14 May 2026
Researchers at Human Technopole developed a novel tool to map the spatial organisation of the nucleus of eukaryotic cells by profiling the radial distribution of the genome from the nuclear periphery to the centre. The experimental procedure is published in Nature Protocols and featured on the cover of the journal.
Imagine visiting a big city where a famous building is located. You want to see it, but you don’t know its precise location. The instructions you get rely on other reference points, whose location is also unknown to you. Exploring this city suddenly feels like crossing a dark, intricated maze. Clearly, you need a map.
The genome of eukaryotic cells can also be a complicated labyrinth for those who are not familiar with its environment: genes, regulatory elements, non-coding regions, (epi)genetic modifications, and single-nucleotide polymorphisms are all packed into a small, specialised cellular compartment called the nucleus. This important feature distinguishes eukaryotic cells from the primordial anucleate prokaryotic cells.
The nuclear compartment stores the cell’s genetic information in the form of chromatin, that is, DNA wrapped around packaging proteins named histones. The nucleus, however, is not only a storage unit for eukaryotic genomes, but also the location where fundamental biological processes, such as DNA replication, transcription and repair, take place.
It has long been thought that the nuclear localisation of different parts of the genome is related to their functions. Indeed, the genome is not randomly organised inside the nucleus. Previous studies have shown that the two-metre-long DNA molecule inside each diploid human cell is efficiently folded to fit a tiny space with a diameter 100,000 times smaller than the genome in its full length: larger chromatin compartments contain smaller structural elements, such as topologically associated domains or TADs, which in turn contain smaller units where gene regulatory elements interact, such as chromatin loops. What is less known, however, is how these structural features are spatially positioned with respect to each other and how the spatial arrangement of the genome in the nucleus affects its functions, if at all.
The Bienko Group at Human Technopole addressed this gap by developing a novel method, called Genomic loci Positioning by Sequencing (GPSeq), specifically designed to map how the genome is, on average, positioned between the periphery and the centre of the cell nucleus—a feature known as ‘genome radiality’.
GPSeq can be used by any laboratory with an intermediate expertise in molecular biology, genomics and microscopy. Briefly, the cells of interest are treated to allow their penetrance by special proteins called restriction enzymes, which recognise and cut (or digest) specific DNA sequences frequently found throughout the genome. These enzymes enter the cell nuclei from the periphery and gradually diffuse inwards. As a result, the DNA will be progressively cut from the outermost to the innermost layer of the nucleus. By stopping this reaction after increasing time intervals, it is possible to obtain snapshots of the progressive radial digestion of DNA.
At each timepoint, special reporters are bound to the cut DNA to enable its visualisation through a microscope for quality control, followed, if successful, by DNA amplification and sequencing. Each sequence is then given a GPSeq score representing its genome radiality, based on which genome-wide radial maps are generated.
By combining the resulting genome maps with data produced by other omics technologies, it is possible to explore the radial distribution of various genomic features, from gene expression levels and (epi)genomic modifications to mutational hotspots and DNA damage profiles.
This method can be applied to any eukaryotic cell of interest, thus allowing the study of genome architecture not only in different model systems, but also with a multi-scale approach spanning biological levels from cells to organs to whole individuals. The versatility of GPSeq highlights its potential to help identify key differences and similarities between distinct cell types, as well as in health and disease.
Nicola Crosetto, Senior Manager at the Genomics Research Centre – Functional Genomics and co-corresponding author of this study, shares: “GPSeq is a powerful approach that complements the Hi-C method widely used for mapping 3D genome architecture. With our new protocol, researchers can now easily implement GPSeq in their labs and use it to obtain high-resolution maps of genome radiality across different cell types and experimental conditions.”
With more advanced updates predicted to come, genomic maps by GPSeq empower researchers to navigate the eukaryotic genome with better orientation — just like geographical maps help us find our destination in our daily life.
Yip WH, Harton K, Castiglioni I, Bouwman BAM, Jiménez C, Georgiades E, Harbers L, Kang W, Wernersson E, Crosetto N, Bienko M. GPSeq maps the radial organization of eukaryotic genomes along the nuclear periphery-center axis. Nat Protoc. 2026 May;21(5):2199-2270. doi: 10.1038/s41596-025-01278-x. Epub 2026 Jan 19. PMID: 41555070.
