A new study published in BMC Genomics provides the first three-dimensional answer, and the result is remarkable. A team led by Martha Valiadi and Adam Monier at the University of Exeter, working with colleagues in Greece and at the Institut Pasteur in Paris, applied high-throughput chromosome conformation capture, or Hi-C, to O. tauri and mapped how its genome folds in space. Hi-C works by chemically cross-linking DNA segments that sit close together in the nucleus, fragmenting the genome, and then sequencing the paired fragments to build a contact map of physical interactions. When the team analysed these maps, they found that the low-GC regions of the two outlier chromosomes fold into self-contained loops of interaction that resemble the topologically associating domains, or TADs, familiar from animal and plant genomes. These TAD-like structures have sharp boundaries that effectively wall the outlier regions off from the rest of their own chromosomes and from the rest of the genome.

The finding is significant because spatial insulation was never previously demonstrated in organisms with genomes this compact. O. tauri holds the record as the smallest known free-living eukaryote, and its genome of roughly thirteen million base pairs is squeezed into a nucleus that occupies only a fraction of the cell. In larger eukaryotes, TADs are thought to help regulate gene expression by limiting the reach of regulatory elements such as enhancers, so that signals from one part of the genome do not bleed into another. Finding TAD-like architecture in an organism with so little genomic real estate suggests that the physical compartmentalisation of DNA is not a luxury of complex life but a fundamental feature that even the most streamlined eukaryotic genomes maintain.

The outlier regions themselves carry a distinctive chromatin fingerprint that the researchers uncovered by mining existing transcriptomic, methylation and nucleosome positioning data across the Mamiellales. Compared with the rest of the genome, the outlier regions are hypomethylated, meaning they carry fewer chemical methyl tags on their cytosine bases, and they are transcriptionally hyperactive, with genes inside them being expressed at unusually high levels. Nucleosome spacing across these regions is also altered, indicating that the DNA is packaged differently around the histone proteins around which it is wound. Taken together, these features describe a chromatin environment that is open, active and chemically distinct from the surrounding genome, and this profile is conserved across the species of the order that the team examined.

Yet the two outlier chromosomes are not identical twins in behaviour. The team found that transcription is consistently elevated in the low-GC region of the big outlier chromosome, which they designate BOC1, in every Mamiellales species they analysed. The small outlier chromosome tells a different story: transcriptional activity in its low-GC region, SOC1, varies from species to species. This asymmetry hints that the two outlier chromosomes may have different evolutionary origins or different functional roles, even though both share the same hallmark sequence composition and the same spatial sequestration within the nucleus. Understanding why one outlier region is universally busy while the other is more permissive remains an open question for future work.

One long-standing hypothesis about outlier chromosomes has been that they serve as repositories for transposable elements, the mobile genetic sequences that can copy and paste themselves around the genome. Because transposable elements often carry different GC compositions than host DNA and can be silenced by methylation, sequestering them in a separate chromatin compartment would be a sensible genome-defence strategy. The new study confirms that outlier regions are indeed enriched in transposable elements in most Mamiellales species, including a variety of element types such as Mutator-like elements and long terminal repeat retrotransposons. But the correlation is not universal, and this is where the study delivers its most conceptually important twist.

In two species, Bathycoccus prasinos and Ostreococcus lucimarinus, the researchers found no substantial enrichment of transposable elements in the outlier regions, yet those regions still retain their characteristic low-GC composition and their elevated BOC1 transcription, and the Hi-C data show that they remain spatially insulated. This decoupling demonstrates that the three-dimensional isolation of outlier chromosomes is not simply a by-product of harbouring mobile DNA. Spatial insulation, in other words, is a property that tracks the chromatin state of these regions rather than their transposable element content alone. It adds a genuine three-dimensional criterion to the list of sequence-based features, such as GC content and gene density, by which outlier chromosomes have traditionally been defined.

To test whether this compartmentalisation extends beyond the Mamiellales, the team reanalysed published Hi-C data from two other compact marine eukaryotes: Mantoniella tinhauana, a close relative within the same order, and Pelagomonas calceolata, a stramenopile alga only distantly related to the green lineage. In both cases, the data revealed consistent patterns of insulation around the outlier regions, suggesting that the spatial sequestration of compositionally distinct chromosome segments may be a recurrent feature of compact picoeukaryotic genomes more broadly. If this holds, it would imply that the physical organisation of the nucleus in these tiny cells follows rules that have evolved independently multiple times, converging on the same solution of walling off unusual DNA into its own neighbourhood.

The technical achievement behind these conclusions should not be understated. Hi-C experiments typically require millions of cells, and working with an organism as small as O. tauri demanded careful optimisation of cross-linking, digestion and ligation steps to recover enough informative contacts from such a tiny genome. The team also used iterative correction to normalise their contact matrices, removing biases introduced by restriction site distribution and read depth, before calling the boundaries of the TAD-like domains. The resulting maps provide the first glimpse of how a eukaryotic genome at the extreme lower limit of cellular complexity arranges itself in three dimensions, and they demonstrate that even a nucleus barely larger than a bacterial cell can sustain organised chromosomal architecture.

For the broader field of genome biology, the study reframes outlier chromosomes from curiosities of sequence composition into bona fide spatial compartments with conserved epigenetic identities. It raises new questions about how their boundaries are established and maintained in an organism that lacks many of the architectural proteins found in larger eukaryotes, and about what functional advantages insulation confers, whether in protecting the core genome from transposable elements, regulating the expression of specialised gene families, or managing the conflicts between different chromatin states within a single nucleus. As sequencing and chromosome conformation capture technologies continue to reach ever smaller and stranger organisms, the humble O. tauri, long a model of genomic minimalism, now also stands as a model of how much organised structure can be packed into the smallest of packages.

Subject of Research: Three-dimensional genome organisation and spatial insulation of outlier chromosomes in the picoeukaryote Ostreococcus tauri

Article Title: Three-dimensional genome organisation reveals spatially insulated outlier chromosomes in Ostreococcus tauri

Article References: Valiadi, M., Harrison, K., Loe-Mie, Y., Williams, B., Ankrett, D., Smirnoff, N., & Monier, A. (2026). Three-dimensional genome organisation reveals spatially insulated outlier chromosomes in Ostreococcus tauri. BMC Genomics. https://doi.org/10.1186/s12864-026-13416-0

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13416-0

Keywords: Ostreococcus tauri, Hi-C, chromosome conformation capture, topologically associating domains, outlier chromosomes, picoeukaryotes, Mamiellales, genome organisation, transposable elements, chromatin, DNA methylation, BMC Genomics

ASFV belongs to the nucleocytoplasmic large DNA viruses, a group of complex viruses whose genomes encode many of their own replication machinery. Although the virus assembles and replicates in cytoplasmic factories, its entry into a macrophage sets off a cascade of events that reaches into the nucleus. Previous work had suggested that ASFV can modulate host gene expression epigenetically, but the scale and dynamics of the nuclear changes during early infection had never been systematically mapped. The new study addresses that gap by tracking the infection at 2, 4, and 6 hours post-infection, a window in which the virus establishes itself before progeny virions begin to spread.

To capture this pivotal phase, the researchers deployed an unusually comprehensive multi-omics strategy. Time-course RNA sequencing charted the host transcriptome as it changed hour by hour. CUT&Tag profiling measured where RNA polymerase II, the enzyme that transcribes protein-coding genes, was sitting across the genome. Immunoprecipitation followed by mass spectrometry identified the proteins that associate with the polymerase during infection. Finally, Hi-C, a method that captures the physical contacts between distant stretches of chromatin, revealed how the genome folds in three-dimensional space. Crucially, the team ran this entire pipeline using both a virulent ASFV strain and its live-attenuated derivative, allowing them to distinguish changes caused by the virus in general from those attributable to specific virulence factors.

The most striking finding concerns the global organization of the genome. In healthy cells, chromatin is partitioned into compartments of active euchromatin and silent heterochromatin, and further subdivided into topologically associating domains, or TADs, which are self-contacting genomic neighborhoods that help regulate which genes talk to which regulatory elements. The study found that early ASFV infection significantly increased heterochromatinization across the host genome, shifted the positions of TAD boundaries, and altered both the intensity of chromatin interactions and the spatial distances between interacting genomic regions. In other words, within hours of the virus entering the cell, the host genome was physically refolded.

One of the most intriguing observations is that viral DNA itself appears to participate in this reorganization. The Hi-C data revealed interactions between viral genomes and host chromatin, suggesting that incoming ASFV DNA does not simply float in the nucleus as an inert passenger. Instead, it seems to make physical contact with host chromosomes, raising the possibility that the virus actively recruits host genomic regions to viral replication compartments or sequesters immune genes into repressive nuclear environments. The authors suggest that this chromatin reorganization may contribute to ASFV immune evasion, though the precise mechanisms linking physical genome folding to immune suppression remain to be worked out.

The transcriptional consequences of this remodeling were equally revealing. The host antiviral transcriptional program, the set of interferon-stimulated genes and inflammatory pathways that normally swing into action when a macrophage detects a pathogen, turned out to be indistinguishable between cells infected with the virulent strain and cells infected with the attenuated virus. This was a surprise, because the attenuated strain lacks MGF-encoded factors, a family of viral genes long associated with virulence and immune modulation. The result demonstrates that the earliest wave of innate immune activation is independent of these virulence determinants, implying that whatever the MGF proteins do to tip the balance toward lethal disease must happen later, or through mechanisms other than silencing the initial antiviral transcriptional response.

RNA polymerase II itself became a focal point of the analysis. The researchers found that the total protein levels of the polymerase did not change appreciably during early infection, yet its behavior was profoundly altered. Its genomic occupancy was redistributed across the genome, and its interactome, the network of proteins it physically associates with, was remodeled. Core polymerase subunits and components of the Mediator complex, a large coactivator that bridges transcription factors to the polymerase, became enriched in the polymerase-associated fraction. In contrast, sequence-specific transcription factors, the proteins that normally direct the polymerase to particular genes in response to signals, were depleted from that fraction.

This shift in the polymerase’s social circle is mechanistically significant. A polymerase that is increasingly bound to Mediator and core subunits but less associated with gene-specific transcription factors suggests a reprogramming of transcriptional control away from signal-responsive gene activation and toward a more basal or virally steered mode. Combined with the increased heterochromatinization and the repositioning of TAD boundaries, the picture that emerges is one of coordinated change: the physical folding of the genome, the distribution of the transcription machinery, and the resulting transcriptome are all being reshaped together during the first six hours of infection.

The implications extend beyond basic virology. African swine fever continues to inflict substantial economic losses on the global swine industry, and the absence of a widely available safe and effective vaccine has made understanding the virus’s evasion strategies a research priority. By showing that ASFV manipulates host chromatin architecture so early and so extensively, the study opens a new dimension for antiviral intervention. If specific host factors mediate the observed heterochromatinization or the redistribution of polymerase occupancy, those factors could become drug targets. Similarly, the finding that early innate immune activation proceeds normally even without MGF-encoded virulence factors suggests that the critical battle between host defense and viral evasion is fought on a chromatin landscape, not merely at the level of individual signaling pathways.

The work also adds ASFV to a growing list of viruses known to touch the three-dimensional genome, but with a distinctive twist. Because ASFV is a cytoplasmic replicator, its nuclear influence must be exerted through delivered proteins, RNAs, or the viral DNA itself, rather than through a nuclear replication cycle. Disentangling which viral components drive the chromatin remodeling, and determining whether blocking that remodeling restores full antiviral gene expression, are the natural next questions. For now, the study provides the most systematic view yet of how a lethal agricultural pathogen rewrites the physical grammar of the host genome in its opening hours, and it suggests that the nucleus, long viewed as a bystander in ASFV infection, is in fact an active battlefield.

Subject of Research: Chromatin architecture remodeling in host cells during early African swine fever virus infection

Article Title: ASFV early infection dynamically remodels host chromatin architecture to evade immune responses

Article References: Xu, Y., Yang, B., Zhu, J., Sunkang, Y., Xing, L., Wang, C., Yang, J., Xu, W., Dai, J., Zhang, J., Cao, G., & Xiao, K. (2026). ASFV early infection dynamically remodels host chromatin architecture to evade immune responses. Cellular and Molecular Life Sciences. https://doi.org/10.1007/s00018-026-06467-9

Image Credits: AI Generated

DOI: 10.1007/s00018-026-06467-9

Keywords: African swine fever virus, ASFV, chromatin architecture, Hi-C, RNA polymerase II, macrophages, immune evasion, topologically associating domains, heterochromatin, innate immunity, virus-host interactions, multi-omics

Conventional Hi-C, first described more than a decade and a half ago, revolutionized genomics by revealing that chromosomes fold into compartments, topologically associating domains, and loops that bring distant regulatory elements into physical proximity. But the technique has always carried a fundamental trade-off. To generate enough material for sequencing, researchers typically dissociate tissues into cell suspensions or grind them into homogenates, destroying the spatial context that makes a brain a brain. Single-cell Hi-C and imaging-based chromatin tracing recovered some of that information, but at the cost of throughput, resolution, or genomic coverage. Spatial transcriptomics, meanwhile, maps gene expression across tissue but says nothing about the physical folding of the DNA that produces that expression. Spatial Hi-C was designed to close precisely this gap.

The technical core of the method is a microfluidic device that performs the Hi-C chemistry in situ on thin tissue sections. The chip contains arrays of parallel channels, with widths of 10, 20, or 50 micrometers depending on the desired resolution, through which barcoded reagents are delivered to spatially defined strips of the section. By running the barcoding in two perpendicular passes, each microscopic spot on the tissue acquires a unique combination of two barcodes, effectively assigning a spatial address to every chromatin contact captured there. The researchers verified that the channels do not leak or diffuse into one another using fluorescent dyes, and demonstrated that valid contact counts concentrate within expected barcode combinations rather than spreading across the chip. The result is a contact map, the raw currency of Hi-C analysis, attached to a coordinate on the tissue.

To validate the approach, the team applied spatial Hi-C to sections of mouse embryos at embryonic day 13. Pseudobulk contact matrices, generated by pooling data across an entire section, showed the expected high-quality features of Hi-C data, including clear compartmentalization and domain structure at resolutions down to 10 kilobases. Unsupervised clustering of the spatial data reproduced the anatomy of the embryo, separating the central nervous system from surrounding mesenchyme and other tissues without any anatomical annotation being provided. When the researchers compared their spatial Hi-C clusters with bulk Hi-C data generated from manually dissected embryonic organs, principal component analysis showed tight agreement, and aggregate compartment and TAD signals were highly consistent. Correlations between replicate sections exceeded 0.95, indicating that the method is both faithful and reproducible.

Integrating spatial Hi-C with spatial transcriptomics on adjacent sections proved particularly powerful. In the E13 embryo, the team identified differential chromatin interactions between the central nervous system and mesenchymal regions, including changes in A/B compartment scores, reorganized TAD boundaries, and distinct chromatin loops. Genes such as Nova1, a neuronal splicing regulator, and Tbx3, a transcription factor involved in developmental patterning, showed spatial expression patterns that aligned with spatially resolved changes in their local chromatin contact landscapes. Differential loop anchors were enriched for genes involved in neural and developmental functions, and examples such as Dner in the nervous system and Gja1 in mesenchyme illustrated how enhancer-promoter wiring differs across tissue regions. The compartment scores derived from spatial Hi-C tracked the expression of marker genes for neural progenitor cells, premature neurons, heart, and liver clusters identified by the transcriptomic data.

The adult mouse cerebellum provided the most striking demonstration of the method’s spatial resolving power. At 20-micrometer resolution, spatial Hi-C distinguished the molecular layer, Purkinje layer, granular layer, and white matter by their 3D genome architectures. Within the granular layer, the analysis revealed subclusters with distinct 3D genomes that aligned with the anatomical lobules of the cerebellum, the repeating folds that organize cerebellar function. Genes such as Dpp6, Gprin3, and Galntl6 showed promoter-region compartment scores that varied systematically across these granule cell subclusters, and the corresponding spatial expression patterns in the transcriptomic data mirrored the chromatin differences. The researchers also documented B-compartment fusion events and differential TAD reorganization between the granular and Purkinje layers, including loops at the Etv1 locus, a regulator of granule cell maturation, whose associated enhancer was validated in an independent in vivo reporter assay.

Pushing resolution further, the team achieved single-spot 3D chromatin reconstruction in the adult cortex at 10 micrometers, a scale comparable to single-cell data. Using the Tensor-FLAMINGO algorithm, they reconstructed distance matrices and 3D structures for individual nuclear spots that closely matched those derived from Dip-C single-cell datasets of the same brain regions. Spatial Hi-C clusters in the cortex corresponded to cortical layers and to cell types identified by single-nucleus transcriptomic references, and spots overlapping segmented nuclei by more than 90 percent provided near-single-cell chromatin contact information. In the hippocampus, the method resolved clusters corresponding to the dentate gyrus, CA1 pyramidal layer, and even the ependymal cell layer lining the ventricles, with compartment scores at loci such as Npas3 and Vit1a varying across these microdomains.

Perhaps the most conceptually significant finding came from the developing brain. Across embryonic days 14.5, 16.5, and 18.5, the researchers measured the ratio of short-range to long-range chromatin interactions on coronal sections and found an increasing radial gradient of this ratio from the germinal zone toward the cortical plate. This gradient tracked neuronal maturity: when compared with CytoTRACE2 developmental potency scores computed from spatial transcriptomic data, the short-versus-long interaction ratio correlated significantly across clusters at 10-micrometer resolution. In other words, the physical compactness of local chromatin packing, readable directly from tissue, serves as a marker of how far a neuron has progressed along its developmental trajectory. Genes such as Sox2 and Notch2, markers of progenitors, and Celf2 and Ank3, associated with maturing neurons, showed spatial expression patterns consistent with the chromatin gradient.

The implications extend well beyond neurobiology. Disease-associated non-coding variants often act through long-range enhancer-promoter contacts that are specific to cell type and tissue context, and a method that preserves both the contact information and the anatomical address could pinpoint where in a tissue a regulatory variant exerts its effect. The data and code from the study have been deposited in public repositories, including the Genome Sequence Archive and Zenodo, with BEDPE contact files ready for standard Hi-C visualization tools, lowering the barrier for other laboratories to adopt the framework. The protocol itself is available through protocols.io, and the underlying microfluidic chip design is included with the supplementary materials.

Spatial Hi-C establishes what its developers call a paradigm for investigating spatially resolved chromatin structures within complex tissue microenvironments. By fusing the contact-mapping power of Hi-C with the positional awareness of spatial omics, it transforms the 3D genome from an abstraction studied in dissociated cells into an anatomical object that can be read layer by layer, lobule by lobule, and spot by spot. As the technology matures and resolution improves further, researchers anticipate applying it to human tissue, pathological specimens, and models of neurological disease, where the folding of the genome in its native spatial context may hold keys to understanding how regulatory architecture goes awry.

Subject of Research: Spatially resolved 3D chromatin architecture mapping in mammalian brain tissue using spatial Hi-C

Article Title: Spatially resolved chromatin architectures in mammalian brain tissues

Article References: Chen, Z., Guo, M., Zhang, L., Yu, H., Wang, X., Yu, X., Chen, M., Lv, J., Chen, Z., Peng, C., Gong, Q., Zhang, Q., Guo, R., Huang, Y., Gao, L., Jiang, S., Wang, J., Zhang, Z., Qian, J., … Chen, X. (2026). Spatially resolved chromatin architectures in mammalian brain tissues. Nature Methods. https://doi.org/10.1038/s41592-026-03218-3

Image Credits: AI Generated

DOI: 10.1038/s41592-026-03218-3

Keywords: spatial Hi-C, 3D genome, chromatin architecture, mouse brain, cerebellum, cortex, spatial transcriptomics, topologically associating domains, A/B compartments, neuronal development, microfluidics, Nature Methods