Polycomb repression operates through two cooperating complexes. PRC1 decorates histone H2A with a single ubiquitin molecule at lysine 119, producing the H2Aub mark, while PRC2 trimethylates histone H3 at lysine 27, producing H3K27me3. Together these marks silence genes that would otherwise trigger premature differentiation. In mouse embryos, previous work had shown that H2Aub and H3K27me3 can be decoupled during preimplantation development, and that maternal H3K27me3 can guide certain imprinted expression patterns. But human embryos posed a puzzle: H3K27me3 is largely erased across the genome after fertilization and only later restored. If the repressive mark disappears, how does the cell know where to put it back?

To answer that question, the team needed to measure H2Aub in samples that are extraordinarily scarce, human sperm, fully grown oocytes, two-cell embryos, eight-cell embryos, blastocysts and embryonic stem cells. They adapted a targeted profiling approach called Stacc-seq, an in situ method derived from CUT&Tag that can map chromatin marks from as few as a handful of cells. The authors validated the technique extensively, showing that profiles from 500, 50 or even 20 cultured cells closely matched conventional ChIP-seq, and confirming in engineered mouse and human stem cells that the signal vanished when PRC1 was acutely degraded. Immunofluorescence on human sperm independently confirmed that H2Aub is present in the paternal genome.

The resulting atlas shows that H2Aub does not simply follow H3K27me3. Instead, it emerges remarkably early, appearing in GC-rich regions of the genome as soon as the two-cell stage, right around the time the embryonic genome switches on. From there it progressively accumulates at both active and inactive genes, and by the blastocyst stage it concentrates strongly at canonical Polycomb target genes, the developmental regulators that must stay silent until the embryo commits to its first lineages. Notably, H2Aub in humans tracks GC content and CpG density far more closely than it does in mice, where the mark is largely confined to inactive genes, revealing a species difference in how Polycomb complexes are recruited to chromatin.

The relationship between the two Polycomb marks changes across development. In oocytes and two-cell embryos, H3K27me3 is only weakly correlated with H2Aub, consistent with the genome-wide erasure of the H3K27me3 landscape after fertilization. By the blastocyst stage, however, the two marks colocalize precisely at inactive Polycomb target genes that lack the active mark H3K4me3. This suggested a causal hypothesis: rather than inheriting H3K27me3 from the gametes, human embryos may rebuild it on a scaffold laid down by PRC1 through H2Aub.

To test that idea, the researchers removed H2Aub in human embryos by overexpressing PR-DUB, the BAP1-containing complex that erases the ubiquitin mark, using microinjection of three-pronuclear zygotes donated through IVF programs. Single-embryo RNA sequencing at day 3 and day 4 showed that losing H2Aub impaired embryonic development and caused moderate derepression of Polycomb target genes, particularly those that are normally silent. More striking was what happened to H3K27me3: its reestablishment at Polycomb targets was abolished, while the mark was instead deposited ectopically at inappropriate regions, including gene-poor, partially methylated domains of the genome. In other words, without the H2Aub scaffold, PRC2 not only failed to find its proper targets but painted the wrong parts of the genome.

The team extended the analysis to human embryonic stem cells using an inducible protein-degradation system that removes PRC1 within hours. Acute loss of H2Aub again collapsed H3K27me3 at Polycomb targets and generated ectopic H3K27me3 domains. The experiments also uncovered a second layer of control: DNA methylation. When the researchers inhibited the maintenance methyltransferase DNMT1, additional ectopic H3K27me3 appeared, and combining DNMT1 inhibition with PRC1 degradation produced the strongest mislocalization. H2Aub and DNA methylation therefore cooperate to keep H3K27me3 confined to its correct domains, a partnership that echoes the known interplay between Polycomb complexes and DNA methylation valleys in pluripotent cells.

The study also clarified how PRC1 itself is recruited in human cells. The variant PRC1 machinery, including components such as RYBP, KDM2B and CBX proteins, binds both the GC-rich active genes and the classical Polycomb targets. Knocking down RYBP in stem cells preferentially affected the active GC-rich genes, while catalytic loss of PRC1 hit both classes, with the strongest transcriptional consequences at silenced Polycomb targets. This dual role, dampening highly active GC-rich promoters while enforcing repression at developmental genes, helps explain why H2Aub accumulates at active genes in human embryos without silencing them outright.

Taken together, the findings sketch a stepwise model for the earliest establishment of Polycomb repression in humans. H2Aub appears first, seeded at GC-rich DNA in two-cell embryos, expands across active and inactive genes, and culminates at Polycomb targets in the blastocyst, where it guides PRC2 to redeposit H3K27me3 on a genome that had been wiped nearly clean. Because the experiments were performed in human gametes and embryos, the work fills a gap that mouse studies could not, and it carries practical weight for assisted reproduction, since errors in this reprogramming are thought to contribute to early developmental failure. The datasets have been deposited in public archives, and the authors suggest that the H2Aub-dependent mechanism they describe represents the foundational step by which human embryos rebuild one of their most important layers of gene control.

Subject of Research: H2Aub-dependent reestablishment of Polycomb repression in human preimplantation embryos

Article Title: Establishing Polycomb regulatory landscapes in human early development

Article References: Hu, X., Zhang, C., Liu, B., Lai, F., Ma, S., Hou, Z., Shao, Q., Liu, L., Lu, X., Yu, G., Liu, H., Yang, Z., Wang, N., Wu, X., Lin, Z., Wang, L., Shan, Y., Pan, G., Chen, D., … Xie, W. (2026). Establishing Polycomb regulatory landscapes in human early development. Nature Genetics. https://doi.org/10.1038/s41588-026-02764-y

Image Credits: AI Generated

DOI: 10.1038/s41588-026-02764-y

Keywords: Polycomb, H2AK119ub, H3K27me3, PRC1, PRC2, human embryos, epigenetics, blastocyst, histone modification, DNA methylation, embryonic stem cells, Stacc-seq

The research, led by teams at St. Jude Children’s Research Hospital in Memphis and the Hopp Children’s Cancer Center in Heidelberg, took a deliberately multi-modal approach. Rather than relying on DNA sequencing alone, the investigators profiled six key histone post-translational modifications across 52 fresh-frozen tumor specimens representing all four consensus subgroups. These modifications—H3K4me1, H3K4me3, H3K27me3, H3K27ac, H3K9me3 and H3K36me3—were assayed by chromatin immunoprecipitation followed by sequencing, generating 254 ChIP-seq experiments, of which 229 were newly produced for the study. The histone data were then integrated with whole-genome sequencing, DNA methylation profiling and RNA sequencing datasets covering hundreds of additional tumors, creating one of the most comprehensive epigenomic portraits of any pediatric cancer to date.

To make sense of this torrent of data, the team applied ChromHMM, a hidden Markov model-based algorithm, using the Roadmap 18-state segmentation framework to annotate the genome of each tumor into combinatorial chromatin states. The results were immediately reassuring: clustering tumors by their chromatin states largely recapitulated known subgroup identity, and active chromatin states accurately predicted well-established subgroup signature genes. The ATOH1 and GLI2 loci, hallmarks of proliferating granule neuron progenitors, carried active chromatin specifically in SHH tumors, while the HLX promoter was active only in Group 3 and EOMES, a marker of unipolar brush cell-fated progenitors in the rhombic lip, was active in both Group 3 and Group 4. In other words, subgroup identity is not merely correlated with transcription—it is epigenetically encoded.

But the most consequential finding emerged when the researchers compared the relative abundance of individual chromatin states across subgroups. One state stood out dramatically: the bivalent enhancer state, or EnhBiv, defined by the coexistence of the enhancer mark H3K4me1 and the Polycomb mark H3K27me3. EnhBiv marks regulatory elements that are poised for activation—silent but ready to fire during development. Its genomic coverage was highest in Group 4, followed by Group 3, and lowest in WNT and SHH tumors. Intriguingly, while the classical bivalent promoter state, TssBiv, was distributed evenly across subgroups, EnhBiv was specifically enriched at promoter-proximal regions in Groups 3 and 4, occupying the flanks of transcription start sites rather than their cores, with distinct DNA methylation, GC content and CpG density profiles that set it apart from canonical poised promoters.

The genes marked by this state told a coherent story. The team identified 666 promoters significantly enriched for EnhBiv in Group 4 tumors, which they designated the Group 4 EnhBiv signature. These genes were expressed at their lowest levels precisely in Group 4, and pathway analysis revealed a striking enrichment for neurogenesis and transcriptional regulation terms—exactly the programs one would expect to be held in developmental checkmate by bivalent chromatin. Genes such as PAX3 and PAX2, regulators of neuronal differentiation, were repressed in Groups 3 and 4 through context-dependent mechanisms, with the PAX3 promoter bearing EnhBiv in Group 4 but a fully repressive Polycomb state in Group 3. The implication was clear: Group 3 and 4 tumors, which share a developmental origin in the rhombic lip subventricular zone, are holding neuronal differentiation genes in a poised, repressed state.

The hunt for the regulator responsible led to a single dominant candidate. Enrichment analysis using publicly available chromatin occupancy datasets identified KDM2B, a histone lysine demethylase and core component of the PRC1.1 Polycomb complex, as the most enriched regulator at EnhBiv-marked promoters. KDM2B was also the most significantly upregulated candidate in Group 4 tumors, the only differentially expressed enzyme among the H3K4 and H3K27 methyltransferases and demethylases, and its own promoter carried active chromatin marks in Groups 3 and 4. Elevated KDM2B expression correlated with somatic alterations in other chromatin-modifying genes, including PRDM6, KDM6A and KMT2C, hinting at layered epigenetic dysregulation. Notably, KDM2B expression is normally highest early in cerebellar development and declines during maturation, but its levels in the unipolar brush cell lineage do not fully explain the tumor-specific elevation—suggesting the tumors are actively maintaining an embryonic chromatin program.

Direct validation followed. Using CUT&RUN, a technique that maps protein-DNA interactions in intact chromatin, the researchers examined KDM2B occupancy in patient-derived xenografts representing SHH, Group 3 and Group 4 medulloblastoma. Group 3 and 4 EnhBiv-enriched promoters showed significantly higher KDM2B binding than SHH tumors, with the strongest signal in Group 4, accompanied by elevated H3K27me3. The functional consequences were equally decisive. CRISPR-mediated knockout of KDM2B in three Group 3 cell lines—D425, D283 and CHLA-01-MED—robustly suppressed growth in competition assays, while SHH medulloblastoma and high-grade glioma models were unaffected. Because authentic Group 4 culture models do not exist, the team turned to two Group 4 xenografts, DMB006 and Med2312FH, and showed in vivo that KDM2B loss impaired tumor growth in mouse cerebellum. KDM2B, in short, is a selective dependency of the high-risk subgroups.

To rule out long-term adaptation artifacts and probe therapeutic potential, the researchers engineered a degradation tag into the endogenous KDM2B alleles of D283 cells. Treatment with dTAG compounds degraded the KDM2B protein within two to four hours, and acute loss of the protein reduced proliferation by roughly twenty percent and slightly increased apoptosis in vitro. In a flank xenograft model, seven weeks of dTAG treatment reduced tumor growth and significantly prolonged survival, with immunohistochemistry confirming reduced proliferation. Transcriptomic analysis revealed what KDM2B was actually doing: its degradation predominantly upregulated gene expression, with PRC2 targets, bivalent-marked genes and neuronal differentiation programs rising to the top of the enrichment lists. At the chromatin level, KDM2B loss stripped H3K27me3 from the promoters of upregulated genes and increased H3K4me3, collapsing the EnhBiv state—while global histone modification levels, measured by mass spectrometry, remained essentially unchanged, indicating locus-specific rather than genome-wide effects.

Mechanistically, the study resolved the order of operations in exquisite temporal detail. KDM2B is known to recruit the PRC1.1 complex to unmethylated CpG islands through its CXXC DNA-binding domain, where PRC1.1 deposits H2AK119 ubiquitination, which in turn instructs PRC2 to deposit H3K27me3. Co-immunoprecipitation confirmed that KDM2B physically interacts with PRC1.1 components BCOR, PCGF1 and RYBP, and more weakly with PRC2 components including EZH2, SUZ12 and JARID2. After acute KDM2B degradation, KDM2B and BCOR were lost from repressed promoters within twelve hours, H2AK119ub and EZH2 occupancy declined in parallel, and H3K27me3 followed. Rescue experiments with domain mutants sealed the argument: wild-type KDM2B and JmjC demethylase-defective mutants fully rescued the growth defect, whereas a mutant lacking the CXXC domain failed entirely. KDM2B sustains malignancy through its DNA-binding scaffolding function, not its catalytic demethylase activity.

The therapeutic implications are profound and, unusually for an epigenetic target, well-defined. Because KDM2B’s demethylase activity is dispensable for tumor maintenance, classical catalytic inhibitors are unlikely to help; instead, the dTAG results point toward degrader technologies—proteolysis-targeting chimeras or molecular glues—that physically eliminate the protein. The study also found that multiple PRC1.1 and PRC2 subunits are highly expressed in Groups 3 and 4 and represent Group 3-selective dependencies in the DepMap CRISPR screen, supporting evaluation of existing EZH2 inhibitors and Polycomb-directed approaches as alternatives. With no effective targeted therapies currently available for Group 3 and 4 medulloblastoma, and with the KDM2B-associated EnhBiv state predicted to contribute to malignancy across a broad fraction of patients, the KDM2B–PRC1.1–PRC2 axis now stands as one of the most compelling candidate vulnerabilities in pediatric brain tumor biology—and the multidimensional datasets generated along the way, freely accessible through an online portal, promise to fuel the next wave of discovery.

Subject of Research: Epigenomic regulation of medulloblastoma subgroups and the role of KDM2B as a selective dependency

Article Title: Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency

Article References: Tao, R., Erkek-Ozhan, S., Xu, B., Matsui, Y., Mittal, P., Smith, K. S., Li, Y., Filipovic, D., Xu, R., Gao, Q., Darrow, E., Kumar, R., Djekidel, N., Bajpai, R., Hadley, J., Batts, M., Lewis, S. A., Soliman, T., Reilly, C., … Northcott, P. A. (2026). Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. Nature Genetics, 58(10), 2590-2604. https://doi.org/10.1038/s41588-026-02745-1

Image Credits: AI Generated

DOI: 10.1038/s41588-026-02745-1

Keywords: medulloblastoma, KDM2B, epigenomics, chromatin states, Polycomb, PRC1, PRC2, bivalent enhancer, pediatric brain tumor, H3K27me3, targeted protein degradation, neuronal differentiation

The heart of the platform is cell-free gene expression, or CFE, a cell-free transcription-translation system rebuilt from E. coli lysate that can synthesize proteins on demand outside any living cell. Rather than using CFE merely to make regulatory proteins that diffuse around a chamber, the researchers embedded the reaction directly inside a dense network of stabilized microtubules. DNA plasmids added to the mixture encode kinesin motors, and as the lysate churns out new kinesin, the motors cluster and attach to the microtubule scaffold. The newly synthesized proteins are not passive reporters of the gene circuit; they become the structural and force-generating components of the material itself. Activity, in other words, stops being a parameter chosen by the experimenter and becomes a dynamic variable governed by the underlying biochemical circuit.

The experimental choreography is striking to watch. At early times, when kinesin levels are still low, the microtubule sheet sits in the well as a mechanically quiescent, load-bearing gel with negligible internal motion. After roughly two hours, accumulated kinesin forms the multimeric clusters needed to slide adjacent filaments, and the flat sheet begins to deform. It first aligns, then buckles out of plane into a labyrinth of blister-like protrusions roughly 50 micrometres wide, spaced about 200 micrometres apart. About half an hour after buckling begins, the blisters fracture near their apexes, where deformation is largest, and the fragments reorganize into independently flowing active bundles that sustain turbulent-like extensile flows for up to eight hours, at speeds of roughly 0.3 to 0.5 micrometres per second. The material has, in effect, bootstrapped itself from a passive gel into self-mixing active turbulence using nothing but its own genetic instructions.

The buckling instability itself follows elegant physics. As kinesin accumulates, motor activity builds an in-plane compressive stress in the sheet. When that stress reaches a critical value scaling with the square root of the product of bending rigidity and gravitational loading, the flat sheet becomes unstable and wrinkles. The selected wavelength is set by the balance between the sheet’s bending rigidity and gravity, and the predicted value of roughly 360 micrometres, for a soft gel with an elastic modulus near one kilopascal and a thickness near ten micrometres, agrees well with the observed 150 to 200 micrometres. Crucially, this wavelength stayed essentially constant across all tested DNA concentrations, even though activation times varied enormously. DNA concentration, the authors conclude, does not simply tune how active the material becomes; it controls the trajectory through mechanical phase space by determining when successive active states become accessible.

That distinction became quantitative when the team varied the kinesin-encoding DNA from 0.1 to 13 nanomolar. Higher DNA concentrations advanced the onset of motion from about four hours down to about one hour and accelerated the rise to steady-state velocity, yet the maximal velocity saturated at roughly 0.5 micrometres per second above three nanomolar DNA, corresponding to an estimated tetrameric kinesin cluster concentration of about 0.7 micromolar. Notably, the onset of flow was not triggered at a fixed kinesin concentration: samples with less DNA accumulated more motor protein before flowing, while samples with more DNA flowed earlier at lower motor levels. The transition to buckling is therefore governed by the kinetics of motor production rather than a single critical threshold, and the mean blister width shrank fourfold, from about 80 to about 20 micrometres, as DNA concentration rose, following a power law consistent with an active length scale set by the competition between motor-generated stress and elastic resistance.

To show that gene-circuit architecture, not just expression level, can program mechanical behaviour, the researchers built three regulatory designs. The first was simple constitutive kinesin expression under a T7 promoter, which produced sustained active turbulence, with onset times tunable from about seven hours at low DNA to about 45 minutes at high DNA. The second added mechanical feedback by co-expressing PRC1, a natural microtubule-bundling protein, under a bacterial sigma-70 promoter. At low PRC1 DNA the material flowed as before; at intermediate concentrations buckling was followed by complete arrest; and at high concentrations the sheet pulsed, entering turbulence briefly before friction from excessive bundling overwhelmed the kinesin-generated stresses and froze the network. A single biochemical dial, the PRC1 DNA dose, thus switched the material between flowing, pulsed and arrested states.

The third and most spectacular circuit introduced delayed negative feedback, the same design principle that drives biological clocks. A kinesin-sigma-28 fusion protein activates expression of the bacteriophage lambda CI repressor, which in turn shuts off kinesin production, while the ssrA degradation tags on both proteins allow the endogenous ClpXP protease to clear them. Depending on the repressor DNA concentration, the material either reached steady turbulence, oscillated rhythmically with a period of about 30 minutes, or delivered a single pulse before arresting. The mechanical oscillations are a direct readout of the genetic oscillator: rising kinesin drives flow, delayed repression cuts it off, degradation resets the loop, and the cycle repeats. A material that pulses on its own schedule, encoded entirely in its DNA, is a genuinely new kind of synthetic object.

Tying everything together is a coarse-grained reaction-mechanics model that couples mRNA and protein dynamics to active flow. Transcription and translation rates, mRNA and protein lifetimes, and the regulatory function of each circuit feed into a mapping from motor and cross-linker abundance onto flow velocity. The model quantitatively reproduced all three experimental architectures, and its simulations revealed subtleties invisible to the microscope, such as the fact that velocity saturation in the constitutive case arises from the nonlinear motor-flow relationship rather than from any cessation of protein production, and that pulses and arrest in the PRC1 circuit emerge despite monotonically accumulating proteins, purely from mechanical coupling. The simulations also confirmed that without ClpXP-mediated degradation, the oscillator collapses back into the constitutive steady-flow solution, pinpointing protein turnover as the ingredient that unlocks oscillatory active matter.

Geometry supplies a second, complementary control layer. When the team confined the active sheet in 3D-printed channels between 100 and 500 micrometres wide, blister-like deformations aligned perpendicular to the channel axis, and their constrained length grew with channel width before saturating near 300 micrometres, while their width stayed near 50 micrometres, an intrinsic active length scale. Patterned ridges imposed anisotropic confinement that accelerated buckling and stretched deformations to millimetre scales along unconstrained directions, independent of ridge curvature. The broader implications reach toward self-morphing engineered materials, autonomous soft robots and artificial cells whose mechanics are programmed like software: gene circuits decide when distinct mechanical states emerge, geometry decides how they are spatially organized, and the material itself carries the instructions for its own transformation.

Subject of Research: Genetically programmed self-morphing microtubule-based active matter driven by cell-free gene expression

Article Title: Gene-driven self-morphing microtubule-based active matter

Article References: Silverman, R., Zerbib, E., Garenne, D., Aharoni, H., Noireaux, V., & Tayar, A. M. (2026). Gene-driven self-morphing microtubule-based active matter. Nature Materials. https://doi.org/10.1038/s41563-026-02767-4

Image Credits: AI Generated

DOI: 10.1038/s41563-026-02767-4

Keywords: active matter, microtubules, kinesin, cell-free gene expression, synthetic biology, gene circuits, molecular motors, self-assembly, buckling instability, PRC1, oscillators, bioinspired materials

Polycomb group proteins first announced themselves in fruit flies, where researchers screening for mutants noticed animals with an extra sex comb, a structure normally restricted to the front legs of males. At least sixteen of these genes were eventually identified as repressors of the homeotic, or Hox, genes, the ancient genetic address system that tells every cell where it sits along the body axis. The discovery revealed a profound biological principle: development depends not only on turning genes on, but on keeping the wrong genes firmly off. That principle has been conserved across hundreds of millions of years of evolution, and in vertebrates Polycomb proteins now appear central to cellular differentiation, proliferation, tissue integrity, homeostasis and stem cell renewal.

The molecular machinery is elegantly modular. Polycomb proteins assemble into two major multi-protein complexes, Polycomb Repressive Complex 1 and Polycomb Repressive Complex 2, each built around a catalytic core plus a variable set of accessory subunits. The catalytic heart of PRC1 is a heterodimer of RING1A or RING1B with one of six PCGF family members, and it stamps histone H2A with a single ubiquitin molecule at lysine 119, a mark abbreviated H2AK119ub. PRC2, whose catalytic engine is the methyltransferase EZH1 or EZH2 working alongside EED, SUZ12 and RBBP4/7, deposits di- and trimethyl marks on lysine 27 of histone H3, known as H3K27me2 and H3K27me3. The two complexes are deeply interdependent. The H3K27me3 mark laid down by PRC2 is recognised by the chromobox subunit of canonical PRC1, which is thereby recruited to the same target sites to spread H2AK119ub and lock genes into a repressed state. Variant PRC1 can operate in the opposite direction, ubiquitinating H2A first and pulling PRC2 in behind it, creating a self-reinforcing loop of silencing.

Studying these complexes in mammals is brutally difficult because embryos lacking Polycomb function typically die around gastrulation, long before organs form. This is precisely where the zebrafish, Danio rerio, earns its reputation as one of developmental biology’s most powerful model organisms. Introduced as a genetic system by George Streisinger in the 1970s, zebrafish combine optical clarity, rapid development, sexual maturity within twelve weeks of fertilisation, ex utero embryonic growth that allows manipulation from the single-cell stage, and clutches of hundreds of offspring per mating. Crucially, maternal gene products sustain the embryo up to roughly the 1000-cell stage, far longer than in mice, giving researchers an extended window to probe early gene regulation. Zebrafish embryos also survive early development even with severe cardiovascular defects, because they obtain oxygen by passive diffusion rather than relying solely on blood circulation, something no mammal can do.

The fish genome adds another layer of opportunity. Around 320 million years ago, the teleost lineage underwent a whole-genome duplication event, generating pairs of duplicate genes called ohnologs, of which roughly 15 to 20 percent were retained after rediploidization. In the zebrafish genome, thirteen Polycomb subunits exist as duplicated pairs, although some, including RING1A, PCGF2, PCGF3, RBBP7 and the accessory subunit HDAC2, were lost during rediploidization. Despite these losses, the diversity and complexity of Polycomb complexes remain intact, and researchers can now dissect their roles using an arsenal of techniques ranging from classical ENU mutagenesis and morpholino knockdowns to zinc-finger nucleases, TALENs and CRISPR/Cas9 gene editing.

When it comes to the heart, the review paints a picture of two complexes with distinct but complementary timing. Embryos lacking either PRC1 or PRC2 develop the striking ‘heart-strings’ phenotype: after 48 hours post-fertilisation, the heart fails to loop and instead remains a string-like tube rather than forming its two chambers, the atrium and ventricle. Loss of rnf2, the sole zebrafish homolog of PRC1’s enzymatic subunit, produces pericardial edema and this stringy heart. Yet early cardiac markers such as nkx2.5, tbx5 and hoxb5b appear at normal levels in the lateral plate mesoderm of rnf2 mutants, indicating that the heart field is specified correctly and that PRC1 acts later in the programme. RNA sequencing of individual mutant hearts by Chrispijn and colleagues showed that T-box transcription factors tbx2a, tbx2b, tbx3a and tbx5 become upregulated over time, while structural genes such as vmhc, myl7, myh6 and nppa are downregulated, pointing to a role for PRC1 in the structural maturation of the organ.

The finer details are remarkable. In homozygous rnf2(f5) mutants, genes involved in smooth muscle and skeletal muscle development, which normally participate in transforming the atrioventricular canal between the two chambers, become dysregulated. Transmission electron microscopy reveals misaligned cardiac sarcomeres, with closely packed myofibrils and abnormally spaced I-bands and Z-discs. Calcium imaging with the fluorescent dye fluo-4 AM shows a weakened calcium signal, and the result is a heart that contracts feebly. The expression of atrioventricular canal markers such as alcama, vcana and bmp4 becomes expanded and diffuse rather than tightly constricted. Together these data establish that PRC1 is essential for cardiac sarcomere assembly, the maintenance of contraction, and the proper constriction of the atrioventricular canal and its valves, largely by repressing inappropriate non-cardiac sarcomere genes. A second non-canonical PRC1 component, mga, adds another twist: morpholino knockdown of mgaa blocks heart tube looping, and the defect can be rescued by co-reducing gata4, whose transcript levels rise two- to four-fold in the mutant, showing that variant PRC1 fine-tunes this key regulator.

PRC2, by contrast, acts earlier. Maternal-zygotic ezh2 mutants, in which the methyltransferase is eliminated from both maternal and zygotic sources, show reduced numbers of nkx2.5-expressing cardiac progenitors, partially reduced chamber markers, and cardiomyocytes that wander away from the cardiac tube, leaving a small, tubular heart that never loops. The atrioventricular canal fails to form properly, possibly because of ectopic expression of has2, a gene that promotes cardiac cell migration. Chromatin immunoprecipitation sequencing shows that both ezh2 and the H3K27me3 mark are absent from heart-development genes such as tbx3a, tbx5 and isl1, and PRC1 peaks are missing from the same loci, consistent with PRC2 recruiting PRC1 to its targets. Intriguingly, ezh1 mutants show no heart defects despite a modest reduction in H3K27me3, and ezh1;ezh2 double mutants resemble ezh2 single mutants, demonstrating that ezh1 cannot compensate for ezh2 in the heart. Pharmacological inhibitors of EZH2, including GSK126, DZNep and PF-06726304 acetate, all induce heart edema, reinforcing the complex’s central role.

The pectoral fin story is equally compelling, and arguably more evolutionarily provocative. Zebrafish pectoral fins are the evolutionary relatives of tetrapod forelimbs, and although a fin and an arm look nothing alike, the underlying regulatory logic is deeply conserved. Retinoic acid, synthesised by the enzyme aldh1a2, initiates the programme by activating wnt2b and tbx5 in the lateral plate mesoderm; tbx5 then triggers the Fgf cascade that drives outgrowth, while shh, hox genes and the apical ectodermal ridge pattern the bud along its anterior-posterior, dorsal-ventral and proximal-distal axes. When PRC1 or PRC2 function is lost, pectoral fins simply fail to form. In rnf2 mutants, early fin markers such as tbx5 and hand2 appear on schedule but vanish from the fin mesenchyme by 40 hours post-fertilisation, the Fgf targets fgf24 and fgf10 shrink to a small patch, and apical ectodermal ridge markers such as dlx2a, fgf8 and versican are absent, so fin initiation occurs but outgrowth collapses.

The epigenetic mechanism behind the missing fins involves a runaway retinoic acid signal. In rnf2 mutants, aldh1a2 is overexpressed and spreads beyond its normal posterior domain, while cyp26a1, which degrades retinoic acid, is reduced, producing excess retinoic acid that the embryo tries to metabolise by upregulating genes such as dhrs3. Hox genes normally restricted to the anterior body, including hoxc6a and hoxc8a, are ectopically expressed in the posterior and throughout the brain, and fin-specific hox expression of hoxa9b, hoxc8a and hoxd9a is lost while their axial domains expand. Patterning markers such as shh, msxc, eng1a and wnt7a are absent or reduced. Even partially suppressing retinoic acid with DEAB restores tbx5 and hand2 only partially, insufficient to restart fin outgrowth. In maternal-zygotic ezh2 mutants the same picture emerges: tbx5 is entirely missing, the hoxab cluster expands beyond its normal domain, and shh is absent from the fin bud. Because PcG-deficient zebrafish survive gastrulation where mice do not, this model opens a unique window onto how epigenetic silencing sculpts organs, and the authors argue that understanding these molecular pathways could ultimately illuminate congenital heart defects and limb abnormalities in humans, and point toward new therapeutic targets in regenerative medicine.

Subject of Research: Polycomb group protein-mediated epigenetic regulation of heart and pectoral fin development in zebrafish

Article Title: Epigenetic regulation in zebrafish development: the roles of polycomb group proteins in heart and pectoral fin development

Article References: Kavade, P. S., Parab, S. S., Capone, V., Carannante, D., Ambrosino, C., Altucci, L., & Carafa, V. (2024). Epigenetic regulation in zebrafish development: the roles of polycomb group proteins in heart and pectoral fin development. Epigenetics Communications, 4(1), Article 7. https://doi.org/10.1186/s43682-024-00030-y

Image Credits: AI Generated

DOI: 10.1186/s43682-024-00030-y

Keywords: Polycomb group proteins, PRC1, PRC2, zebrafish, epigenetics, heart development, pectoral fin development, Hox genes, histone modification, retinoic acid signaling, EZH2, developmental biology

Polycomb repressive complexes were first discovered in fruit flies through mutations that transformed body segments, a striking phenotype that hinted at their role in maintaining the expression patterns of developmental genes. In mammals, the two major Polycomb systems, PRC1 and PRC2, work in concert to silence lineages-inappropriate genes. PRC2 deposits the histone mark H3K27me3, a chemical flag on lysine 27 of histone H3, while PRC1 deposits a complementary mark, monoubiquitinated lysine 119 on histone H2A, abbreviated H2AK119ub. Both marks are hallmarks of facultative heterochromatin, the compacted but still potentially reversible form of chromatin that keeps developmental regulators quiet without permanently altering the underlying DNA sequence.

Canonical PRC1 is not a single protein but a holocomplex built from four families of subunits. At its catalytic heart sits a heterodimer of a RING-family E3 ubiquitin ligase component, RING1A or RING1B, paired with one of six PCGF proteins, most commonly PCGF2 or PCGF4 in the canonical form. Surrounding this catalytic core are the Polyhomeotic proteins PHC1, PHC2 or PHC3, which mediate higher-order chromatin interactions, and the chromodomain proteins of the CBX family, CBX2, CBX4, CBX6, CBX7 or CBX8, which read the H3K27me3 mark laid down by PRC2 and help recruit PRC1 to its genomic destinations. This modular organisation has made PRC1 notoriously difficult to study as an intact entity: the complex flexes, adopts multiple compositions, and interacts dynamically with its nucleosome substrate.

Cryo-electron microscopy is uniquely suited to this challenge. The technique flash-freezes purified protein complexes in a thin film of vitreous ice and images thousands of individual particles, computationally sorting the views into a three-dimensional map at near-atomic resolution. For PRC1, the technical hurdles were formidable. The complex must be purified in a homogeneous state, yet its different subunit paralogs generate compositional heterogeneity that can blur reconstructions. By isolating a defined canonical holocomplex and pushing the limits of particle classification and map refinement, Ciapponi and colleagues were able to visualise the architecture of the entire assembly, resolving how each subunit docks onto its neighbours and where the catalytic machinery sits relative to the rest of the complex.

The resulting structure reveals a striking spatial economy. The RING1 catalytic subunit and its PCGF partner form a central scaffold onto which the Polyhomeotic and CBX subunits assemble in a defined arrangement. Critically, the positions of these accessory modules explain why they are not passive passengers. The chromodomain subunit projects away from the catalytic core, positioned to reach out and engage neighbouring nucleosomes bearing the H3K27me3 mark, thereby coupling recognition of the PRC2 histone code to the placement of the PRC1 ligase. The Polyhomeotic subunits, meanwhile, occupy an architecture consistent with their established role in bridging distant chromatin regions, the process of chromatin compaction that physically reinforces gene silencing.

Beyond the static snapshot, the study directly interrogated enzymatic function. The catalytic RING1B-containing core acts as an E3 ubiquitin ligase, transferring ubiquitin from an E2 conjugating enzyme onto lysine 119 of histone H2A within the nucleosome. In experiments with reconstituted nucleosomes and purified complex variants, the authors examined how mutations or perturbations that disrupt the interfaces seen in the structure affect H2A monoubiquitination activity. The results support a model in which the holocomplex architecture coordinates substrate engagement: the catalytic module must be correctly positioned relative to the nucleosome acidic patch, the docking surface on the histone disc where RING1B binds, while the peripheral subunits stabilise the active conformation and mediate the multivalent contacts that make targeting efficient.

Perhaps the most consequential aspect of the work concerns genome targeting. How does PRC1 find the hundreds of genomic loci it represses, including the CpG islands that overlap promoters of developmental regulators? The prevailing model holds that recruitment depends on combinatorial recognition: CBX chromodomains bind H3K27me3 deposited by PRC2, while additional factors recognise unmethylated CpG DNA. The new structure shows how the CBX subunit is oriented within the holocomplex such that its chromodomain can sample adjacent nucleosomes, and how the overall geometry of the complex allows multiple weak interactions to cooperate into a stable, specific engagement with its chromatin substrate. This multivalent design explains how PRC1 achieves both specificity, favouring the correct genomic loci, and stability, maintaining silencing through cell divisions.

The biological stakes of this work are considerable. Aberrant Polycomb function is implicated in a long list of human diseases. Overexpression of BMI1, the mammalian homolog of PCGF4, drives proliferation in numerous cancers and is a recognised marker of tumour-initiating stem-like cells. Loss-of-function mutations in Polycomb components cause developmental syndromes, including Weaver syndrome and other overgrowth disorders linked to EZH2 and EED of PRC2, and Shashi-Penman syndrome linked to EED and EZHIP, while somatic alterations in PRC1 genes recur across lymphoma, leukaemia and solid tumours. Understanding the assembly pathway and enzymatic mechanism of canonical PRC1 at structural resolution therefore provides a rational foundation for therapeutic intervention, informing the design of molecules that destabilise pathological complexes or block their catalytic activity.

The study also resolves longstanding debates about the relationship between structure and function in Polycomb biology. Earlier biochemical work established the individual interactions, RING1B with PCGF subunits, CBX chromodomains with H3K27me3, Polyhomeotic with chromatin, but it remained unclear how these pieces fit together in the intact holocomplex and whether the intact assembly behaves differently from its parts. By presenting the architecture of the canonical PRC1 holocomplex alongside enzymatic assays and genome-targeting data within a single integrated analysis, Ciapponi and colleagues provide the kind of mechanistic completeness that individual fragment studies could not. Their structure serves as a framework onto which decades of genetic, biochemical and genomic observations can now be mapped.

Future work will build on this foundation in several directions. Cryo-EM structures of PRC1 variants containing different PCGF, CBX and Polyhomeotic paralogs will reveal how compositional diversity translates into functional specialisation. Higher-resolution reconstructions of the complex bound to nucleosome substrates will clarify the exact geometry of ubiquitin transfer onto H2A lysine 119. And comparative studies with the non-canonical PRC1 complexes, which lack CBX subunits and rely instead on KDM2B and other recruitment factors, will illuminate how evolution has tuned the same catalytic core to serve distinct targeting strategies. For now, the structure determined by Ciapponi and colleagues stands as a landmark: the first comprehensive view of one of the cell’s most important gene-silencing machines, and a vivid demonstration of how cryo-electron microscopy is transforming our understanding of the molecular logic of chromatin regulation.

Subject of Research: Cryo-EM structure, enzymatic activity and genome targeting of canonical Polycomb repressive complex 1

Article Title: Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1

Article References: Ciapponi, M., Cafiso, M., Schkölziger, S., Benda, C., Bonnet, J., & Müller, J. (2026). Cryo-EM structure, enzymatic activity and genome targeting of canonical PRC1. Nature Structural & Molecular Biology, 33(10), 1516-1526. https://doi.org/10.1038/s41594-026-01885-6

Image Credits: AI Generated

DOI: 10.1038/s41594-026-01885-6

Keywords: PRC1, cryo-EM, Polycomb, chromatin, epigenetics, gene silencing, H2A ubiquitination, RING1B, structural biology, histone modification, genome targeting, structure

The review centers on CBX7, a member of the Chromobox protein family and a core subunit of Polycomb Repressive Complex 1, one of the two major Polycomb complexes that shape the epigenetic landscape of mammalian cells. Epigenetics, a field now seventy years old, concerns heritable changes in gene expression that occur without altering the underlying DNA sequence, chiefly through DNA methylation and histone modifications. Polycomb group proteins sit at the heart of this regulatory architecture, controlling cell fate decisions by modulating the expression of genes responsible for development, differentiation and, when things go wrong, cancer. Genome-wide studies have established that Polycomb Repressive Complex 1 and Polycomb Repressive Complex 2 function as crucial transcriptional regulators targeting a wide range of genes involved in tumor development, and the chromodomain-containing CBX proteins are the molecular anchors that tether Polycomb activity to specific chromatin regions.

Structurally, CBX7 is a study in molecular precision. Its chromodomain, spanning amino acids 9 to 48, descends from a conserved 37-amino acid sequence first identified in the Polycomb and heterochromatin protein 1 proteins of the fruit fly Drosophila melanogaster. Phylogenetic analyses show that the CBX7 chromodomain is more closely related to other Polycomb group proteins such as CBX2, CBX4, CBX6 and CBX8 than to the HP1 family members CBX1, CBX3 and CBX5, and unlike HP1 proteins, CBX7 lacks a chromoshadow domain. Instead, its chromodomain carries unique conserved residues exclusive to Polycomb proteins that are necessary for Polycomb dimer formation and for recognizing the tri-methylated lysine 27 mark on histone H3, known as H3K27me3. Thanks to the stable geometry of this domain, CBX7 preferentially binds H3K27me3, a mark laid down by the PRC2 complex through its core subunits EZH2, SUZ12 and EED. Once anchored, CBX7 recruits the canonical PRC1 complex, whose catalytic core ubiquitinates lysine 119 on histone H2A, compacting chromatin and silencing target genes. In this way, CBX7 acts as a functional bridge between PRC2 activity and stable transcriptional repression.

The protein also exists in two isoforms with strikingly divergent behavior. The 36-kilodalton nuclear form, p36CBX7, is expressed in proliferating cells and drives gene regulation, while the 22-kilodalton cytoplasmic form, p22CBX7, is induced by serum deprivation and restrains cell proliferation. This context- and tissue-specific duality foreshadows the protein’s complex role in cancer. Across human tumors, CBX7 behaves as either an oncogene or a tumor suppressor depending on the dominant signaling pathways and the genetic and epigenetic makeup of each tumor type. In lymphomas and gastric cancer, overexpressed CBX7 represses tumor-suppressive genes such as Ink4a/Arf and Trail, allowing malignant cells to evade senescence and apoptosis. In contrast, cancers of the breast, pancreas, lung, thyroid, colon, bladder and brain, including glioblastoma, consistently show reduced CBX7 expression compared with normal tissue, pointing to a tumor-suppressive function in these settings.

In glioblastoma specifically, the evidence for CBX7 as a tumor suppressor is compelling. High-grade gliomas exhibit significantly lower CBX7 levels than low-grade gliomas, and this downregulation correlates with aggressive disease and poor prognosis. When lost CBX7 is restored in glioma cells, tumor growth is inhibited and the cell cycle arrests at the G0/G1 phase. One well-characterized mechanism involves competition with the architectural transcription factor HMGA1 for control of the CCNE1 promoter, which encodes cyclin E1, a key driver of the G1/S transition. Under normal conditions, CBX7 partners with histone deacetylase 2 to form a repressive complex on the CCNE1 promoter. When CBX7 is lost, HMGA1 evicts this complex, cyclin E1 expression surges, and glioblastoma cells proliferate uncontrollably. HMGA1 also directly binds the CBX7 promoter itself, adding a further layer of antagonism.

The tumor-suppressive reach of CBX7 extends well beyond cell-cycle control into the machinery of invasion and stemness. CBX7 directly binds the promoter of CDH1, the gene encoding the adhesion molecule E-cadherin, where it restrains HDAC2 activity and promotes activating acetylation and methylation marks on histones H3 and H4, stabilizing the epithelial phenotype. Loss of CBX7 silences CDH1, promotes epithelial-to-mesenchymal transition and drives the invasiveness that typifies glioblastoma progression. CBX7 also prevents HMGA1 from transcriptionally activating SPP1, the gene encoding osteopontin, another potent EMT stimulator. Perhaps most strikingly, recent work shows that CBX7 engages PRC1 to facilitate ubiquitin-proteasome degradation of myosin heavy chain 9, thereby suppressing NF-kappaB signaling and stripping glioblastoma cells of their stem-like characteristics. Restoring MYH9 reverses this effect, re-establishing stemness, proliferation and invasion, and defining a CBX7-MYH9-NF-kappaB regulatory axis that researchers regard as a desirable therapeutic target.

Two further oncogenic pathways fall under CBX7’s control. The Wnt/beta-catenin pathway, aberrantly activated in many glioblastomas, is dampened when CBX7 binds the promoter of DKK1, a Wnt inhibitor, upregulating its expression and simultaneously reducing ZEB1, a transcription factor that promotes invasion, metastasis and epithelial-to-mesenchymal transition. Restoring CBX7 in glioblastoma cells suppresses both Wnt signaling and ZEB1, curtailing tumor growth and metastatic potential. CBX7 likewise modulates the Hippo pathway through connective tissue growth factor, encoded by CTGF, a key component of the YAP/TAZ signaling axis. When CBX7 is lost, PRC1-mediated gene suppression fails, YAP/TAZ signaling becomes hyperactive, TEAD-dependent transcription rises and CTGF is overexpressed, activating kinases such as SAPK/JNK and fueling glioma cell invasion and migration. Ectopic CBX7 expression additionally reduces the matrix metalloproteinases MMP2 and MMP9, major markers of glioblastoma invasiveness, angiogenesis and immune modulation.

How does such a critical tumor suppressor get silenced in the first place? The review details two principal mechanisms. The first is epigenetic: hypermethylation of the CBX7 promoter, confirmed by bisulfite sequencing in glioblastoma tissues, glioma-derived cell lines and normal brain, with clear enrichment of methylation in tumor samples. Knockdown studies identified the DNA methyltransferases DNMT1 and DNMT3A, but not DNMT3B, as the enzymes responsible for this silencing, and treatment with a methylation inhibitor restored CBX7 mRNA expression in glioma cell lines. The second mechanism is post-transcriptional, mediated by microRNAs. The MYC-responsive microRNA miR-9 lowers CBX7 protein levels, while CBX7 in turn binds the miR-9 promoter and represses its expression, creating an autoregulatory loop that also feeds into the control of p16-INK4a, a key effector of replicative senescence. Separately, the oncogenic miR-18a, highly expressed in glioblastoma, directly targets CBX7 mRNA, and silencing miR-18a in animal models markedly slows tumor growth and prolongs survival.

The translational implications are substantial, though tempered by caution. No CBX7-targeted therapy is yet in clinical use for glioblastoma, and the review’s authors stress that the protein’s role in normal cells must be fully understood before therapeutic modulation is attempted. Nevertheless, pharmacological proof of concept already exists in other malignancies: chromodomain-targeting inhibitors such as UNC3866, UNC4976, MS452, EC-134 and BDA-41 have dislodged overexpressed CBX7 from chromatin in lymphoid leukemia models, inducing differentiation and growth arrest. For glioblastoma, the therapeutic logic runs in the opposite direction, toward restoring rather than inhibiting CBX7 function, using epigenetic drugs, miRNA-based approaches or targeted modulation of CBX7-associated complexes and downstream pathways. Beyond therapy, CBX7’s consistent downregulation and correlation with tumor aggressiveness make it a promising prognostic biomarker, measurable through immunohistochemistry, methylation profiling or miRNA expression analysis to classify patients and guide treatment decisions. As the authors conclude, CBX7 represents a particularly promising starting point for developing more accurate and potent targeted treatments, and for deepening our understanding of glioblastoma biology in a disease that urgently needs both.

Subject of Research: The role of the Polycomb protein CBX7 as an epigenetic tumor suppressor in glioblastoma and its therapeutic potential.

Article Title: Epigenetic regulation by CBX7 in glioblastoma: molecular mechanisms and translational perspectives

Article References: Fayyaz, F., Favale, G., Capasso, L., Casalino, R., Mele, D., Verrilli, G., Conte, M., Carafa, V., Nebbioso, A., & Altucci, L. (2025). Epigenetic regulation by CBX7 in glioblastoma: molecular mechanisms and translational perspectives. Epigenetics Communications, 6(1), Article 2. https://doi.org/10.1186/s43682-025-00043-1

Image Credits: AI Generated

DOI: 10.1186/s43682-025-00043-1

Keywords: CBX7, glioblastoma, epigenetics, Polycomb, PRC1, PRC2, chromodomain, DNA methylation, microRNA, Wnt signaling, Hippo pathway, tumor suppressor