Publications

Les 20 dernières publications

Automated mapping of DNA replication fork progression in human cells with ForkML: Author(s) : Rojat V, Ciardo D, Tourancheau A, Proux F, Jean E, Arbona J, Audit B, Millot G, Bonhomme F, Arimondo P, others,; Journal : Nature communications; 2026
Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids: Author(s) : D’Asaro D, Arbona J, Vaillant C, Jost D,; Journal : Nucleic Acids Research; 2026; Following DNA replication, cohesion maintains sister chromatids (SCs) in spatial proximity with a certain degree of alignment. This tethering, mediated by the cohesin complex, may facilitate DNA repair and enable proper chromosome individualization and segregation during mitosis. However, it is still unclear how cohesion is established and how it reshapes the relative organization of replicated chromosomes to achieve its functions. In this study, we address these questions in the biological context of budding yeast by disentangling the interplay between two major structural functions of cohesin: organizing individual chromatids through loop extrusion and SCs through cohesion. Combining polymer modeling and detailed analysis of recent experimental data of replicated chromosomes in G2/M, we show that extruding and cohesive cohesins are sparsely distributed, leading to mildly compacted and loosely aligned SCs. Genome-wide analysis of inter-chromatid contact maps in wild-type and mutant conditions suggests that cohesion is asymmetric, favoring the tethering between non-homologous cohesin-enriched regions. Our work highlights the dual role played by cohesin in structuring the replicated genome and questions the functions of cohesion in the context of asymmetric, partial alignment of SCs.
Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.: Author(s) : Dufour A, Duplus-Bottin H, Boukéké-Lesplulier T, Casassa E, Triqueneaux G, Tarbouriech L, Darthenay-Kiennemann C, Dumont A, Moali C, Vittoz F, Jost D, Yvert G,; Journal : Biol Open; 2026; Advances in optogenetics now allow specific modifications to the DNA of livecells with light. However, successfully using these technologies requires knowingtheir properties in terms of sensitivity, efficiency, kinetics and mechanism. Wepreviously developed an optogenetic tool made of a single chimeric protein calledLiCre that enables the induction of specific changes in the genome with bluelight via DNA recombination between loxP sites ( Duplus-Bottin et al., 2021).Here, we used in vitro and in vivo experiments combined with kinetic modeling toprovide a deeper characterization of the photoactivated LiCre-loxP recombinationreaction. We find that LiCre binds DNA with high affinity in the absence of alight stimulus and that this binding is cooperative, although not as much as forthe Cre recombinase from which LiCre was derived. In yeast, the addition ofriboflavin to the culture medium had no effect on LiCre's efficiency, even whencells over-expressed riboflavin kinase, suggesting that the abundance of theflavin mononucleotide cofactor is not limiting for the reaction. However, LiCre'sefficiency in yeast gradually increased when raising the temperature from 20°C to37°C. The recombination kinetics observed in live cells are best explained by amodel where the photoactivation of two or more DNA-bound LiCre units (happeningin seconds) can produce (in several minutes) a functional recombination synapse.This model was able to capture the effect of a point mutation altering LiCre'slight cycle. This deeper understanding of the LiCre-loxP system providesadditional knowledge for designing experiments where specific genetic changes areinduced in live cells with light.
Editorial overview: Genome Architecture and Expression: Author(s) : Giorgetti L, Jost D,; Journal : Current opinion in genetics & development; 2026
Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.: Author(s) : Dufour A, Duplus-Bottin H, Boukéké-Lesplulier T, Casassa E, Triqueneaux G, Tarbouriech L, Darthenay-Kiennemann C, Dumont A, Moali C, Vittoz F, Jost D, Yvert G,; Journal : Biol Open; 2026; Advances in optogenetics now allow specific modifications to the DNA of livecells with light. However, successfully using these technologies requires knowingtheir properties in terms of sensitivity, efficiency, kinetics and mechanism. Wepreviously developed an optogenetic tool made of a single chimeric protein calledLiCre that enables the induction of specific changes in the genome with bluelight via DNA recombination between loxP sites ( Duplus-Bottin et al., 2021).Here, we used in vitro and in vivo experiments combined with kinetic modeling toprovide a deeper characterization of the photoactivated LiCre-loxP recombinationreaction. We find that LiCre binds DNA with high affinity in the absence of alight stimulus and that this binding is cooperative, although not as much as forthe Cre recombinase from which LiCre was derived. In yeast, the addition ofriboflavin to the culture medium had no effect on LiCre's efficiency, even whencells over-expressed riboflavin kinase, suggesting that the abundance of theflavin mononucleotide cofactor is not limiting for the reaction. However, LiCre'sefficiency in yeast gradually increased when raising the temperature from 20°C to37°C. The recombination kinetics observed in live cells are best explained by amodel where the photoactivation of two or more DNA-bound LiCre units (happeningin seconds) can produce (in several minutes) a functional recombination synapse.This model was able to capture the effect of a point mutation altering LiCre'slight cycle. This deeper understanding of the LiCre-loxP system providesadditional knowledge for designing experiments where specific genetic changes areinduced in live cells with light.
PRC1 nanoglobules organize Hox chromatin during Drosophila embryogenesis.: Author(s) : Cheutin T, Akilli N, Di Stefano M, Puel P, Fritsch L, Jost D, Cavalli G,; Journal : Cell Discov; 2026; Polycomb group (PcG) proteins are required to maintain the silencing of keydevelopmental genes during development. In Drosophila, they bind to discretegenomic elements named Polycomb response elements (PREs). PcG proteins form twoclasses of complexes. Polycomb repressive complex 2 (PRC2) deposits H3K27me3, ahistone mark that covers large chromatin domains. The canonical PRC1 complex canbind to PREs as well as to the H3K27me3 mark. Inside the cell nucleus, whenanalyzed by confocal microscopy, the PcG subunits and associated chromatin arelocalized to polycomb foci. However, the lack of spatial resolution of thismethod impedes the precise localization of the polycomb machinery relative to itstarget chromatin. To resolve this long-standing problem, we analyzed Drosophilaembryos by superresolution stimulated emission depletion microscopy. We observedthat polycomb foci associated with Hox gene clusters are composed of multipledynamic PRC1 substructures, which we named "PRC1 nanoglobules". PREs are moreassociated with these nanoglobules than the surrounding H3K27me3 chromatin. Byimaging the entire Bithorax complex (BX-C) locus, we identified chromatinsubstructures that partially overlap with PRC1 nanoglobules, indicating that theyform different assemblies. Furthermore, polymer simulations suggest thatinteractions between PREs and PRC1 nanoglobules can drive the compaction andpositioning of the BX-C domain. Taken together, these data suggest that byestablishing the three-dimensional architecture of their target loci, PRC1nanoglobules are key molecular assemblies that maintain polycomb-dependentsilencing.
Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.: Author(s) : Akilli N, Puel P, Stefano M, Muzzopappa F, Fritsch L, Erdel F, Jost D, Cheutin T, Cavalli G,; Journal : Nucleic Acids Res; 2026; Polycomb repressive complex 1 (PRC1) forms nuclear condensates that organizetarget chromatin domains. SUMOylation modulates PRC1 clustering, but its impacton condensate properties and 3D genome architecture remains unclear. Here, weshow that depletion of small ubiquitin-like modifier (SUMO) in Drosophila wingimaginal discs transforms PRC1 condensates into large structures with reducedmolecular dynamics. Biophysical modeling suggests that the changes in PRC1self-interactions are responsible for the formation of large PRC1 condensateswhen SUMO is depleted. Interestingly, this biophysical reorganization occurswithout global loss of the H3K27me3 mark. Instead, Hi-C reveals widespreadrewiring of topologically associating domain (TAD) interactions. PRC1-bound TADslose specific long-range contacts with each other while gaining ectopicinteractions with active chromatin. These topological shifts correlate with genemisregulation independently of changes in Polycomb histone modifications. Ourresults establish SUMOylation as a critical regulator of PRC1 condensates,demonstrating that post-translational control of biomolecular condensationmodulates 3D genome architecture and transcriptional output through mechanismsseparable from histone mark deposition.
Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.: Author(s) : Piveteau V, Dupont C, Salari H, Dumont A, Savocco J, Jost D, Piazza A,; Journal : EMBO J; 2026; The in vivo mechanism, cis-acting roadblocks, and biological functions of DNAloop extrusion by eukaryotic SMC complexes remain incompletely defined. Here, weidentify condensin-dependent Hi-C contact stripes at the recombination enhancer(RE) and at rDNA in S. cerevisiae. The RE is an autonomous condensin loading siteonly active in MATa cells from which oriented, unidirectional loop extrusionproceeds with an estimated processivity ~150-250 kb and a density ~0.04-0.18 thatvaries across the cell cycle. Centromeres, replication forks, and highlytranscribed RNA PolII-dependent genes represent roadblocks for condensin. Cohesinis not an obstacle for condensin, while Top2 promotes its loop extrusionactivity. A DNA double-strand break (DSB) at MAT blocks loop extrusion, resultingin the establishment of a ~170 kb-long RE-MAT loop. The RE and the DSB arerequired and sufficient to form this site-specific loop, which promotesRE-proximal homology identification in the early stages of recombinational DNAbreak-repair. We propose that juxtaposition of the broken MATa site and itstarget HMLα donor is the relevant structure by which condensin promotes a-to-αmating-type switching.
Cohesin forms fountains at active enhancers in C. elegans.: Author(s) : Lüthi B, Semple J, Haemmerli A, Thapliyal S, Ghadage K, Stojanovski K, D'Asaro D, Das M, Gilbert N, Glauser D, Towbin B, Jost D, Meister P,; Journal : Nat Commun; 2025; Transcriptional enhancers must locate target genes with precision. In mammals,topologically associating domains (TADs) guide this process, but the C. elegansgenome lacks such organization despite containing over 30,000 putative enhancers.Using high-resolution Hi-C, we identify distinct 3D chromatin structures aroundactive enhancers, termed fountains. These ~38 kb cohesin-dependent structures areunique to active enhancers and enriched for topoisomerases and negativelysupercoiled DNA, indicating topological stress. Disrupting cohesin collapsesfountains and leads to transcriptional upregulation of nearby genes, suggestingfountains act as spatial repressors controlling enhancer-promoter communication.This repression preferentially affects neuronal genes, including skn-1/Nrf, whichchanges isoform usage upon cohesin loss in ASI neurons. Cohesin cleavage alsoalters nematode movement and foraging behavior, linking 3D genome architecture toneural function and behavior. Thus, fountains represent a distinctive chromatinfeature that may ensure enhancer specificity in a TAD-less genome.
Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.: Author(s) : Paldi F, Szalay M, Dufau S, Di Stefano M, Reboul H, Jost D, Bantignies F, Cavalli G,; Journal : Nat Genet; 2026; Epigenetic memory enables the propagation of gene expression patterns followingtransient stimuli. Although three-dimensional chromatin organization is emergingas a key regulator of genome function, it is unknown whether it contributes tocellular memory. Here we establish that acute perturbation of the epigenome caninduce cellular memory of gene expression in mouse embryonic stem cells. Weuncover how a pulse of histone deacetylase inhibition translates to changes intranscription, histone modifications and genome folding. While most epigenomicand transcriptional changes are initially reversed once the perturbation isremoved, some loci remain transcriptionally deregulated and genome architecturepartially maintains its perturbed conformation. Consequently, a second pulse oftransient hyperacetylation induces stronger memory of transcriptionalderegulation. Using ultradeep Micro-C, we associate memory of gene expressionwith repressive Polycomb-mediated chromatin topology. These results demonstratehow cells can record transient stresses in their genome architecture, therebyenabling an enhanced response to subsequent perturbations.
Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes: Author(s) : D’Asaro D, Arbona J, Piveteau V, Piazza A, Vaillant C, Jost D,; Journal : Genome Biology; 2025
The mechanistic and evolutionary diversity of programmed DNA elimination.: Author(s) : Duharcourt S, Ross L, Suh A, Dedukh D, Delattre M, Houben A, Kokko H, Reifova R, Richard Albert J, Roze D, Smith J, Wang J,; Journal : Nat Rev Genet; 2026; Beyond somatic mutations, the genetic makeup of an organism is often assumed toremain constant across all cells or nuclei within individuals. However, someorganisms exhibit programmed DNA elimination (PDE), whereby specific celllineages lose DNA segments or whole chromosomes. Building evidence indicates thatPDE occurs in a wide range of eukaryotes and is linked to diverse cellularprocesses including gene silencing, germline differentiation, genome defence andsex determination. Here we compare PDE across broad phylogenetic groups,highlighting the mechanistic diversity, overlooked plasticity in genome integrityand the considerable gaps in our understanding of why PDE emerged recurrently andis maintained across the Tree of Life.
Emergence and stabilization of a neo-Y chromosome in nematode species with rare males: Author(s) : Letcher B, Stevens L, Saclier N, Hsiao A, Kieninger M, Wenger E, Launay C, Blaxter M, Delattre M,; Journal : Molecular Biology and Evolution; 2026; How do sex chromosomes evolve in the transition to asexuality? So far, species that depart from canonical sexual reproduction—for example, parthenogens with rare sex or species where the paternal genome is set aside—have been found to carry either no sex chromosomes or sex chromosomes but no male-specific sex chromosome (i.e. no Y). Here we reveal that, in Mesorhabditis nematodes, a new Y chromosome evolved once, from sexual ancestors, in species that have transitioned into an unconventional mode of reproduction called autopseudogamy. In this reproductive system, females produce clonal females plus rare (∼10\%) males that are needed for fertilization but that do not contribute to the female genome. Analyzing the Y chromosomes of two autopseudogamous species, we found high levels of degeneration, most likely due to loss of recombination, and two additional conserved features: (i) they accumulated male-beneficial genes, and (ii) they display a strong fertilization drive, in that mainly Y-bearing sperm fertilize female oocytes. Both features are likely evolutionarily favorable in the context of autopseudogamy. Our results suggest that male-specific chromosomes can still be maintained in systems with rare, and possibly “genetically useless,” males.
Revealing ancient macroH2A features through in vivo analysis in the cricket Gryllus bimaculatus: Author(s) : Gonzalez-Sqalli E, Caron M, Loppin B,; Journal : Proceedings of the National Academy of Sciences; 2026; macroH2A is one of the most atypical histone variants, being three times larger than canonical H2A due to its unique extranucleosomal macrodomain. Once thought to be vertebrate-specific, macroH2A is in fact an evolutionary ancient histone, encoded by two genes in vertebrates and a single gene in other eukaryotes. However, the absence of macroH2A in Drosophila and Caenorhabditis elegans have precluded its functional characterization beyond vertebrates. Here, we report the functional characterization of macroH2A in an invertebrate, enabled through genome editing in the cricket Gryllus bimaculatus . Endogenous tagging of the cricket macroH2A gene revealed a highly dynamic distribution of macroH2A during gametogenesis and a general association with heterochromatin. In embryos, macroH2A shows a remarkable enrichment in differentiating cells, particularly in the nervous system and muscles. Interestingly, complete gene deletion reveals that macroH2A is dispensable for viability but critical for survival after irradiation. We further show that embryos lacking the linker and macrodomain of macroH2A are equally hypersensitive to DNA damage, demonstrating that this nonhistone region safeguards genome integrity beyond vertebrates. Finally, removing the extranucleosomal domain of macroH2A unexpectedly disturbs its chromatin incorporation in a cell-type-specific manner. This study thus reveals deeply conserved features of macroH2A, shared between insects and vertebrates, but also provides insights about the regulation of its chromatin incorporation.
ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments: Author(s) : Mendiboure N, Modolo L, Janczarski S, Piazza A,; Journal : Bioinformatics; 2026; Single-strand DNA-specific Hi-C (ssHi-C) is a recently developed technique enabling the capture of chromatin interactions involving single-stranded DNA (ssDNA), an intermediate of various DNA metabolic processes. ssHi-C entails the restoration of restriction sites in ssDNA regions of interest upon introduction of designer, internally barcoded “annealing oligonucleotides” prior to the restriction digestion step of Hi-C. The design of these “annealing oligonucleotides,” as well as the analysis of the resulting ssHi-C data presents specific challenges, such as (i) differentiating ssDNA from dsDNA-derived contacts, (ii) tracking probe-specific interactions, and (iii) calibrating the amount of ssDNA contacts across biological samples. Dedicated computational tools are therefore needed to facilitate the design of, and extract biological information from, ssHi-C experiments.We present ssHiCstuff, a Rust- and Python-based package for the design of key reagents for ssHi-C experiments and for the analysis of ssHi-C data. ssHiCstuff provides (i) an automated annealing oligonucleotides design module, (ii) an end-to-end analyses pipeline, and (iii) a graphical user interface. ssHiCstuff simplifies the high-resolution analysis of ssDNA interactions at genome-wide scale. A graphical user interface (GUI) implemented in Python is also available for biologists without coding skills.ssHiCstuff is freely available at https://github.com/Piazzalab/ssHiCstuff and https://zenodo.org/records/19677479 (https://doi.org/10.5281/zenodo.19677479) under the GPL 3.0 license. The annealing oligonucleotides design and the visualization modules are additionally freely available on a web browser at https://bioshiny.ens-lyon.fr/public/app/sshicstuff. A test dataset is available at https://zenodo.org/records/20035366 (https://doi.org/10.5281/zenodo.20035366).
Somatic Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes: Author(s) : Launay C, Wenger E, Letcher B, Delattre M,; Journal : eLife; 2026; All cells of a multicellular organism usually share an identical genome, faithfully transmitted through successive divisions. Yet, a number of animal species deviate from this dogma, as parts of their DNA are systematically eliminated in all their somatic nuclei, in a process called Programmed DNA Elimination (PDE). PDE leads to the unexpected reorganisation of the genome at every generation in all somatic cells but its molecular mechanism, evolutionary origins, and functional significance remain unknown. This lack of understanding partially stems from limitations in genetically tractable model species.PDE can target an entire chromosome, or involve chromosome fragmentation followed by selective fragment retention and elimination, raising further questions on genome stability, genome integrity and mechanisms of DNA repair. PDE by chromosome fragmentation has been described in parasitic nematodes in the family Ascarididae, copepods in the genus Cyclops and unicellular ciliates. More recently, PDE has been discovered in three non-parasitic, lab-tractable nematode species from the Rhabditidae family, opening new perspectives.In this study, we used cytological approaches to screen 25 new Rhabditidae species for PDE. We found evidence of PDE in 17 species. Our work reveals that PDE is present in 12 out of 17 tested genera, demonstrating its widespread presence in Rhabditidae nematodes, with the notable exception of C. elegans. Genetic tools have already been established for some species. This work provides a collection of lab-tractable species that can be used to test many aspects of somatic Programmed DNA Elimination by chromosome fragmentation in animals.
Spatial controls of homology search: Author(s) : Piazza A, Taddei A,; Journal : Current Opinion in Genetics and Development; 2026; Homologous recombination is a conserved DNA double-strand break (DSB) repair pathway that uses an intact dsDNA molecule as a template. A filament of the RecA/Rad51 protein family catalyzes the search for this homologous template, in a process that minimally requires the collision of these two partners in the nuclear space. Orthogonal methodological developments recently revealed that this search for homology is a choreographed process under control by both 3D chromatin organizers of the structural maintenance of chromosomes (SMC) family and the structure and dynamics of the RecA/Rad51 filament. Here we review these advances that establish a novel framework for homology search, highlight the commonalities and distinctions between search facilitation strategies in eukaryotes and bacteria, and discuss outstanding open questions.
Selfish chromosomes exploit a germline checkpoint to eliminate competing gametes: Author(s) : Ridges J, Bladen J, King T, Brown N, Large C, Cooper J, Jones A, Loppin B, Dubruille R, Phadnis N,; Journal : Nature Communications; 2026

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Publications

Automated mapping of DNA replication fork progression in human cells with ForkML

Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids

Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.

Editorial overview: Genome Architecture and Expression

Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP.

PRC1 nanoglobules organize Hox chromatin during Drosophila embryogenesis.

Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3.

Condensin loop extrusion properties, roadblocks, and role in homology search during recombination in S. cerevisiae.

Cohesin forms fountains at active enhancers in C. elegans.

Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

The mechanistic and evolutionary diversity of programmed DNA elimination.

Emergence and stabilization of a neo-Y chromosome in nematode species with rare males

Revealing ancient macroH2A features through in vivo analysis in the cricket Gryllus bimaculatus

ssHiCstuff: a package for the design and analysis of ssDNA-specific Hi-C experiments

Somatic Programmed DNA Elimination is widespread in free-living Rhabditidae nematodes

Spatial controls of homology search

Selfish chromosomes exploit a germline checkpoint to eliminate competing gametes

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