Biology subjects

Ceppi, I.

Publications and source records attributed to Ceppi, I..

6 recordsLinked to original sources

bioRxiv2026

Non-canonical ATR signalling via NBS1 phosphorylation propagates fork slowing from stressed to unperturbed nuclear regions

DNA replication forks frequently encounter obstacles and remodel into four-way junctions to actively slow DNA fork progression. Fork slowing can also spread to undamaged forks via an ATR-dependent mechanism that remained elusive. Here, using mild genotoxic stress, we show that fork slowing and reversal require full ATR activity, but no canonical ATR activators and signalling partners, defining a non-canonical ATR pathway distinct from origin firing control. Phospho-proteomics in S-phase cells under checkpoint-blind replication stress identified a subset of ATR-dependent phospho-sites, such as S343 on NBS1, the regulatory subunit of the MRN complex. This residue is essential to stimulate MRN exonuclease activity in vitro and required in cells for global fork slowing upon mild DNA damage. Ultimately, local UV-C micro-irradiation reveals that ATR-dependent MRN-stimulated resection dampens DNA synthesis at lesions and propagates fork slowing to undamaged chromatin, supporting MRN-mediated ssDNA exposure as a mean to coordinate replication slowdown across the nucleus.

cell biology↗

bioRxiv2026

Meiotic pairing through barcode-like satellite DNA repeats

During meiosis, chromosomes must find, pair, and synapse with their homologous partners in the crowded milieu of the nucleus1. Although homology detection is generally attributed to recombination, pairing and synapsis can occur in its absence2-10, suggesting alternate mechanisms that discriminate between homologous and non-homologous chromosomes. In many eukaryotes, tandem repeats known as satellite DNA facilitate inter-chromosomal associations11. Notably, their non-uniform distribution across chromosomes gives rise to homologue-specific satellite DNA barcodes12-14, which have been speculated to enable meiotic pairing15-18. However, satellite DNA function remains actively debated since these repeats cannot be manipulated in most model organisms. Here, we use satellite DNA deletion, duplication, and translocation strains that are unique to Drosophila to demonstrate that repeat mismatches perturb meiotic pairing, particularly at centromeres and pericentromeres. In the absence of satellite DNA homology, pairing is antagonized by the HORMAD protein, Mad2, while a Pachytene checkpoint 2 (Pch2)-dependent meiotic delay restores pairing. Remarkably, pairing defects are also observed in the progeny of D. melanogaster natural populations that have diverged in their satellite DNA content. Finally, compromised meiotic pairing is strongly correlated with mid-oogenesis cell death, a quality control mechanism that likely culls defective oocytes to prevent chromosome mis-segregation and aneuploidy. These findings resolve a long-standing debate on satellite DNA functionality by demonstrating a barcode-like role in homology detection. We propose that this repeat-based pairing mechanism exerts an underappreciated selective pressure, constraining the divergence of rapidly evolving satellite DNA within interbreeding natural populations.

genetics↗

bioRxiv2025

Nuclear mechanostability emerges from satellite DNA condensation into chromocenters

As the largest organelle, the nucleus endures significant mechanical stresses over the cellular lifespan, and mechanostability, i.e. the ability to resist deformation, is critical for genome integrity and function. Here, we reveal that nuclear mechanostability is an emergent property arising from the clustering of satellite DNA repeats into nuclear condensates known as chromocenters. Targeted chromocenter disruption in Drosophila testes subjected to natural and artificial mechanical stress compromises nuclear mechanostability, leading to deformed nuclei, DNA damage, and chromosome breaks. Conversely, enhancing chromocenter coalescence through genetic means improves mechanostability. Molecular dynamics simulations suggest that chromocenters enable physically linked chromosomes to respond collectively, rather than individually, to mechanical challenge, and dissipate external forces over a larger nuclear surface. We propose that the satellite DNA-dependent mechanostability framework described here likely extends to other cells and tissues facing mechanical stress, and offers an explanation for the evolutionary success of these non-coding repeats across eukaryotes.

cell biology↗

bioRxiv2025

IFI16 senses and protects stalled replication forks

Replication stress is a key driver of DNA damage and genome instability. Replication stress-induced fork remodelling generates a new DNA end that is vulnerable to the action of nucleases, and which is protected by a range of factors including the canonical tumour suppressors BRCA1 and BRCA2. Here we report that replication stress drives elevated production of cytokines and chemokines in the absence of DNA damage. The DNA sensor IFI16 binds nascent DNA at stalled replication forks and signals via the DNA sensing adaptor STING, to induce the activation of NF-{kappa}B and the production of pro-inflammatory cytokines in response to replication stress. IFI16 also acts directly at stalled replication forks to protect nascent DNA from degradation by the nucleases MRE11 and DNA2. Furthermore, IFI16 is required for the interferon-mediated rescue of fork protection in BRCA-deficient cells, highlighting the critical role of IFI16 in the cross-talk between innate immunity and fork protection during replication stress. HighlightsO_LIReplication stress induces an early innate immune response, which is dependent on the DNA sensing factors IFI16 and STING, but not cGAS C_LIO_LIIFI16 binds directly to nascent DNA at stalled replication forks C_LIO_LIIFI16 prevents nucleolytic degradation of reversed forks C_LIO_LIIFI16 is required for interferon-mediated fork protection in BRCA-deficient cells C_LI

cancer biology↗

bioRxiv2024

The PIN1-p38-CtIP signaling axis protects stalled replication forks from deleterious degradation

Human CtIP plays a critical role in homologous recombination (HR) by promoting the resection of DNA double-strand breaks. Moreover, CtIP maintains genome stability through protecting stalled replication forks from nucleolytic degradation. However, the upstream signaling mechanisms governing the molecular switch between these two CtIP-dependent processes remain largely elusive. Here, we show that phosphorylation of CtIP by the p38 stress kinase and subsequent PIN1-mediated CtIP cis-to-trans isomerization is required for fork stabilization but dispensable for HR. We found that stalled forks are degraded in cells expressing non-phosphorylatable CtIP or lacking PIN1-p38 activity, while expression of a CtIP trans-locked mutant overcomes the requirement for PIN1-p38 in fork protection. We further reveal that Brca1-deficient mammary tumor cells that have acquired PARPi resistance regain chemosensitivity after PIN1 or p38 inhibition. Collectively, our findings identify the PIN1-p38-CtIP signaling pathway as a critical regulator of replication fork integrity.

molecular biology↗

bioRxiv2019

CtIP promotes the motor activity of DNA2 to accelerate long-range DNA end resection

BLM or WRN helicases function with the DNA2 helicase-nuclease to resect DNA doublestrand breaks and initiate homologous recombination. Upon DNA unwinding by BLM/WRN, RPA directs the DNA2 nuclease to degrade the 5-strand, revealing the 3 overhang needed for recombination. RPA bound to ssDNA also represents a barrier, explaining the need for the motor activity of DNA2 to displace RPA prior to resection. Using ensemble and single molecule biochemistry, we show that phosphorylated CtIP dramatically stimulates the ATP hydrolysis driven motor activity of DNA2. This activation in turn strongly promotes the degradation of RPA-coated ssDNA by DNA2. The domains of CtIP required to stimulate DNA2 are separable from those that regulate the MRN complex. These results establish that CtIP couples both MRE11-dependent short and DNA2-dependent long-range resection, and show how the motor activity of DNA2 promotes resection. Our data explain the less severe resection defects of MRE11 nuclease-deficient cells compared to those lacking CtIP.\n\nHighlightsO_LIPhosphorylated CtIP stimulates the motor activity of DNA2\nC_LIO_LIThe activated DNA2 translocase facilitates degradation of RPA-coated ssDNA\nC_LIO_LICtIP promotes both MRN and DNA2 nucleases coupling short and long-range resection\nC_LIO_LIThe CtIP domains required to promote DNA2 and MRN are distinct and fully separable\nC_LI

biochemistry↗