The core idea is elegantly simple. The researchers designed photocleavable hashtag oligonucleotides, or PHOs, short synthetic DNA molecules conjugated to cholesterol so that they insert themselves into the fatty membranes of living cells. Each PHO carries two distinct barcode sequences, an inner and an outer tag, joined through a chemical bond that snaps apart when illuminated with ultraviolet light. Because the tags sit on the cell surface, they do not perturb the cell’s internal biochemistry, and because they are cleaved by light, they can be erased selectively wherever a researcher chooses to shine a beam.

To convert this chemistry into spatial information, the team used a digital micromirror device, the same light-engine found in many projectors, to cast user-defined patterns of ultraviolet light onto cultures of PHO-labeled cells. Cells bathed in light lose their outer tag; cells kept in shadow retain it. After several minutes of patterned exposure, the researchers dissociate the sample and run it through standard single-cell sequencing workflows, including droplet-based platforms such as 10x Genomics. In the resulting data, the ratio of outer to inner barcode reads recovered from each cell encodes how much light that cell received, and therefore where it sat in the original culture. In effect, the light pattern is stamped onto the cells as a molecular memory.

The precision of this stamping is tunable. Because photocleavage scales monotonically with light dose, a smoothly graded illumination pattern produces a continuous gradient of barcode cleavage across the sample, allowing cells to be assigned positions along an axis rather than sorted into coarse bins. Sequential rounds of labeling push resolution further: by applying different photomasks in succession with distinct PHO species, each carrying its own fluorophore and barcode, the team generated combinatorial codes that distinguish multiple spatial quadrants within a single dish. A refined second-generation tag, held in place by bridging oligonucleotides that prevent cleaved fragments from washing away, preserves earlier labeling patterns through subsequent rounds, expanding the encoding capacity exponentially with each additional exposure.

Critical to any method that douses living cells with ultraviolet light is demonstrating that the light itself does not distort the biology being measured. The researchers addressed this directly. Comparing transcriptomes of illuminated and non-illuminated cells, they found correlations approaching unity, with principal component analysis showing no separation between the two groups and differential expression testing revealing essentially no genes significantly altered by saturating UV exposure. They also showed that PHOs linger on cell membranes with a half-life of roughly nine hours, defining a practical window for live-cell experiments, and that the method works equally well on fixed samples, broadening its applicability to precious clinical specimens that cannot be kept alive.

Where scSTAMP-seq truly distinguishes itself is in its modularity. Rather than reading out gene expression alone, the team extended the approach to scSTAMP-MAT-seq, which jointly profiles messenger RNA, DNA accessibility, and DNA methylation from the same individual cell, all while retaining the spatial barcode. The workflow combines the light-stamped tags with a methyltransferase that marks open chromatin and a methylation-sensitive restriction enzyme that fragments the genome at methylated sites. Benchmarking showed that the multiomic version recovers tens of thousands of accessible GpC sites and endogenous methylated CpG sites per cell, comparable to the non-spatial predecessor, meaning spatial resolution came at little cost to data quality.

To showcase the method’s power, the researchers applied it to two-dimensional human gastruloids, micropatterned colonies of induced pluripotent stem cells that recapitulate the spatial patterning of the early embryo. During gastrulation, the embryonic disc organizes itself into domains fated to become different germ layers, and understanding how position and gene regulation intertwine during this process is a central question in developmental biology. Using a radial light gradient that decayed nonlinearly from the colony edge toward the center, the team encoded continuous positional information across each gastruloid and then read out the transcriptome of thousands of individual cells.

The resulting spatial maps revealed that canonical lineage markers such as CDX2, SOX17, EOMES, and DNMT3B each occupied characteristic radial positions, reproducing the epiblast-like, primitive streak-like, and extraembryonic-like domains seen in real gastrulating embryos. More strikingly, when the researchers grouped genes by their spatial expression profiles and examined the behavior of chromatin regulators, the enzymes and binding proteins that chemically modify and interpret histones and DNA, they found that these regulators themselves were spatially patterned. Histone editors, histone readers, DNA modifiers, ATP-dependent remodelers, and Polycomb group proteins each showed distinct distributions across the radial axis, suggesting that the epigenetic machinery governing cell fate is itself organized by position within the emerging tissue.

This observation speaks to a long-standing challenge in genomics. Studies from the ENCODE project and numerous single-cell atlases have catalogued gene expression and epigenetic states across cell types, but disentangling whether epigenetic differences drive spatial organization or merely reflect it requires measurements that capture both simultaneously in an intact spatial context. By coupling spatial barcoding with joint multiomic readout, scSTAMP-seq offers a way to ask these questions directly, correlating chromatin state, DNA methylation, and transcription as functions of position within a developing or diseased tissue.

The practical accessibility of the method may prove as influential as its scientific results. Unlike purpose-built spatial transcriptomics instruments that require specialized arrays or imaging systems, scSTAMP-seq piggybacks on standard single-cell sequencing platforms and a digitally addressable light source found in many microscopy facilities. The team has deposited its sequencing data in the Gene Expression Omnibus and released its analysis code on GitHub, lowering the barrier for other laboratories to adopt the approach. With a patent application pending and demonstrated compatibility with both live and fixed cells, plate-based and droplet-based workflows, and transcriptomic plus epigenomic readouts, light-stamped barcoding stands to bring spatial reasoning to single-cell genomics labs that could never justify a dedicated spatial platform, potentially reshaping how developmental biology, neuroscience, and cancer research map the molecular landscapes of complex tissues.

Subject of Research: A light-encoded barcoding method for spatially resolved single-cell transcriptomics and epigenomics

Article Title: Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics

Article References: Piscopio, R. A., Chialastri, A., Wang, C., Godzik, M., Heom, K. A., Wang, W., Li, L. J., Saxena, N., Wilson, M. Z., & Dey, S. S. (2026). Photolabile oligonucleotides with topological light gradients enable spatially resolved single-cell transcriptomics and epigenomics. Nature Biotechnology. https://doi.org/10.1038/s41587-026-03328-5

Image Credits: AI Generated

DOI: 10.1038/s41587-026-03328-5

Keywords: scSTAMP-seq, spatial transcriptomics, single-cell sequencing, photocleavable oligonucleotides, epigenomics, DNA methylation, chromatin accessibility, gastrulation, human gastruloids, digital micromirror device, multiomics, Nature Biotechnology