The work, published in the journal Molecular Cell, was led by researchers at the Centre for Genomic Regulation (CRG) in Barcelona together with the City University of Hong Kong and the Guangdong Provincial People’s Hospital of the Guangdong Academy of Medical Sciences at Southern Medical University. The team describes a new class of fluorescent probes, called HoTs, which are small enough to slip into living cells unaided and bind directly to DNA. What makes them special is their blinking behaviour: rather than glowing continuously, they flicker intermittently, like strings of fairy lights switching on and off at random.

That flickering is not a quirk but the key to the entire technique. Conventional light microscopes hit a hard physical limit at roughly 200 nanometres, the diffraction barrier that blurs anything packed more tightly than that. If every dye molecule in a sample lit up simultaneously, even the most advanced microscope would simply record an overlapping glow. But if molecules emit one at a time, or in small sparse groups, each flash can be localised individually. Thousands of snapshots, each capturing a scattered subset of blinking probes, can then be stitched together by software into a reconstructed image far sharper than any single exposure. This is the principle behind single-molecule localisation microscopy, and the new probes were engineered specifically to deliver the right blinking dynamics for it.

With the HoT dyes, the researchers deployed STORM, a stochastic optical reconstruction microscopy technique, to visualise DNA inside living human cells at a resolution of 20 nanometres. That is a tenfold improvement over the conventional limit, achieved not on fixed and chemically treated samples but on cells that were alive throughout the imaging. The team demonstrated the approach in living human skin cells and in living HeLa cancer cells grown in the laboratory. In parallel, they pushed the technology even further on preserved cells, using MINFLUX, an ultra-high-resolution method that tracks individual fluorophores, to pinpoint single dye molecules to within three nanometres. The diameter of the DNA double helix is approximately two nanometres, so a localisation precision of three nanometres brings imaging to the very doorstep of the molecule itself.

The significance of that achievement becomes clear when one considers what biologists have been missing. Every human cell contains roughly two metres of DNA, folded and compressed into a nucleus only a few micrometres across. The degree to which that DNA is wound tightly or left loose is not decorative; it is one of the principal layers of biological control. Tightly packed DNA tends to be silent, while loosely packed regions are accessible to the molecular machinery that reads genes. Yet almost all existing images of DNA folding come from dead, fixed cells, because the powerful microscopy techniques needed to track individual genomic components typically require harsh chemicals and intense laser illumination that living cells cannot survive. The new probes sidestep that constraint, allowing chromatin, the natural state of DNA in cells, to be watched in motion.

Professor Hongyan Sun of the City University of Hong Kong, co-senior author of the study, highlighted the central design problem: the key challenge was to create fluorophores with the right blinking behaviour for super-resolution imaging. ICREA Research Professor Pia Cosma of the CRG, senior author, explained the dual power of the system: with the same dye, researchers can watch DNA moving in a living cell, revealing how chromatin behaves, and zoom into preserved cells until they are almost at the scale of the DNA molecule itself. Combining both approaches, she noted, allows one of the main layers of control in human biology to be seen at unprecedented resolution.

The team did not stop at laboratory cell lines. In a striking demonstration of clinical relevance, they applied the probes to ordinary wax-preserved tissue slices taken from three bowel cancer patients, the same kind of samples hospitals routinely store after biopsies. In the tumour tissue, the DNA was noticeably looser and more spread out than in the healthy tissue sitting immediately beside it. This observation aligns with earlier findings that DNA unpacks progressively as cancer takes hold, and it suggests a provocative possibility: how loosely a cell’s DNA is folded could eventually serve as a measurable indicator of how far a tumour has progressed or how aggressive it is. Today, doctors examine these biopsies largely by eye using staining methods more than a century old. The ability to add a three-dimensional readout of how DNA occupies space inside cells could one day become an additional diagnostic clue.

The probes also proved useful beyond human tissue. The researchers imaged slices of zebrafish eye, an animal famous for its ability to regrow damaged retina. Retinal regeneration in these fish is thought to involve cells loosening their DNA packaging in order to become flexible again, and the new dyes offer a way to observe that process directly at nanometre scale. Such experiments hint at a broader future for the technology in regenerative medicine, where identifying which cells have entered a plastic, stem-like state is a central challenge.

Artificial intelligence enters the story as a force multiplier. The same team had previously unveiled a program called AINU, short for AI of the Nucleus, in 2024, which scans super-resolution images of cellular DNA and detects patterns far too subtle for the human eye. Originally, AINU could only analyse cells that had been killed and preserved. Trained on the new living-cell images produced with the HoT probes, the AI correctly distinguished skin cells from stem cells between 96 and 98 per cent of the time. The two cell types carry identical genomes but fold their DNA differently, and the algorithm could see that difference in living material. The researchers hope the same principle could eventually be turned to distinguishing cancerous from healthy tissue, or to selecting the most promising stem cells to accelerate regenerative medicine.

The technology is not without limits, and the authors are candid about them. The probes coat the entirety of the DNA rather than highlighting any single gene, so they reveal global packaging architecture rather than gene-specific organisation. The very sharpest pictures, at the three-nanometre scale, required preserved rather than living cells, although the team reports that follow-up studies are already under way and that MINFLUX has the potential to image the probes in living cells as well. Even so, the combination demonstrated here, live-cell chromatin dynamics at 20 nanometres and near-helix-scale localisation in preserved clinical samples, marks a genuine step change. A staining method from the nineteenth century may soon share the microscope bench with blinking molecular probes and AI readers, giving clinicians and researchers a view of the genome not as a static blueprint but as a living, breathing three-dimensional structure whose shape itself carries diagnostic information.

Subject of Research: Super-resolution fluorescence imaging of DNA packaging in living and preserved cells using self-blinking probes

Article Title: Self-blinking ‘fairy lights’ allow DNA to be imaged at almost double helix width resolution

Article References: Self-blinking ‘fairy lights’ allow DNA to be imaged at almost double helix width resolution. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: super-resolution microscopy, STORM, MINFLUX, chromatin, DNA packaging, fluorescent probes, cancer diagnostics, biopsy imaging, artificial intelligence, stem cells, zebrafish, Molecular Cell

Now, an international research team led by the Institute for Research in Biomedicine (IRB Barcelona), the University of Cambridge, UT Southwestern Medical Center and the Howard Hughes Medical Institute has unveiled a tool that promises to change how scientists study this hidden world. Called OpenCGChromatin, the software works as what the researchers describe as a computational microscope. Rather than using lenses and light, it uses computer simulations to explore how chromatin folds, how its molecular components interact with one another, and which physical forces hold its structures together. The tool is described in a study published in Nature Communications, and it has been released as open-source software so that researchers anywhere can use it to investigate the physical principles underlying genome organisation.

The central problem the team set out to solve is one of scale. Experiments can reveal individual molecular interactions in exquisite detail, or they can capture the behaviour of large stretches of chromatin in bulk, but connecting the two levels has remained stubbornly difficult. The challenge, as Dr. Modesto Orozco, head of the Molecular Modeling and Bioinformatics Laboratory at IRB Barcelona, ICREA Academia researcher and professor at the University of Barcelona, who co-led the study, explains, is to connect interactions between individual molecules with the behaviour of much larger stretches of chromatin. The new tool allows researchers to study both within the same framework, and to understand how small molecular changes can alter DNA packaging across the entire system.

Technically, OpenCGChromatin is a coarse-grained model, a class of simulation approaches that simplifies the representation of atoms and molecules while preserving the essential physics of their interactions. In this case, the tool combines a detailed representation of DNA and proteins with far greater computational efficiency than previous models could achieve. The practical consequence is striking: researchers can now study chromatin systems more than ten times larger than those accessible to earlier models at comparable resolution. That includes assemblies containing hundreds of nucleosomes, the basic units of DNA packaging, which means simulations can finally reach the scale of gene-sized structures rather than remaining confined to small fragments.

The design of the model was not developed in isolation from experimental reality. Professor Rosana Collepardo-Guevara of the University of Cambridge, who co-led the study, notes that OpenCGChromatin was inspired by beautiful cryo-electron tomography experimental work from the group of Professor Michael Rosen at UT Southwestern Medical Center and the Howard Hughes Medical Institute, who co-led the study. Cryo-electron tomography is an imaging technique that can visualise the three-dimensional organisation of biological molecules inside cells at near-atomic resolution, and grounding the model in such data helps ensure that the simulations reflect genuine biology rather than purely theoretical constructs.

A crucial test for any computational model is whether it reproduces what experiments actually show. According to the research team, the simulations generated by OpenCGChromatin reproduce observations from microscopy and biochemical experiments, providing confidence that the model captures real physical behaviour. But the simulations go a step further, revealing movements of flexible histone regions that are difficult to resolve experimentally. These histone tails, the protein segments that protrude from the nucleosome core, are known to play important roles in chromatin behaviour, yet their constant motion makes them elusive targets for laboratory imaging. The computational microscope can track them in ways that bench-top instruments cannot.

This ability to observe the unobservable is where the tool earns its microscope nickname. In the simulations, researchers can watch how nucleosomes shift position, how DNA unwraps and rewraps around histone cores, and how chemical modifications to histone proteins propagate their effects through large chromatin assemblies. David Farré-Gil, also an author of the paper, explains that the simulations help scientists understand why changing the spacing between nucleosomes, or adding chemical modifications to histones, can make chromatin behave differently. These are precisely the kinds of changes that cells use naturally to regulate gene activity, and that go awry in diseases such as cancer.

The significance of this work extends into one of the hottest areas of contemporary cell biology: biomolecular condensates. These are membrane-less compartments that form inside cells when proteins and nucleic acids cluster together, and chromatin is increasingly understood to participate in their formation and function. Collepardo-Guevara highlights that the tool now allows researchers to connect the chemical makeup of chromatin to its organisation across scales, from molecular interactions to gene-sized structures and biomolecular condensates, while remaining closely grounded in experiment. Bridging those scales within a single computational framework is what makes the approach genuinely new, rather than an incremental improvement on existing models.

The achievement behind the software is also a story of technical persistence. Collepardo-Guevara credits Kieran Russell, first author of the study, with pushing the state of the art in chromatin modelling, allowing simulations at a scale and level of molecular detail that were previously out of reach. In her view, OpenCGChromatin opens up a completely new range of questions that can now be addressed computationally. That shift matters because questions that once required years of painstaking experimental work can now be explored in silico first, generating hypotheses that experiments can then test, and allowing researchers to scan through many possible chromatin configurations far faster than laboratory methods would permit.

By releasing OpenCGChromatin as open-source software, the team has invited the wider scientific community to build on their work. Open availability means that laboratories studying gene regulation, DNA repair, genome architecture or the biophysics of condensates can adapt the model to their own questions without needing to develop the underlying technology from scratch. As chromatin research moves from describing static structures to understanding dynamic, force-driven behaviour, tools that connect molecular chemistry to large-scale genome organisation are likely to become indispensable. This computational microscope offers a way to watch the genome breathe, fold and reorganise itself, one nucleosome at a time, and to finally link the smallest molecular events to the grand architecture of our DNA.

Subject of Research: Development of a coarse-grained computational simulation tool for studying chromatin organisation and dynamics

Article Title: A new “computational microscope” to explore chromatin

Article References: A new “computational microscope” to explore chromatin. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: chromatin, nucleosome, histones, molecular dynamics simulation, coarse-grained modelling, genome organisation, OpenCGChromatin, DNA packaging, biomolecular condensates, cryo-electron tomography, computational biology, epigenetics

A study published on September 22 in the journal Molecular Cell by researchers at The Ohio State University and the University of Zurich shows that linker histone H1 wanders aimlessly inside the cell even when its target, a nucleosome with spooled-up segments of DNA, is directly in front of it. Although H1 binds readily to two DNA strands that stick out from the nucleosome, it struggles to bind to the nucleosome itself. Only when a chaperone protein escorts it does H1 successfully load onto the nucleosome and carry out its gene-silencing role. The finding fills a long-standing gap in scientists’ understanding of how one of the genome’s most important architectural proteins finds its proper place.

The research team, led by first author Ehsan Akbari, a research scientist in the laboratory of senior author Michael Poirier, professor of physics at The Ohio State University, tackled the question with single-molecule experiments. Rather than averaging the behavior of millions of molecules together, single-molecule methods allow researchers to quantify molecular motions and interactions one molecule at a time, watching individual H1 proteins and their nucleosome targets before, during and after H1 bound to the DNA and to the center of the nucleosome. The team combined optical tweezer instrumentation, which uses highly focused laser light to manipulate and measure single molecules, with single-molecule fluorescence measurements to visualize the process in real time.

“Many proteins are dynamic, and the way you get at mechanistic dynamic information is by doing these single-molecule studies where you literally can watch in real time what individual molecules are doing,” Poirier said. This approach proved essential for a protein whose behavior defied expectations. When the researchers observed H1 in action, they found that the protein continues to move around even after it binds to DNA. More strikingly, instead of loading onto the nucleosome by way of the DNA it had attached to, the protein reflects away from the nucleosome entirely.

“It moves around and doesn’t even go to the nucleosome, which I didn’t believe,” Poirier said. That unexpected observation prompted the team to hypothesize that a chaperone protein might be the missing link in the loading process. Chaperone proteins are known to assist other proteins in folding, targeting and assembly, and three linker histone chaperone proteins were already known to science. When the researchers added these chaperones to their experiments, the results were dramatic.

“Amazingly, the chaperones did a bunch of things to regulate how H1 goes around and how it actually finds and gets onto nucleosomes. And that’s the main point, that people have not understood how H1 loads and gets onto a nucleosome,” Poirier said. “What we found was that it actually will directly load and likes to slide along DNA – we also didn’t even know that it would do that – but it needs a chaperone to help get onto the actual nucleosome.” The experiments revealed that H1 can load directly onto DNA and slide along it, a previously unknown behavior, but the final step of binding to the nucleosome core requires chaperone assistance.

The biological stakes of this process are considerable. Every cell in a plant, animal or human contains the organism’s entire genome, and nucleosomes fold in on each other, clumping together to form chromatin. Linker histone H1’s job is to facilitate chromatin compaction, ensuring that DNA segments containing genes the cell is not using stay wrapped up and unavailable for expression. “We know that H1 is important for compacting the genome, which is important for regulating gene expression,” Poirier said. “In the genome, regions that are going to be compacted are loaded with a lot of H1, while regions that are more open are going to have less H1.”

Most genes in any given cell are turned off at any moment, because only a small fraction of the genome is active in a particular cell type. Maintaining the silent majority in compacted states is therefore a fundamental requirement of cellular life, and H1 is a central player in that maintenance. “H1 is a key regulator of which genes are being used by a cell and which genes are not,” Poirier said. “If you want to understand how disease develops because gene expression is no longer working properly, then you need to understand how H1 works. Once you understand this, then you open up the possibility for new therapies that counteract this cause of disease.”

The connection to disease is not hypothetical. H1 is well known for its role in compacting genes and for its connection to cancer when it undergoes mutation. Mutations in linker histone genes and alterations in how H1 is deployed across the genome can disrupt the careful balance between open, active chromatin and closed, silent chromatin, contributing to the misregulated gene expression that characterizes cancer cells. Understanding the mechanics of how H1 reaches nucleosomes in the first place gives researchers a new handle on where this process could go wrong.

Though the work does not tell the entire H1 story, the step-by-step visualizations offer concrete directions for future research. Poirier’s laboratory has previously studied H1 variants and the post-translational modifications that can change H1 targeting and function after the protein has been fabricated by the cell. “One very natural thing to do next is to look at how these variants, post-translational modifications, and, most importantly, cancer-relevant mutations influence H1 properties and function that we are now in a position to measure,” he said. With single-molecule tools now capable of watching H1’s loading pathway in detail, the effects of disease-linked alterations can be tested directly.

The study, titled “Linker histone H1.0 loads onto nucleosomes through multiple pathways that are facilitated by histone chaperones,” was funded by the National Institutes of Health and the U.S. National Science Foundation. In addition to Akbari and Poirier, the co-authors included Nathaniel Burge of Ohio State and Matti Valdimarsson, Aritra Chowdhury and Benjamin Schuler of the University of Zurich. Together, their findings reframe a seemingly simple question – how does a protein find its binding site? – into a multi-step journey involving DNA sliding, unexpected reflection away from targets, and an essential chaperone handoff, deepening the mechanistic picture of how cells keep their vast genomes organized and their genes properly silenced.

Subject of Research: How linker histone H1 is targeted to nucleosomes with the help of histone chaperone proteins

Article Title: Protein key to cells’ gene regulation needs a chaperone to do its job

Article References: Protein key to cells’ gene regulation needs a chaperone to do its job. (n.d.). Original publication

Image Credits: AI Generated

DOI: Not provided

Keywords: linker histone H1, nucleosome, chromatin compaction, gene regulation, histone chaperones, single-molecule imaging, optical tweezers, epigenetics, cancer mutations, Molecular Cell, Ohio State University, DNA packaging