Biology subjects

Bernard, P.

Publications and source records attributed to Bernard, P..

13 recordsLinked to original sources

bioRxiv2026

Understanding the role of chromatin accessibility and compaction on loop extrusion dynamics

Loop extrusion by SMC complexes is a fundamental mechanism regulating the three-dimensional genome organization, but how these molecular motors navigate through the crowded, nucleosome-covered chromatin fiber remains an open question. Here, we develop a stochastic biophysical model of loop extrusion that explicitly couples motor stepping dynamics to chromatin accessibility and compaction. First, we systematically analyze the role of accessibility on its dynamics across homogeneous, periodic, and random roadblock positioning along chromatin. This comprehensive analysis reveals distinct dynamic regimes: phase-dependent kinetics in periodic arrays where motor step size aligns with obstacle spacing, and anomalous sub-linear progression in disordered environments due to rare but long-lived trapping events. Then, we contextualize our framework to nucleosome-like arrays. Our simulations reveal a non-intuitive dual role for nucleosomes: while they hinder extruder progression by blocking access to linker DNA, their high compaction packs more base pairs per physical distance, enabling larger genomic displacements per step. Strikingly, the resulting base-pair extrusion speed displays a non-monotonic dependence on nucleosome spacing, reaching a maximum at intermediate linker lengths (10-70 bp) that can exceed the speed on naked DNA. Finally, in support of this mechanism, analysis of yeast genomic data shows that a higher nucleosome occupancy between cohesin-associated regions correlates with stronger contact enrichment, consistent with compaction-enhanced extrusion efficiency in vivo. These findings establish chromatin architecture as a tunable regulator of loop extrusion, explaining the comparable speeds observed in vitro and in vivo and providing a quantitative framework for understanding how genome organization emerges from the interplay between motor kinetics and chromatin structure.

biophysics↗

bioRxiv2026

The rapid delivery of RNase H variants reveals distinct classes of RNA:DNA hybrids

Multiple lines of evidence suggest that RNase H1-sensitive RNA:DNA hybrids (thereafter referred to as hybrids) could disrupt the stability and restart of stalled replication forks. The prolonged over-expression of RNase H1 is the most popular method to manipulate hybrids in situ but it cannot discriminate between direct and indirect effects resulting from their loss. To overcome this limitation, we developed iCoRD (in Cellulo RNase H Delivery) to rapidly deliver comparable amounts of either Escherichia coli RNase H1 (RnhA) or control proteins in live cells, with a negligible impact on the transcriptome. iCoRD-delivered RnhA recognises hybrids in situ, is enriched in the vicinity of active replication forks and rescues replication fork progression in different stress conditions. While iCoRD-delivered RnhA had a clear impact on stress-induced, fork-proximal hybrids and R-ChIP signals, it had no effect on DRIP or S9.6 Cut&Tag signals, even when these were induced by stress. Our results strongly suggest the existence of distinct populations of hybrids that are best mapped by different methods and are differently sensitive to RNase H1 activity in situ.

molecular biology↗

bioRxiv2026

Single-Cell Cross-Species Profiling identifies Conserved Transcriptional Networks in Early Pancreatic Tumourigenesis.

Pancreatic ductal adenocarcinoma (PDAC) is the most common form of pancreatic cancer and carries the poorest prognosis among all cancers, largely because it is frequently diagnosed at metastatic stages. It is therefore critical to identify reliable markers of preinvasive stages and to decipher the network driving preinvasive lesions to invasive carcinoma. Here, we generated a zebrafish model in which KRASG12D is specifically expressed in pancreatic acinar cells, inducing acinar-to-ductal metaplasia that faithfully mirrors mammalian tumorigenesis. Single cell RNA-seq allowed us to capture transcriptional changes occurring at early stages of the disease. Cross-species comparison with mouse and human scRNAseq transcriptomes revealed a striking conservation of the genes upregulated during metaplasia, triggering common signalling pathways and regulatory programs. Notably, metaplastic cells reactivate a broad set of developmental genes expressed in multipotent pancreatic progenitors. Mapping the acinar-to-cancer trajectories revealed a set of cytoskeletal and migration-related genes specifically upregulated during the late phase of metaplasia, immediately prior to malignant transformation, likely conferring invasive potential to these cells. SCENIC analysis further identified regulatory networks that become progressively activated as cells transition toward cancer, suggesting their involvement in the acquisition of malignant traits. In conclusion, our cross-species comparison demonstrates a high degree of conservation in the molecular mechanisms driving pancreatic cancer progression from early to late stages across evolutionarily distant species, including zebrafish, mouse, and human, highlighting critical pathways that should be targeted to prevent cancer progression. To allow researchers to easily explore gene expression profiles during pancreatic cancer progression across all three species, the datasets are publicly accessible via a user-friendly web platform (https://www.zddm.page.gd/)

cancer biology↗

bioRxiv2025

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

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

molecular biology↗

bioRxiv2023

RNA Pol II antagonises mitotic chromatin folding and chromosome segregation by condensin

Condensin shapes mitotic chromosomes by folding chromatin into loops but whether it does so by DNA-loop extrusion remains speculative. While loop-extruding cohesin is stalled by transcription, no conclusive evidence has been provided regarding the impact of transcription on condensin despite its conserved enrichment at highly expressed genes. Using degrons of Rpb1 or the torpedo nuclease Dhp1XRN2, we depleted or displaced RNAP2 on chromatin in fission yeast metaphase cells. We show that RNAP2 does not load condensin on DNA but instead retains condensin and hinders its ability to fold mitotic chromatin and to support chromosome segregation, consistent with the stalling of a loop-extruder. Transcription termination by Dhp1 limits such a hindrance. Our results shed a new light on the integrated functioning of condensin and we argue that a tight control of transcription underlies mitotic chromosome assembly by loop-extruding condensin.

genomics↗

bioRxiv2022

Condensin positioning at telomeres by Taz1 promotes telomere disjunction in anaphase

The localization of condensin along chromosomes is crucial for their accurate segregation in anaphase. Condensin is enriched at telomeres but how and for what purpose had remained elusive. Here we show that fission yeast condensin accumulates at telomere repeats through the balancing acts of Taz1, a core component of the shelterin complex that ensures telomeric functions, and Mit1, a nucleosome-remodeler associated with shelterin. We further show that condensin takes part in sister-telomere separation in anaphase, and that this event can be uncoupled from the prior separation of chromosome arms, implying a telomere-specific separation mechanism. Consistent with a cis-acting process, increasing or decreasing condensin occupancy specifically at telomeres modifies accordingly the efficiency of their separation in anaphase. Genetic evidence suggests that condensin promotes sister-telomere separation by counteracting cohesin. Thus, our results reveal a shelterin-based mechanism that enriches condensin at telomeres to drive in cis their separation during mitosis.

cell biology↗

bioRxiv2020

RNA polymerase backtracking drives the accumulation of fission yeast condensin at active genes

The mechanisms leading to the accumulation of the SMC complexes condensins around specific transcription units remain unclear. Observations made in bacteria suggested that RNA polymerases (RNAP) constitute an obstacle to SMC translocation, particularly when RNAP and SMC travel in opposite directions. Here we show in fission yeast that gene termini harbour intrinsic condensin-accumulating features whatever the orientation of transcription, which we attribute to the frequent backtracking of RNAP at gene ends. Consistent with this, to relocate backtracked RNAP2 from gene termini to gene bodies was sufficient to cancel the accumulation of condensin at gene ends and to redistribute it evenly within transcription units, indicating that RNAP backtracking may play a key role in positioning condensin. Formalization of this hypothesis in a mathematical model suggests that the inclusion of a sub-population of RNAP with longer dwell-times is essential to fully recapitulate the distribution profiles of condensin around active genes. Taken together, our data strengthen the idea that dense arrays of proteins tightly-bound to DNA alter the distribution of condensin on chromosomes.

cell biology↗

bioRxiv2020

Aurora B and Condensin are dispensable for chromosome arm and telomere separation during meiosis II

In mitosis, while the importance of kinetochore-microtubule attachment has been known for many years, increasing evidence suggests that telomere dysfunctions also perturb chromosome segregation by contributing to the formation of chromatin bridges at anaphase. Recent evidence suggests that Aurora B ensures proper chromosome segregation during mitosis not only by controlling kinetochore-microtubule attachment but also by regulating telomere and chromosome arm separation. However, whether and how Aurora-B governs telomere separation during meiosis has remained unknown. Here, we show that fission yeast Aurora B localizes at telomeres during meiosis I and promotes telomere separation independently of the meiotic cohesin Rec8. In meiosis II, Aurora-B controls kinetochore-microtubule attachment but appears dispensable for telomere and chromosome arm separation. Likewise, condensin activity is nonessential in meiosis II for telomere and chromosome arm separation. Thus, in meiosis, the requirements for Aurora-B are distinct at centromeres and telomeres, illustrating the critical differences in the control of chromosome segregation between mitosis and meiosis II.

cell biology↗

bioRxiv2019

The sequence of the extruded non-template strand determines the architecture of R-loops.

Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the sequence of the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.

biophysics↗

bioRxiv2019

Sen1 is required for RNA Polymerase III transcription termination in an R-loop independent manner.

R-loop disassembly by the human helicase Senataxin contributes to genome stability and to proper transcription termination at a subset of RNA polymerase II genes. Whether Senataxin-mediated R-loop disassembly also contributes to transcription termination at other classes of genes has remained unclear. Here we show in fission yeast that SenataxinSen1 promotes efficient termination of RNA Polymerase III (RNAP3) transcription in vivo. In the absence of SenataxinSen1, RNAP3 accumulates downstream of the primary terminator at RNAP3-transcribed genes and produces long exosome-sensitive 3-extended transcripts. Importantly, neither of these defects was affected by the removal of R-loops. The finding that SenataxinSen1 acts as an ancillary factor for RNAP3 transcription termination in vivo challenges the pre-existing view that RNAP3 terminates transcription autonomously. We propose that Senataxin is a cofactor for transcription termination that has been co-opted by different RNA polymerases in the course of evolution.

molecular biology↗

bioRxiv2018

Condensin controls cellular RNA levels through the accurate segregation of chromosomes instead of directly regulating transcription

Condensins are genome organisers that shape chromosomes and promote their accurate transmission. Several studies have also implicated condensins in gene expression, although the mechanisms have remained enigmatic. Here, we report on the role of condensin in gene expression in fission and budding yeasts. In contrast to previous studies, we provide compelling evidence that condensin plays no direct role in the maintenance of the transcriptome, neither during interphase nor during mitosis. We further show that the changes in gene expression in post-mitotic fission yeast cells that result from condensin inactivation are largely a consequence of chromosome missegregation during anaphase, which notably depletes the RNA-exosome from daughter cells. Crucially, preventing karyotype abnormalities in daughter cells restores a normal transcriptome despite condensin inactivation. Thus, chromosome instability, rather than a direct role of condensin in the transcription process, changes gene expression. This knowledge challenges the concept of gene regulation by canonical condensin complexes.

molecular biology↗

bioRxiv2017

The affinity of the S9.6 antibody for double-stranded RNAs impacts the mapping of R-loops in fission yeast.

R-loops, which result from the formation of stable DNA:RNA hybrids, can both threaten genome integrity and act as physiological regulators of gene expression and chromatin patterning. To characterize R-loops in fission yeast, we used the S9.6 antibody-based DRIPc-seq method to sequence the RNA strand of R-loops and obtain strand-specific R-loop maps at near nucleotide resolution. Surprisingly, preliminary DRIPc-seq experiments identified mostly RNase H-resistant but exosome-sensitive RNAs that mapped to both DNA strands and resembled RNA:RNA hybrids (dsRNAs), suggesting that dsRNAs form widely in fission yeast. We confirmed in vitro that S9.6 can immuno-precipitate dsRNAs and provide evidence that dsRNAs can interfere with its binding to R-loops. dsRNA elimination by RNase III treatment prior to DRIPc-seq allowed the genome-wide and strand-specific identification of genuine R-loops that responded in vivo to RNase H levels and displayed classical features associated with R-loop formation. We also found that most transcripts whose levels were altered by in vivo manipulation of RNase H levels did not form detectable R-loops, suggesting that prolonged manipulation of R-loop levels could indirectly alter the transcriptome. We discuss the implications of our work in the design of experimental strategies to probe R-loop functions.

molecular biology↗

bioRxiv2017

Membrane Proteins Significantly Restrict Exosome Mobility

Exosomes are membrane nanovesicles that intermediate cell-to-cell signaling through the transfer of their molecular cargo. The exosomes small size facilitates rapid migration through the extracellular matrix and into and out of circulation. Here we report that the mobility of the exosomes is much lower than would be expected from the size of their membrane vesicles. The difference is broadly distributed and caused by surface proteins, which significantly impede exosome migration. The observed wide range in the mobility implies that a subpopulation of hydrodynamically small exosomes is more likely to participate in signaling. The extracellular environment amplifies the size-dependent hindrance to the exosomes migration. The significant contribution of surface proteins to the transport resistance make the exosome mobility a dynamic property that changes with the extracellular environment which affects the membrane protein conformation, glycosylation, specific, and non-specific surface adsorption.

biochemistry↗