Biology subjects

Franchitto, A.

Publications and source records attributed to Franchitto, A..

14 recordsLinked to original sources

bioRxiv2026

A novel imaging biosensor for the detection of reversed replication forks and four-way junctions in human cells

Replication fork reversal and recombination-dependent replication protect perturbed forks by forming four-way DNA junctions. Despite their central role, detecting these intermediates in intact cells has historically required electron microscopy of bulk extracted DNA. Here, we describe a genetically encoded biosensor for four-way junctions based on nuclear-targeted bacterial RuvA tagged with GFP or Spot-tag. Combined with SIRF, RuvA selectively accumulates at nascent DNA following hydroxyurea- or camptothecin-induced replication stress. Recruitment requires fork-reversal factors and is abolished by a non-binding mutant (K84E/K119E), confirming specificity. The biosensor dynamically tracks reversed fork abundance, capturing MRE11-mediated fork degradation in BRCA2- or RAD52-deficient cells and its functional rescue. Finally, RuvA reveals RAD51-dependent four-way junctions at nucleolar rDNA arrays in unperturbed and stressed cells. This tool converts a bulk population measurement into a visualizable readout with single-cell and subnuclear resolution, enabling direct spatial analysis of DNA structures in situ.

cell biology↗

bioRxiv2026

Subthreshold perturbation of DNA replication induces a secretory response and a bystander effect in naïve human fibroblasts

Replication stress is a hallmark of cancer, where it drives DNA damage and genome instability. Yet subtle, subthreshold perturbations of DNA synthesis likely occur routinely in normal proliferating tissues, and their consequences for cell homeostasis are unknown. Using primary human fibroblasts, we show that doses of the DNA polymerase inhibitor aphidicolin, too low to engage the replication checkpoint, or produce detectable DNA breaks, nonetheless elicit low-level, ATM-dependent {gamma}H2AX phosphorylation uncoupled from overt damage. This near-silent perturbation reprograms gene expression, inducing replication-associated genes together with a discrete secretory programme dominated by matrix-remodelling proteases and matricellular factors. This output is not a senescence-associated secretory phenotype: the NF-{kappa}B/IL-1/IL-6 axis is co-ordinately repressed rather than induced, p53 target genes including CDKN1A are unchanged, and cells remain proliferative and non-senescent. Conditioned medium from exposed cells reproduces ATM-{gamma}H2AX activation in naive fibroblasts without DNA damage, defining a "perturbed-replication bystander effect" (PeRBE). PeRBE is ROS-independent and mediated by heat-labile, proteinaceous factors, and in recipient cells it induces an extracellular-matrix programme that culminates in increased collagen production, without loss of proliferative capacity. A perturbation invisible to every standard replication-stress assay therefore generates a transmissible, protein-borne signal that instructs fibrogenic matrix remodelling in cells that never experienced it.

cell biology↗

bioRxiv2026

WRNIP1-ATM signaling promotes G-quadruplex resolution by preserving FANCJ stability

G-quadruplexes (G4s) are non-canonical DNA structures that regulate transcription, replication, and DNA repair but, when unresolved, hinder replication fork progression and compromise genome stability. Here, we identify a WRNIP1-dependent mechanism that promotes the resolution of R-loop-associated G4 structures. Loss of WRNIP1 or disruption of its ubiquitin-binding zinc finger (UBZ) domain causes persistent G4/R-loop accumulation, leading to transcription-replication conflicts, DNA damage, and genome instability. We further show that WRNIP1 interacts with the G4 helicase FANCJ and that mutation of the UBZ domain disrupts this interaction, impairing FANCJ stability and recruitment to G4 sites. Mechanistically, WRNIP1 acts upstream of FANCJ by promoting ATM-dependent signaling required for FANCJ stabilization and chromatin association. ATM-mediated phosphorylation of FANCJ at Ser990 protects the helicase from ubiquitin-dependent proteasomal degradation. Together, these findings define a WRNIP1-ATM-FANCJ regulatory axis that promotes G4 resolution during DNA replication and preserves genome stability.

cell biology↗

bioRxiv2023

PHOSPHORYLATION-DEPENDENT ASSOCIATION OF WRN WITH RPA IS REQUIRED FOR RECOVERY OF REPLICATION FORKS STALLED AT SECONDARY DNA STRUCTURES

The WRN protein mutated in the hereditary premature aging disorder Werner syndrome plays a vital role in handling, processing, and restoring perturbed replication forks. One of its most abundant partners, Replication Protein A (RPA), has been shown to robustly enhance WRN helicase activity in specific cases when tested in vitro. However, the significance of RPA-binding to WRN at replication forks in vivo has remained largely unexplored. In this study, we have identified several conserved phosphorylation sites in the acidic domain of WRN that are targeted by Casein Kinase 2 (CK2). Surprisingly, these phosphorylation sites are essential for the interaction between WRN and RPA, both in vitro and in human cells. By characterizing a CK2-unphosphorylatable WRN mutant that lacks the ability to bind RPA, we have determined that the WRN-RPA complex plays a critical role in fork recovery after replication stress whereas the WRN-RPA interaction is not necessary for the processing of replication forks or preventing DNA damage when forks stall or collapse. When WRN fails to bind RPA, fork recovery is impaired, leading to the accumulation of single-stranded DNA gaps in the parental strands, which are further enlarged by the structure-specific nuclease MRE11. Notably, RPA-binding by WRN and its helicase activity are crucial for countering the persistence of G4 structures after fork stalling. Therefore, our findings reveal for the first time a novel role for the WRN-RPA interaction to facilitate fork restart, thereby minimizing G4 accumulation at single-stranded DNA gaps and suppressing accumulation of unreplicated regions that may lead to MUS81-dependent double-strand breaks requiring efficient repair by RAD51 to prevent excessive DNA damage.

cell biology↗

bioRxiv2023

WRNIP1 prevents transcription-associated genomic instability

R-loops are non-canonical DNA structures that form during transcription and play diverse roles in various physiological processes. Disruption of R-loop homeostasis can lead to genomic instability and replication impairment, contributing to several human diseases, including cancer. Although the molecular mechanisms that protect cells against such events are not fully understood, recent research has identified fork protection factors and DNA damage response proteins as regulators of R-loop dynamics. In this study, we identify the Werner helicase-interacting protein 1 (WRNIP1) as a novel factor that counteracts transcription-associated DNA damage upon replication perturbation. Loss of WRNIP1 leads to R-loop accumulation, resulting in collisions between the replisome and transcription machinery. We observe co-localization of WRNIP1 with transcription/replication complexes and R-loops after replication perturbation, suggesting its involvement in resolving transcription-replication conflicts. Moreover, WRNIP1-deficient cells show impaired replication restart from transcription-induced fork stalling. Notably, transcription inhibition and RNase H1 overexpression rescue all the defects caused by loss of WRNIP1. Importantly, our findings highlight the critical role of WRNIP1 ubiquitin-binding zinc finger (UBZ) domain in preventing pathological persistence of R-loops and limiting DNA damage, thereby safeguarding genome integrity.

cell biology↗

bioRxiv2023

RAD52 prevents accumulation of Polalpha-dependent replication gaps at perturbed replication forks in human cells

Replication gaps can arise as a consequence of perturbed DNA replication, and their accumulation might undermine the stability of the genome. Loss of RAD52, a protein involved in the regulation of fork reversal, promotes accumulation of parental ssDNA gaps during replication perturbation. Here, we demonstrate that this is due to the engagement of Pol downstream of the extensive degradation of perturbed replication forks after their reversal and is not dependent on PrimPol. Pol is hyper-recruited at parental ssDNA in the absence of RAD52, and this recruitment is dependent on fork reversal enzymes and RAD51. Of note, we report that the interaction between Pol and RAD51 is stimulated by RAD52 inhibition, and Pol-dependent gap accumulation requires formation of the RAD51 nucleoprotein filaments. Our data indicate that the RAD51/Pol-dependent repriming is essential to support fork progression, limit DNA damage and improve viability of RAD52-deficient cells when replication is perturbed. Altogether, this study shows that RAD51/Pol-dependent repriming is a genuine fork recovery mechanism activated to overcome loss of RAD52 function at replication forks.

cell biology↗

bioRxiv2022

WRNIP1 PREVENTS G4/R-LOOP-ASSOCIATED GENOMIC INSTABILITY

Maintenance of genome integrity is essential for cell viability and depends on complete and accurate DNA replication. However, G4/R-loops may provide significant obstacles for DNA replication, as they can cause collisions between replication fork and the transcription machinery. Hence, cells require mechanisms to counteract the presence of persistent G4/R-loops, most of which remain poorly understood. Here, we demonstrate an involvement of the Werner helicase-interacting protein 1 (WRNIP1) in preventing DNA damage induced by G4/R-loop-associated transcription-replication conflicts. We discovered that the ubiquitin-binding domain of WRNIP1 is required to efficiently avoid pathological persistence of G4/R-loops upon replication stress. Also, we observed that G4s reside within R-loops and that WRNIP1 colocalises with these structures. Furthermore, WRNIP1 plays a role in restarting replication from transcription-induced fork stalling. More importantly, we characterized the interplay between WRNIP1 and the DNA helicase FANCJ in counteracting R-loop-dependent G4 formation in response to replication stress. Collectively, our findings propose a mechanisms whereby WRNIP1, contributing to stabilise FANCJ to G4 sites, mitigates the G4/R-loop-mediated transcription-replication conflicts and protects against DNA damage accumulation.

cell biology↗

bioRxiv2022

CHK2 Regulates MUS81-EME2 Function in Response to Replication Stress and BRCA2 Deficiency

MUS81 is a structure-specific endonuclease that processes DNA intermediates in mitosis and in S-phase following replication stress. MUS81 is crucial to cleave deprotected reversed forks in BRCA2-deficient cells. However, how MUS81 is regulated during replication stress in human cells remains unknown. Our study reveals that CHK2 binds the MUS81-EME2 complex and positively regulates formation of DSBs upon replication stress or in the absence of BRCA2. The association with MUS81 occurs through the FHA domain of CHK2 and is disabled by the I157T mutation but not by the R117A mutation. The CHK2-MUS81 complex forms downstream fork reversal and degradation, and phosphorylation of MUS81 at CHK2-targeted sites is crucial to introduce DSBs at deprotected replication forks ensuring the replication fork recovery in BRCA2-deficient cells. Collectively, our work sheds light into the regulation of the MUS81 complex and identifies a novel function of the ATM-CHK2 axis in the response to deprotected replication forks in the absence of BRCA2.

cell biology↗

bioRxiv2022

PHOSPHORYLATION STATUS OF MUS81 IS A MODIFIER OF OLAPARIB SENSITIVITY IN BRCA2-DEFICIENT CELLS

The MUS81 complex is crucial for preserving genome stability through resolution of branched DNA intermediates in mitosis and also for the processing of deprotected replication forks in BRCA2-deficient cells. Because of the existence of two different MUS81 complexes in mammalian cells that act in M or S-phase, whether and how the PARPi sensitivity of BRCA2-deficient cells is affected by loss of MUS81 function is unclear. Here, using a mutant of MUS81 that impairs its function in M-phase, we show that viability of BRCA2-deficient cells but not their PARPi sensitivity requires a fully-functional MUS81 complex in mitosis. In contrast, expression of a constitutively-active MUS81 is sufficient to confer PARPi resistance. From a mechanistic point of view, our data indicates that deregulated action of the mitotic active form of MUS81 in S-phase leads to the cleavage of stalled replication forks before their reversal, bypassing fork deprotection, and engaging a Pol{theta}-dependent DSBs repair. Collectively, our findings describe a novel mechanism leading to PARPi resistance that involves unscheduled MUS81-dependent cleavage of intact, unreversed replication forks. Since this cleavage occurs mimicking the phosphorylated status of S87 of MUS81, our data suggest that hyperphosphorylation of this residue in S-phase might represent a novel biomarker to identify resistance to PARPi.

cell biology↗

bioRxiv2019

Checkpoint defects require WRNIP1 to counteract R-loop-associated genomic instability

Conflicts between replication and transcription are common source of genome instability and many factors participate in prevention or removal of harmful R-loops. Here, we demonstrate that a WRNIP1-mediated response plays an important role in counteracting accumulation of aberrant R-loops. Using human cellular models with compromised ATR-dependent checkpoint activation, we show that WRNIP1 is stabilised in chromatin and is needed for maintaining genome integrity by mediating the ATM-dependent phosphorylation of CHK1. Furthermore, we show that loss of WRN or ATR signalling leads to accumulation of R-loop-dependent parental ssDNA, which is covered by RAD51. We demonstrate that WRNIP1 chromatin retention is also required to stabilise the association of RAD51 with ssDNA in proximity of R-loops. Therefore, in these pathological contexts, ATM inhibition or WRNIP1 abrogation is accompanied by increased levels of genomic instability. Overall our findings reveal a novel function of WRNIP1 in preventing R-loop-driven genome instability, providing new clues to understand the way replication-transcription conflicts are resolved.

cancer biology↗

bioRxiv2019

Generation of inducible SMARCAL1 knock-down iPSC to model severe Schimke immune-osseous dysplasia reveals a link between replication stress and altered expression of master differentiation genes

The Schimke immuno-osseous dysplasia is an autosomal recessive genetic osteochondrodysplasia characterized by dysmorphism, spondyloepiphyseal dysplasia, nephrotic syndrome and frequently T cell immunodeficiency. Several hypotheses have been proposed to explain pathophysiology of the disease, however, the mechanism by which SMARCAL1 mutations cause the syndrome is elusive. Indeed, animal models of the disease are absent or useless to provide insight into the disease mechanism, since they do not recapitulate the phenotype. We generated a conditional knockdown model of SMARCAL1 in iPSCs to mimic conditions of cells with severe form the disease. Here, we characterize this model for the presence of phenotype linked to the replication caretaker role of SMARCAL1 using multiple cellular endpoints. Our data show that conditional knockdown of SMARCAL1 in human iPSCs induces replication-dependent and chronic accumulation of DNA damage triggering the DNA damage response. Furthermore, they indicate that accumulation of DNA damage and activation of the DNA damage response correlates with increased levels of R-loops and replication-transcription interference. Finally, we provide data showing that, in SMARCAL1-deficient iPSCs, DNA damage response can be maintained active also after differentiation, possibly contributing to the observed altered expression of a subset of germ layer-specific master genes. In conclusion, our conditional SMARCAL1 iPSCs may represent a powerful model where studying pathogenetic mechanisms of severe Schimke immuno-osseous dysplasia, thus overcoming the reported inability of different model systems to recapitulate the disease.

cell biology↗

bioRxiv2018

SWITCH-LIKE PHOSPHORYLATION OF WRN INTEGRATES END-RESECTION WITH REPAIR OF DSBs AT REPLICATION FORKS

Replication-dependent DNA double-strand breaks are harmful lesions preferentially repaired by homologous recombination; a process that requires processing of DNA ends to allow RAD51-mediated strand invasion. End-resection and subsequent repair are two intertwined processes, but the mechanism underlying their execution is still poorly appreciated. The WRN helicase is one of the crucial factors for the end-resection and is instrumental to select the proper repair pathway. Here, we reveal that ordered phosphorylation of WRN by the CDK1, ATM and ATR kinases define a complex regulatory layer that is essential for correct long-range end-resection connecting it to repair by homologous recombination. We establish that long-range end-resection requires an ATM-dependent phosphorylation of WRN at Ser1058 and that phosphorylation at Ser1141, together with dephosphorylation at the CDK1 site Ser1133, is needed for the correct metabolism of RAD51 foci and RAD51-dependent repair. Collectively, our findings suggest that regulation of WRN by multiple kinases functions as molecular switch to allow a timely execution of end-resection and repair at replication-dependent DNA double-strand breaks.

cell biology↗

bioRxiv2018

RAD51 AND MITOTIC FUNCTION OF MUS81 ARE ESSENTIAL FOR RECOVERY FROM LOW-DOSE OF CAMPTOTHECIN IN THE ABSENCE OF THE WRN EXONUCLEASE

Stabilisation of the stalled replication fork is crucial to prevent excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is a human RecQ helicase that participates in the processing and recovery of perturbed replication forks. WRN is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined, and little is known about an involvement in the response to perturbed replication. Recently, the WRN exonuclease has been linked to protection of stalled forks from MRE11-dependent degradation in response to clinically-relevant nanomolar doses of the Topoisomerase I inhibitor camptothecin. Alternative processing of perturbed forks has been associated to chemoresistance of BRCA-deficient cancer cells, thus, we used WRN exonuclease-deficiency as a model to investigate the fate of perturbed replication forks undergoing degradation, but in a BRCA wild-type condition. We find that, upon nanomolar doses of camptothecin, loss of WRN exonuclease stimulates fork inactivation and accumulation of parental gaps, which engages RAD51. Such alternative mechanism affects reinforcement of CHK1 phosphorylation and causes persistence of RAD51 during recovery from treatment. Notably, in WRN exonuclease-deficient cells, persistence of RAD51 correlates with elevated mitotic phosphorylation of MUS81 at Serine 87, which is essential to avoid accumulation of mitotic abnormalities. Altogether, these findings indicate that aberrant fork degradation, in the presence of a wild-type RAD51 axis, stimulates RAD51-mediated post-replicative repair and engagement of the MUS81 complex to limit genome instability and cell death.\n\nAUTHOR SUMMARYCorrect progression of the molecular machine copying the chromosomes is threatened by multiple causes that induce its delay or arrest. Once the replication machinery is arrested, the cell needs to stabilise it to prevent DNA damage. Many proteins contribute to this task and the Werners syndrome protein, WRN, is one of them.\n\nDefining what happens to replication machineries when they are blocked is highly relevant. Indeed, destabilised replication machineries may form upon treatment with anticancer drugs and influence the efficacy of some of them in specific genetic backgrounds. We used cells that lack one of the two enzymatic functions of WRN, the exonuclease activity, to investigate the fate of destabilised replication machineries. Our data show that they are handled by a repair pathway normally involved in fixing DNA breaks but, in this case, recruited to deal with regions of the genome that are left unreplicated after their destabilisation. This alternative mechanism involves a protein, RAD51, which tries to copy DNA from the sister chromosome. In so doing, however, RAD51 produces a lot of DNA interlinking that requires upregulation of a complex, called MUS81/EME1, which resolves this interlinking prior cell division and prevents accumulation of mitotic defects and cell death.

cell biology↗

bioRxiv2018

Phosphorylation By CK2 Regulates MUS81/EME1 In Mitosis And After Replication Stress

The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.

cell biology↗