Rapid delivery of RNase H1 enables replication fork progression under stress independently of R-loop resolution

Basille, A.; Lin, Y.-L.; Kirke, C.; Cluet, D.; Bawadi, Y.; Vachez, L.; Dervieux, V.; Guiguettaz, L.; Bernard, P.; Hamperl, S.; Pasero, P.; Ricci, E. P.; Vanoosthuyse, V.

doi:10.1101/2025.02.27.640516

bioRxiv · 10.1101/2025.02.27.640516

Rapid delivery of RNase H1 enables replication fork progression under stress independently of R-loop resolution

Basille, A.·Lin, Y.-L.·Kirke, C.·Cluet, D.·Bawadi, Y.·Vachez, L.·Dervieux, V.·Guiguettaz, L.·Bernard, P.·Hamperl, S.·Pasero, P.·Ricci, E. P.·Vanoosthuyse, V.

View original source ↗Export metadata ↓

Abstract

The over-expression of RNase H1 enables the progression of replication forks under stress and safeguards genome stability. The most common interpretation of these observations is that RNase H1 over-expression removes R-loops, whose formation would hinder replication fork progression. Here we challenge this model using an innovative strategy to rapidly deliver ready-made Escherichia coli RNase H1 (RnhA) in live cells. We show that RnhA is enriched in the vicinity of active replication forks and that it rescues replication fork progression in different stress conditions. However, RnhA had no impact on R-loops mapped by the DRIP or Cut&Tag methods. Our results reveal the existence of distinct populations of RNA:DNA hybrids that are differently sensitive to RnhA and invites new interpretations of well-established observations. HIGHLIGHTSO_LIRapid delivery of R-loop sensors and regulators in live cells C_LIO_LIRapid delivery of RnhA rescues replication fork progression in stress conditions C_LIO_LIRapid delivery of RnhA does not impact R-loops C_LIO_LIDRIP detects RNA:DNA species insensitive to RNase H1 in cells C_LI

Explore related subjects

molecular biology Preprint

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Basille, A., Lin, Y.-L., Kirke, C., Cluet, D., Bawadi, Y., Vachez, L., Dervieux, V., Guiguettaz, L., Bernard, P., Hamperl, S., Pasero, P., Ricci, E. P., Vanoosthuyse, V.. 2025-03-02. Rapid delivery of RNase H1 enables replication fork progression under stress independently of R-loop resolution. https://doi.org/10.1101/2025.02.27.640516

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Simvastatin and Primaquine Identified as Potential Endometriosis Therapeutics via a Novel Epithelial-Stromal Assembloid Drug Screening Assay

Background: Endometriosis is an estrogen-driven, inflammatory disorder affecting ~10% of menstruators, causing severe pain. Current treatments that reduce estrogen or inflammation have inconsistent efficacy and poor tolerability. Therapies identified via drug-repositioning methods, which target patient-specific pathways, offer a promising alternative. Simvastatin and primaquine were identified as potential treatments, strongly reversing endometriosis-associated gene expression pathways, and behavioral testing in an animal model showed that these drugs diminish endometriosis-associated pain. This paper examines their effects in human assembloids to provide proof-of-concept validation and insights into their mechanisms of action relevant to endometriosis. Methods: We established human endometrial assembloids using immortalized epithelial (12Z) and stromal fibroblast (iEc) cell lines, as well as primary tissue from patients. Assembloids were generated in 96-well agarose molds with both cell types. We tested ibuprofen, fenoprofen, primaquine, and simvastatin. Following a 24-hour exposure, assembloids and monolayer cultures were harvested and stranded mRNA-seq libraries were sequenced on an Illumina NovaSeqX Plus System. Results: Gene set enrichment analysis showed key pathway reversals: Primaquine reversed the chemical carcinogenesis ROS pathway in assembloids. Simvastatin reversed cytokine-cytokine receptor interaction in both epithelial and stromal cell lines, and the cytoskeleton in muscle cells pathway in stromal cell lines. Fenoprofen reversed the calcium signaling pathway in stromal cell lines. Conclusion: Simvastatin induced the most significant gene expression changes, notably reversing cytokine-cytokine receptor interactions in both cell lines, mirroring findings from our rat model. Despite the small sample size limitation, these experiments highlight the promise of assembloid models to test therapeutic candidates for endometriosis.

molecular biology↗

bioRxiv2026

A feed-forward UHRF1 read-write mechanism supports H3 multi- mono-ubiquitination and DNA methylation maintenance at CpG-sparse regions

The epigenetic inheritance of mammalian DNA methylation requires DNMT1 and its E3 ligase cofactor UHRF1. At newly replicated chromatin, UHRF1 recognition of hemi-methylated DNA and histone H3 N-terminal tails directs catalysis of H3K14, H3K18, and/or H3K23 mono-ubiquitination to recruit DNMT1. While it is appreciated that UHRF1 can deposit multiple mono-ubiquitin marks on a single H3 tail and that DNMT1 recognizes this state through tandem ubiquitin interacting motifs, the mechanism that promotes successive ubiquitination and the biological function of multi-mono-ubiquitination are unknown. Here, we show that UHRF1 directly binds its mono-ubiquitinated H3 products through a previously uncharacterized LGDDSL loop in Tudor 2 of its tandem Tudor domain (TTD) to promote further ubiquitin deposition. Disruption of this ubiquitin reading activity impairs H3 multi-mono-ubiquitination and accelerates DNA methylation loss within late-replicating, CpG-sparse genomic regions that are characteristic of partially methylated domains (PMDs) in cancer and aging cells. These methylation defects overlap those observed by disruption of UHRF1 ubiquitin ligase activity, providing convergent evidence that both writing and reading of H3 ubiquitination support CpG-sparse DNA methylation maintenance. Together, these findings establish a feed-forward ubiquitin read-write mechanism that generates multi-mono-ubiquitinated H3 and safeguards DNMT1-dependent DNA methylation maintenance at vulnerable genomic regions of the mammalian methylome.

molecular biology↗

bioRxiv2026

Calcium dysregulation amplifies fibrotic responses to TGFβ in human Friedreich's ataxia fibroblasts

Friedreich's ataxia (FA) is an inherited disease caused by loss of frataxin (FXN) and characterized by neurodegeneration and fatal cardiomyopathy. Cardiac fibrosis contributes to cardiomyopathy by stiffening the heart wall, yet the underlying mechanisms remain unknown. Here, we investigated pro-fibrotic predisposition in FA patient-derived fibroblasts, focusing on the role of cytosolic calcium (Ca) in TGF{beta}-driven fibroblast-to-myofibroblast transition (FMT). We found pro-fibrotic transcriptional priming in FA fibroblasts, alongside elevated expression of genes controlled by the Ca-responsive transcription factor NFAT. Upon FMT, FA myofibroblasts showed amplified induction of pro-fibrotic (CCN2, NOX4) and suppression of anti-fibrotic (CCN3) genes, which were inversely correlated with residual FXN. Mechanistically, FA fibroblasts exhibited elevated cytosolic Ca and strongly downregulated expression of the Na-Ca exchanger NCX1, which directly correlated with FXN. Furthermore, NCX1 inhibition in control fibroblasts recapitulated FA Ca phenotypes, whereas NCX1 transduction in FA fibroblasts normalized Ca dynamics and blunted CCN2 induction in FMT. These findings highlight NCX1 as a modulator of fibrotic reprogramming in FA and identify Ca dyshomeostasis as an intrinsic mechanism of fibrosis that could be targeted therapeutically.

molecular biology↗