specific interactions between promoters and regulatory elements like super-enhancers, primarily mediated by the cohesin complex and CTCF protein. Cohesin extrudes chromatin loops until arrested by convergently oriented CTCF binding sites at TAD boundaries, thereby promoting intra-domain contacts that enhance gene activation. Super-enhancers, clusters of enhancers often enriched with transcription factors and mediators, preferentially loop to target promoters within the same TAD, amplifying transcriptional output in a cell-type-specific manner. Recent studies from 2023 have highlighted the role of tissue-specific TADs in wiring enhancers to their cognate genes, revealing dynamic reconfiguration of domain structures across cell types to support precise regulatory interactions. These investigations demonstrate that variations in TAD insulation strength correlate with tissue-specific enhancer-gene contacts, enabling adaptive gene expression programs without cross-talk between domains.^[37] Quantitative analyses of chromatin interactions within TADs show that contact probabilities decay following a power-law relationship, approximated as P(s) \sim s^{-1}, where s is the genomic distance. This decay pattern reflects the constrained polymer-like behavior of chromatin inside TADs, contrasting with steeper declines across boundaries and underscoring how TAD architecture optimizes local regulatory efficiency.

Relations to Other Chromatin Domains

Topologically associating domains (TADs) are typically nested within the larger-scale A and B chromatin compartments, which represent broad organizational units of the genome identified through chromosome conformation capture (3C)-derived methods like Hi-C. The A compartments, associated with euchromatin, are enriched for open chromatin structures and active histone modifications such as H3K4me3 and H3K27ac, facilitating higher levels of transcriptional activity and gene expression. In contrast, B compartments correspond to heterochromatin regions with more compact folding and repressive marks like H3K9me3. This hierarchical embedding positions TADs as subcompartments that respect and subdivide these larger patterns, with most TADs residing entirely within a single compartment type. Recent comprehensive benchmarking of computational tools has illuminated the hierarchical nature of TADs, revealing nested sub-TADs (often tens to hundreds of kilobases) within canonical TADs and larger meta-TADs extending up to several megabases. These nested domains, also termed domain-within-domain structures, emerge dynamically during cell cycle phases and differentiation, influenced by factors like CTCF and cohesin binding at boundaries. Such organization underscores TADs' role in multi-scale chromatin folding, where inner levels correlate with finer regulatory control and outer levels align with broader compartmental features.^[21] TADs differ from chromatin loops in scale, stability, and function: TADs form stable, self-interacting regions spanning ~100 kb to 1 Mb that insulate chromosomal interactions across cell types, whereas loops are more dynamic, shorter-range contacts (typically 10-500 kb) mediated by cohesin extrusion between convergent CTCF sites, often linking enhancers to promoters within a TAD. While loops contribute to fine-tuned regulatory specificity inside TADs, the domains themselves provide a persistent scaffold that limits ectopic contacts. TAD boundaries often align with A/B compartment transitions, particularly at the A-side edges, reinforcing the interplay between these structural layers.^[2]^[5]

Biological Functions

Role in Gene Expression

Topologically associating domains (TADs) serve as regulatory hubs that organize chromatin to facilitate coordinated gene expression within their boundaries. By confining cis-regulatory elements, such as enhancers, to interact preferentially with promoters of genes in the same domain, TADs promote the co-regulation of functionally related genes, forming stable regulatory landscapes that integrate developmental and environmental signals.^[38] For instance, genes within a TAD often exhibit synchronized expression patterns, as seen in the Hox gene clusters where TAD insulation ensures precise collinear activation during embryogenesis.^[39] This compartmentalization restricts ectopic interactions, thereby enhancing the specificity and efficiency of transcriptional outputs.^[40] TAD organization displays cell-type specificity, with dynamic strengthening observed during cellular differentiation. In pluripotent stem cells, TAD boundaries are generally weaker and more numerous, resulting in smaller domains that allow broader regulatory flexibility.^[39] As cells differentiate, such as in endothelial lineages, TAD boundaries reinforce, leading to fewer but larger domains that stabilize lineage-specific expression programs.^[41] This maturation process converges chromatin architecture on cell-state-appropriate configurations, reducing promiscuous enhancer-promoter contacts and promoting robust, tissue-specific transcription.^[42] Disruption of TAD integrity increases transcriptional variability. Targeted deletions or mutations at TAD borders lead to ectopic enhancer-promoter interactions, causing variable transcriptional responses in magnitude and direction across tissues.^[32]^[43] Recent single-cell studies highlight cell-to-cell variability in intra-TAD contacts, with TADs emerging as population-level patterns from dynamic chromatin movements.^[44]

Involvement in Development

Topologically associating domains (TADs) emerge during early embryonic development in close coordination with zygotic genome activation (ZGA), marking a pivotal transition in chromatin organization. In human embryos, this process initiates at the 8-cell stage, where ZGA-dependent TAD formation establishes insulation and promotes initial transcriptional programs from a previously diffuse chromatin state inherited from the gametes. Studies in mammalian models, including mice and humans, show that TAD boundaries begin to form concurrently with ZGA, often at loci associated with housekeeping and developmental genes, thereby facilitating the spatial segregation of regulatory elements essential for the first waves of zygotic transcription. This timing ensures that genome architecture supports the rapid cell divisions and differentiation cues in preimplantation embryos.^[45]^[46] Targeted deletion experiments in mice have underscored the critical role of TAD boundaries in developmental processes, particularly those involving organ formation. A 2023 study using CRISPR/Cas9 to excise eight TAD boundaries near embryonically active genes revealed widespread disruptions, including embryonic lethality in 63% of cases and altered chromatin insulation leading to TAD merging. Specifically, deletions near the Tbx5 locus caused a 44% reduction in Tbx5 expression and severe lung malformation in 60% of homozygous mutants, demonstrating how boundary loss permits ectopic enhancer-promoter interactions that misregulate developmental genes. These findings affirm that intact TAD boundaries are indispensable for coordinating developmental gene networks in vivo.^[47]^[48] TADs exhibit dynamic remodeling during cell differentiation, with compartment shifts and the emergence of new boundaries driving lineage commitment from pluripotent stem cells. As embryonic stem cells differentiate into specific lineages, such as neural or muscle progenitors, genomic regions transition between active A compartments and repressive B compartments, affecting approximately 13% of the genome and correlating with stable switches that lock in cell identity. This reorganization includes the strengthening or de novo formation of TAD boundaries, which refines enhancer-gene contacts to activate lineage-specific programs while silencing pluripotency factors. For instance, in skeletal muscle stem cell differentiation, multiscale TAD restructuring accompanies transcriptome changes, enabling myogenic gene activation through enhanced loop formation within TADs. Such plasticity ensures that chromatin topology adapts to developmental cues, supporting progressive restriction of cellular potential.^[49] Hierarchical folding dynamics of TADs, involving nested subdomains, play a key role in maintaining pluripotency during early embryogenesis, as revealed by 2025 analyses of preimplantation stages. In mouse and human embryos, these multi-level TAD structures form progressively from the zygote through the blastocyst, with higher-order interactions influencing pluripotency gene expression, such as Oct4 and Nanog. Disruptions in hierarchical folding impair the compartmentalization needed for balanced self-renewal and poise cells for differentiation, linking TAD organization directly to the totipotent-to-pluripotent transition. This layered architecture provides robustness to the genome, allowing coordinated regulation of developmental competence before lineage specification.^[45]^[50]

Dysregulation and Disease

TAD Alterations in Cancer

Structural variants (SVs), such as deletions, inversions, and translocations, frequently disrupt topologically associating domain (TAD) boundaries in cancer genomes, leading to the fusion of adjacent TADs and aberrant enhancer-promoter interactions known as enhancer hijacking. This rewiring allows enhancers from one TAD to ectopically activate oncogenes in neighboring domains, promoting tumor progression by overriding normal insulation mechanisms. In cancer cells, these SVs alter chromatin folding, with studies showing that up to 98% of TAD boundaries can be affected by somatic rearrangements across various tumor types.^[36] A notable example occurs in acute myeloid leukemia (AML), where inversions within the HOXA locus disrupt TAD boundaries, enabling enhancers to hijack and upregulate HOXA cluster genes, such as HOXA9 and MEIS1, which drive leukemogenesis. This enhancer hijacking results in increased 3D contacts between regulatory elements and target promoters, as revealed by Hi-C analysis in patient samples. Similarly, in colorectal cancer, TAD fusions caused by SVs facilitate cross-domain interactions that activate the MYC oncogene, enhancing proliferation and invasion through strengthened enhancer-MYC promoter loops. These events underscore how TAD boundary disruptions contribute to oncogene overexpression in solid tumors.^[51] Epigenetic modifications also play a critical role in weakening TAD boundaries, with changes like DNA hypermethylation at CTCF binding sites reducing insulator strength and promoting enhancer promiscuity in over 100 boundaries across hypermethylated tumors. Boundary elements, such as CTCF motifs, are particularly vulnerable to these epigenetic shifts.^[52] Recent 2024 studies have further connected TAD instability to metastasis, demonstrating that altered 3D topology in metastatic colorectal carcinoma involves weakened boundaries and novel long-range interactions that upregulate genes involved in invasion and immune evasion. In breast cancer progression models, metastatic samples exhibit abundant weakened TAD boundaries, correlating with enhanced chromatin accessibility at oncogenic loci and poorer prognosis. These findings highlight TAD alterations as drivers of metastatic potential through dynamic changes in genome architecture.^[53]^[54]

Implications in Other Disorders

Topologically associating domains (TADs) play a critical role in insulating enhancers from inappropriate promoters during limb development, and their disruption through structural variants has been implicated in congenital limb malformations. For instance, deletions or inversions at the EPHA4-PAX3 locus on chromosome 2q35-36 alter TAD boundaries, leading to enhancer miswiring that ectopically activates PAX3 expression in the anterior limb bud, resulting in preaxial polydactyly and syndactyly.^[55] Similarly, a 12 kb homozygous deletion near the LMBR1 gene on chromosome 7q removes three CTCF binding sites, impairing interactions between the zone of polarizing activity regulatory sequence (ZRS) enhancer and the SHH promoter, which reduces SHH expression and causes acheiropodia, a severe form of limb truncation.^[56] These findings underscore how TAD boundary disruptions can redirect long-range regulatory elements, contributing to congenital disorders by perturbing precise spatiotemporal gene expression patterns essential for limb patterning. In neurological disorders, TAD alterations contribute to synaptic gene dysregulation, particularly in autism spectrum disorder (ASD). De novo copy number variants (CNVs) and promoter variants within TADs containing ASD-associated genes, such as those involved in synaptic transmission, are enriched in individuals with ASD, leading to altered gene expression across multiple loci within the same domain.^[57] For example, mutations in CTCF, a key TAD insulator protein, disrupt chromatin looping at loci like the clustered protocadherins (PCDH), downregulating genes critical for neuronal connectivity and increasing ASD risk through impaired synaptic pathway assembly.^[58] This dysregulation manifests in accelerated neuronal maturation and altered proportions of neural progenitor cells, as observed in patient-derived cortical organoids, highlighting TADs' role in maintaining balanced synaptic function. TAD disruptions also underlie certain rare diseases, such as facioscapulohumeral muscular dystrophy (FSHD), where contraction of the D4Z4 macrosatellite repeat array on chromosome 4q35 modifies chromatin organization. In FSHD type 1, the repeat contraction to 1-10 units relaxes chromatin compaction, altering long-range interactions within TADs at the 4q35 locus and derepressing the DUX4 gene, which drives toxic expression in skeletal muscle.^[59] This leads to loss of specific intra-TAD contacts (e.g., between D4S139 and SORBS2) and gain of ectopic ones (e.g., with FAT1), correlating with upregulation of nearby genes like FRG1 and progressive muscle weakness. In FSHD type 2, mutations in epigenetic regulators like SMCHD1 compound these effects by further destabilizing TAD insulation around the contracted array.^[60] Recent single-cell analyses have revealed mosaic TAD disruptions in neurodevelopmental conditions, providing insights into cellular heterogeneity underlying disease phenotypes. In Smith-Magenis syndrome, a 17p11.2 deletion disorder featuring intellectual disability and autism-like traits, patient-derived brain organoids exhibit altered intra- and inter-TAD contacts via Hi-C, with single-nucleus RNA sequencing showing mosaic disruptions in neuronal maturation and cell-cycle progression across cell populations.^[61] These 2025 studies emphasize how single-cell resolution uncovers variable TAD integrity in neurodevelopmental disorders, linking mosaic chromatin changes to diverse clinical manifestations such as impaired cortical growth and synaptic deficits.

Lamina-Associated Domains

Lamina-associated domains (LADs) are genomic regions that interact with the nuclear lamina, a meshwork of intermediate filaments lining the inner nuclear membrane, and are characterized as gene-poor, heterochromatic areas primarily involved in gene repression.^[62] These domains are tethered to the lamina through interactions mediated by proteins such as the lamin B receptor (LBR) and lamin B, which bind to heterochromatin marks and facilitate peripheral positioning.^[62] Lamin A/C may also contribute to tethering in certain contexts, though lamin B and LBR are central to heterochromatin attachment.^[62] LADs typically range in size from 0.1 to 10 megabases (Mb), with a median of approximately 0.5–1 Mb, and they cover 30–50% of the genome depending on cell type.^[63] They are enriched in repressive histone modifications, such as H3K9me2 and H3K9me3, and exhibit low gene density (about 2–3 genes per Mb, compared to the human genome average of ~8).^[62] These features position LADs as stable, peripheral structures that maintain heterochromatin integrity and silence associated genes.^[64] In relation to topologically associating domains (TADs), LADs often span multiple TADs due to their larger scale, with partial alignment of boundaries showing 30–50% co-localization in mammalian cells.^[64] This overlap reflects LADs' association with B compartments, which are inactive and peripheral, contrasting with the more modular, internally regulated nature of TADs that facilitate enhancer-promoter interactions in active genomic regions.^[62] Functionally, while LADs enforce transcriptional silencing through peripheral sequestration, TADs support dynamic gene regulation; disruptions in LAD organization, such as those seen in laminopathies from LMNA mutations, lead to loss of normal LADs, ectopic heterochromatin formation, and altered gene expression.^[65]

Chromatin Compartments and Loops

A/B compartments represent large-scale chromatin domains identified through principal component analysis (PCA) of Hi-C contact matrices, segregating the genome into active A compartments enriched in euchromatin and inactive B compartments dominated by heterochromatin, typically spanning 1-5 Mb in resolution. This compartmentalization arises from differential interactions between open and closed chromatin states, with A compartments exhibiting higher intra-compartment contacts and gene activity, while B compartments show stronger self-association and repression.^[66] These compartments complement TADs by providing a coarser organizational layer that influences overall chromatin folding beyond local domain boundaries.^[66] Chromatin loops, in contrast, operate at a finer scale of 10-100 kb and facilitate precise long-range interactions, primarily mediated by the architectural proteins CTCF and cohesin through a loop extrusion mechanism.^[66] In this process, cohesin extrudes chromatin fibers until stalled by convergent CTCF motifs, forming loops that often connect enhancers to promoters for targeted gene regulation.^[67] Unlike the broader compartmental segregation, these loops enable specific functional pairings within the genome, enhancing regulatory specificity.^[68] The 3D genome architecture exhibits a hierarchical organization where individual chromatin loops nest within TADs, and TADs in turn aggregate into A/B compartments, creating nested layers of interaction from kilobase to megabase scales.^[66] Recent studies, including a 2025 analysis in T lymphocytes, have further revealed meta-loops that span multiple TADs, forming larger regulatory structures up to multi-megabase sizes, particularly in immune cells like T lymphocytes.^[69] This nesting ensures that local loop-mediated interactions respect TAD insulation while contributing to compartment-level patterning. In terms of dynamics, A/B compartments remain largely stable across cell types and conditions, reflecting persistent epigenetic states, whereas chromatin loops display high fluctuation rates, with many forming and dissolving on timescales of minutes to hours during processes like transcription.^[67] These dynamic properties align with phase separation models, where heterochromatic B compartments may condense via liquid-liquid phase separation driven by multivalent interactions, while active A compartments and loops support fluid, reversible associations to accommodate regulatory responses.^[70]

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Nov 19, 2014 · Here we localize boundaries of replication domains to the early-replicating border of replication-timing transitions and map their positions in 18 human and 13 ...
[6]
Chromatin architecture reorganization during stem cell differentiation
Feb 18, 2015 · Previous studies indicated that chromosomes are composed of cell-type-invariant TADs. Across the six lineages analysed in this study, we ...
[7]
Hi-C: A Method to Study the Three-dimensional Architecture of ... - NIH
May 6, 2010 · We developed Hi-C, an extension of 3C that is capable of identifying long range interactions in an unbiased, genome-wide fashion.
[8]
Systematic evaluation of chromosome conformation capture assays
Sep 3, 2021 · We used this knowledge to develop a greatly improved Hi-C protocol (Hi-C 3.0) that can detect both loops and compartments relatively effectively ...
[9]
Single cell Hi-C reveals cell-to-cell variability in chromosome structure
Here we introduce single cell Hi-C, combined with genome-wide statistical analysis and structural modeling of single copy X chromosomes.
[10]
Single‐Cell Hi‐C Technologies and Computational Data Analysis
Jan 30, 2025 · Nagano et al. developed the first scHi-C protocol in 2013 and updated it in 2017. Their procedure ...<|separator|>
[11]
Droplet Hi-C enables scalable, single-cell profiling of chromatin ...
Oct 18, 2024 · We used Droplet Hi-C to identify ecDNA and mapped their chromatin interactome in tumor cells at single-cell resolution. Finally, we extended ...
[12]
deepTAD: an approach for identifying topologically associated ...
Mar 25, 2025 · In this work, we propose a new TAD identification method, called deepTAD, based on a CNN-transformer model for feature extraction from the Hi-C ...
[13]
HTAD: a human-in-the-loop framework for supervised chromatin ...
Dec 2, 2024 · We introduce HTAD, a human-in-the-loop TAD caller that combines machine learning with human supervision to achieve high accuracy.
[14]
The 3D Genome Browser: a web-based browser for visualizing 3D ...
Oct 4, 2018 · A fast web-based browser that allows users to smoothly explore both published and their own chromatin interaction data.
[15]
TADKB: Family classification and a knowledge base of topologically ...
Mar 14, 2019 · Topologically associating domains (TADs) are DNA segments that are considered the structural and functional units of the mammalian genomes [1, 2] ...
[16]
A comprehensive benchmarking with interpretation and operational ...
May 23, 2024 · Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain ...
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Formation of Chromosomal Domains by Loop Extrusion - PMC - NIH
Here we propose that loop extrusion underlies TAD formation. In this process, cis-acting loop-extruding factors, likely cohesins, form progressively larger ...Missing: seminal | Show results with:seminal
[18]
Mechanism of phase condensation for chromosome architecture ...
Apr 25, 2024 · In this review, we introduce patterns underlying the molecular mechanisms of chromosomal phase separation and present various examples.
[19]
Phase-separated chromatin compartments: Orchestrating gene ...
These findings suggest that phase separation driven by multivalent H3K9me3/CD interactions is a general principle for HP1-mediated constitutive heterochromatin ...
[20]
Shaping of the 3D genome by the ATPase machine cohesin - Nature
Dec 2, 2020 · Here, we review the current understanding of interphase genome organization with a focus on the major regulator of genome structure, the cohesin complex.
[21]
Cohesin: behind dynamic genome topology and gene expression ...
Cohesin plays a pivotal role regulating highly dynamic chromatin interactions linked to transcription control.
[22]
Multi-feature clustering of CTCF binding creates robustness for loop ...
Sep 12, 2023 · TADs are formed by Cohesin-mediated loop extrusion, with many TAD boundaries consisting of clustered binding sites of the CTCF insulator protein ...Missing: seminal | Show results with:seminal
[23]
Insulation between adjacent TADs is controlled by the width of their ...
Most boundaries between TADs contain CTCF binding sites (CBSs), which individually contribute to the blocking of Cohesin-mediated loop extrusion. Using genome- ...
[24]
Towards a predictive model of chromatin 3D organization - PMC - NIH
Furthermore, YY1 is enriched with CTCF at TAD borders [21]. As is the case in Drosophila, TFIIIC colocalizes with CTCF, cohesin, and the DNA-binding tumor ...Missing: LDB1 | Show results with:LDB1
[25]
ZNF143 mediates CTCF-bound promoter–enhancer loops required ...
Jan 4, 2021 · TADs are detected with a pair of strong boundaries, or insulation scores, and typically span a distance from approximately 100 kb to 1 Mb in ...
[26]
LDB1 establishes multi-enhancer networks to regulate gene ... - NIH
These data suggest that LDB1 may have a unique role in enhancer connectivity and function through distinct mechanisms compared to other architectural proteins.
[27]
TAD border deletion at the Kit locus causes tissue-specific ectopic ...
May 28, 2024 · We found that although Kit is highly active in both mast cells and melanocytes, deletion of the TAD boundary between the Kit and Kdr genes results in ectopic ...
[28]
TAD conservation in vertebrate genomes is driven by stabilising ...
Aug 5, 2025 · Here, we investigated the evolutionary conservation of TADs by analysing Hi-C data from 12 vertebrate species. We examined TAD numbers, borders, ...
[29]
Topologically associating domains and the evolution of three ...
May 19, 2025 · Conserved TADs are gene‐rich, actively transcribed regions In the first approach, we identified sets of high‐confidence TADs, which resulted in ...
[30]
Topologically Associating Domains and Regulatory Landscapes in ...
The first HiC data comparing TADs in human and mouse cells found a general conservation of their boundaries (Dixon et al., 2012) and an in-depth analysis of ...<|control11|><|separator|>
[31]
Disruption of chromatin folding domains by somatic genomic ...
Feb 5, 2020 · TADs are considered to represent functional domains because a given TAD encompasses the regulatory elements for the genes inside the same domain ...
[32]
Topologically Associating Domains and Regulatory Landscapes in ...
Jul 6, 2021 · In this review, we discuss the connections of the 3D genome with gene expression, the relationship between TADs and RLs, and their dynamics in ...Missing: paper | Show results with:paper<|control11|><|separator|>
[33]
Making sense of the linear genome, gene function and TADs
Jan 29, 2022 · TADs are thought to act as functional units in the genome. TADs co-localise genes and their regulatory elements as well as forming the unit of genome switching.
[34]
TADs as modular and dynamic units for gene regulation by hormones
May 24, 2015 · 4.2 Stable and dynamic contacts within TADs. Chromatin loops between enhancers and promoters are probably highly dynamic and an active ...2 Modulation Of Gene... · 3 Tads As Modular Units For... · 4.2 Stable And Dynamic...
[35]
Dynamic chromatin organization and regulatory interactions in ...
Dec 8, 2022 · Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene ...
[36]
The dynamics of three-dimensional chromatin organization and ...
Dec 21, 2022 · The number of TAD boundaries decreases, and the average size of TADs increases during differentiation. Most TAD boundaries are highly conserved ...
[37]
Direction and modality of transcription changes caused by TAD ...
Aug 12, 2025 · As shown by Hi-C experiments, the disruption of the TAD boundary led to the emergence of ectopic long-range interactions between the Cdh23 gene ...
[38]
Transcriptional programs of cell identity and p53-induced stress ...
Jul 8, 2025 · Moreover, both recent single-cell Hi-C studies and chromatin tracing experiments coupled with super-resolution microscopy show that intra-TAD ...
[39]
Transcriptional coregulation in cis around a contact insulation site ...
Mar 6, 2025 · At the single-cell level, where transcription occurs in sporadic bursts, transcriptional coordination has been observed between proximal ...
[40]
The hierarchical folding dynamics of topologically associating ...
Jul 1, 2025 · Our study sheds light on the folding dynamics of hierarchical TADs during early embryo development and underscores their close relationship with ...Missing: paper | Show results with:paper
[41]
The establishment of the 3D genome structure during zygotic ...
Mar 3, 2025 · Zygotic genome activation (ZGA) coincides with a dramatic reorganization of chromatin architecture. We describe mechanisms of 3D genome ...
[42]
Topologically associating domain boundaries are required ... - Nature
Apr 20, 2023 · Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories.
[43]
Topologically associating domain boundaries are required for ... - NIH
Apr 20, 2023 · Here we demonstrate that targeted deletions of TAD boundaries cause a range of disruptions to normal in vivo genome function and organismal ...
[44]
Multiscale 3D genome reorganization during skeletal muscle stem ...
Feb 17, 2023 · Our results uncover that 3D chromatin extensively reorganizes at multiple architectural levels and underpins the transcriptome remodeling during SC lineage ...
[45]
The hierarchical folding dynamics of topologically associating ... - NIH
Jul 1, 2025 · In this study, we examined the hierarchical topological association domain (TAD) during early embryo development and its relationship with ...Missing: pluripotency maintenance
[46]
3D genome landscape of primary and metastatic colorectal ...
Mar 4, 2025 · 3D genome landscape of primary and metastatic colorectal carcinoma reveals the regulatory mechanism of tumorigenic and metastatic gene expression.
[47]
Genome reorganization and its functional impact during breast ...
Sep 10, 2025 · On a finer scale, structural changes in TADs occur more often during later stages of metastasis. We also find an abundance of weakened TAD ...
[48]
https://pmc.ncbi.nlm.nih.gov/articles/PMC10119121/
[49]
Deletion of CTCF sites in the SHH locus alters enhancer–promoter ...
Apr 16, 2021 · As homozygous deletions of the ZRS, which regulates SHH expression in the developing limb, were shown to lead to truncated limbs in mice and ...
[50]
https://pmc.ncbi.nlm.nih.gov/articles/PMC12210587/
[51]
CTCF mutation at R567 causes developmental disorders via 3D ...
Jul 1, 2024 · This study elucidates the influence of the CTCF R567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.
[52]
Analysis of the 4q35 chromatin organization reveals distinct long ...
Jul 17, 2019 · Shortening of the D4Z4 array at the 4q35 locus is linked to Facio-Scapulo-Humeral Dystrophy (FSHD), the third most common hereditary myopathy.
[53]
SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat ...
Jun 28, 2023 · In 5% of FSHD cases, D4Z4 chromatin relaxation is due to germline mutations in one of the chromatin modifiers SMCHD1, DNMT3B or LRIF1. The ...
[54]
Lamina-associated domains: peripheral matters and internal affairs
Apr 2, 2020 · Lamin B receptor (LBR) binds lamin B and the H3K9me3-binding chromobox protein homolog 5 (CBX5) [47], providing a tether for heterochromatin ...
[55]
Choreography of lamina‐associated domains: structure meets ...
Nov 12, 2023 · Lamina-associated domains are large regions of heterochromatin positioned at the nuclear periphery. These domains have been implicated in ...
[56]
Lamina-associated domains: links with chromosome architecture ...
Such lamina-associated domains (LADs) are thought to help organize chromosomes inside the nucleus and have been associated with gene repression.
[57]
Aberrant chromatin organization at the nexus of laminopathy ...
Dec 11, 2022 · LMNA mutations have been shown to cause extensive changes in LAD organization, including both the loss of normal LADs and the formation of ...
[58]
Mapping the 3D genome architecture - ScienceDirect.com
TADs and subTADs are self-interacting genomic domains, appearing as squares along the diagonal, indicating frequent local chromatin interactions. Chromatin ...
[59]
Dynamics of CTCF- and cohesin-mediated chromatin looping ...
Apr 14, 2022 · Functionally, CTCF- and cohesin-mediated looping and TADs play critical roles in multiple nuclear processes, including regulation of gene ...Dynamics Of Ctcf- And... · Fleeting Chromatin Loops · Abstract
[60]
Enhancer–promoter interactions and transcription are ... - Nature
Dec 5, 2022 · We find that enhancer–promoter (E–P) interactions are largely insensitive to acute (3-h) depletion of CTCF, cohesin or WAPL.
[61]
Generation of dynamic three-dimensional genome structure through ...
We propose that phase separation induced by heterogeneous repulsive interactions among chromatin chains largely determines dynamic genome organization.