Biology subjects

Rocher, V.

Publications and source records attributed to Rocher, V..

9 recordsLinked to original sources

bioRxiv2026

Single-cell resolution of resection-dependent chromatin accessibility in response to DNA double-strand breaks reveals specific gene expression programs

Chromatin structure is extensively modified and remodeled to allow for efficient signaling and repair of DNA double-strand breaks (DSBs), a process which is influenced by the nature and properties of the damaged locus or the repair pathway involved. However, the extent of cell-to-cell variability in these DSB-induced chromatin modifications remains poorly characterized. Here, we report how chromatin accessibility is reshuffled at the damaged locus at high resolution. Notably, we identify a long-range increase in chromatin accessibility which is dependent on functional resection. We report that resection-dependent chromatin remodeling events at individual damaged loci display significant heterogeneity in single cells which are only partly explained by the cell cycle, and can frequently be detected as asymmetric and unidirectional. Moreover, we identify strong transcriptional phenotypes upon sustained DNA damage as well as subpopulations of S and G2/M cells for which similar resection-dependent chromatin accessibility patterns occur simultaneously at multiple DSBs. These coordinated chromatin accessibility patterns at multiple DSBs are associated with specific gene expression programs, including DNA damage checkpoint signaling, inflammation and apoptosis. Altogether, our results highlight the heterogeneity in chromatin remodeling during DSB repair and suggest unexpected links between DNA end resection and specific gene expression programs mounted in response to genotoxic stress.

cell biology↗

bioRxiv2025

A deeper study on propionic acid-related inhibition during anaerobic digestion: insights on methane production and identification of biomarker candidates for an early warning

Propionic acid (HPr) accumulation is a major indicator of anaerobic digestion (AD) dysfunction, yet the relative contributions of acidity, undissociated HPr, and propionate ions (Pr-) to process inhibition remain poorly understood. We investigated these effects in mesophilic batch AD microcosms fed with municipal sewage sludge, using a comparative design involving HPr, sodium propionate (NaPr), NaCl, and HCl treatments across two series of experiments. While 20 mM HPr caused a 22% reduction in the maximal methane production rate, 81 mM HPr led to complete inhibition, with the initial pH dropping to 5.1. By contrast, 81 mM NaPr reduced methane production rate by only 40%, and 81 mM NaCl caused no inhibition, demonstrating that acidity is the dominant inhibitory factor, with Pr- exerting a secondary concentration-dependent effect. 16S rRNA gene amplicon sequencing revealed strong, compound-specific shifts in microbial community composition, affecting key functional groups including syntrophs and methanogenic archaea. The proportion of methanogens dropped from 2-3% in control reactors to less than 0.2% under 81 mM HPr, consistent with the observed methane production inhibition. Under HPr81, over 100 ASVs were differentially abundant compared to controls, a pattern largely shared with HCl-treated reactors, further confirming the predominant role of acidity. The number of differentially abundant ASVs was negatively correlated with methane production rates (R{superscript 2} = 0.97), underscoring the link between community reshaping and process impairment. These results provide a unifying framework for propionate inhibition in AD and suggest that microbial community profiling could serve as an early warning tool for process imbalance detection.

bioengineering↗

bioRxiv2023

Circadian PERIOD complex regulates TC-DSB repair through anchoring to the nuclear envelope

Repair of DNA Double-Strand Breaks (DSBs) produced in transcriptionally active chromatin occurs through a poorly characterized pathway called Transcription-Coupled DSB repair (TC-DSBR). Here, using a screening approach scoring multiple outputs in human cells, we identified proteins from the PERIOD complex, a key module ensuring circadian oscillations, as novel TC-DSBR players. We show that the core PER complex protein PER2 is recruited at TC-DSBs and that it contributes to the targeting of TC-DSBs at the nuclear envelope (NE). At the NE, SUN1 and the Nuclear Pore Complex (NPC) act as docking sites for TC-DSBs and TC-DSB anchoring fosters RAD51 assembly. Impaired DSB localization at the NE results in elevated DSB clustering and translocation rate. In agreement, the circadian clock regulates TC-DSB anchoring to the NE, RAD51 assembly, and DSB clustering. Our study shows that DSB localization to the NPC is a conserved molecular pathway that also occurs in human cells and provides a direct link between the circadian rhythm and the response to DSBs occurring in active genes. This opens new therapeutic strategies for chemotherapies based on drugs that are inducing DSBs in active loci such as topoisomerase poisons.

molecular biology↗

bioRxiv2021

ATM-dependent formation of a novel chromatin compartment regulates the Response to DNA Double Strand Breaks and the biogenesis of translocations

DNA Double-Strand Breaks (DSBs) repair is essential to safeguard genome integrity but the contribution of chromosome folding into this process remains elusive. Here we unveiled basic principles of chromosome dynamics upon DSBs in mammalian cells, controlled by key kinases from the DNA Damage Response. We report that ATM is responsible for the reinforcement of topologically associating domains (TAD) that experience a DSB. ATM further drives the formation of a new chromatin sub-compartment ("D" compartment) upon clustering of damaged TADs decorated with {gamma}H2AX and 53BP1. "D" compartment formation mostly occurs in G1, is independent of cohesin and is enhanced upon DNA-PK pharmacological inhibition. Importantly, a subset of DNA damage responsive genes that are upregulated following DSBs also physically localize in the D sub-compartment and this ensures their optimal activation, providing a function for DSB clustering in activating the DNA Damage Response. However, these DSB-induced changes in genome organization also come at the expense of an increased translocations rate, which we could also detect on cancer genomes. Overall, our work provides a function for DSB-induced compartmentalization in orchestrating the DNA Damage Response and highlights the critical impact of chromosome architecture in genomic instability.

molecular biology↗

bioRxiv2021

First evidence of SARS-CoV-2 genome detection in zebra mussel (Dreissena polymorpha).

The uses of bivalve molluscs in environmental biomonitoring have recently gained momentum due to their ability to indicate and concentrate human pathogenic microorganisms. In the context of the health crisis caused by the COVID-19 epidemic, the objective of this study was to determine if the SARS-CoV-2 ribonucleic acid genome can be detected in zebra mussels (Dreissena polymorpha) exposed to raw and treated urban wastewaters from two separate plants to support its interest as bioindicator of the SARS-CoV-2 genome contamination in water. The zebra mussels were exposed to treated wastewater through caging at the outlet of two plants located in France, as well as to raw wastewater at laboratory scale in controlled conditions. Within their digestive tissues, our results showed that SARS-CoV-2 genome was detected in zebra mussels, whether in raw and treated wastewaters. Moreover, the detection of the SARS-CoV-2 genome in such bivalve molluscans appeared even with low concentrations in raw wastewaters. This is the first detection of the SARS-CoV-2 genome in the tissues of a sentinel species exposed to raw and treated urban wastewaters. Despite the need for development for quantitative approaches, these results support the importance of such invertebrate organisms, especially zebra mussel, for the active surveillance of pathogenic microorganisms and their indicators in environmental waters. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=71 SRC="FIGDIR/small/446136v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@781087org.highwire.dtl.DTLVardef@853128org.highwire.dtl.DTLVardef@5e667forg.highwire.dtl.DTLVardef@19b243e_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2020

DeepG4 : A deep learning approach to predict active G-quadruplexes

DNA is a complex molecule carrying the instructions an organism needs to develop, live and reproduce. In 1953, Watson and Crick discovered that DNA is composed of two chains forming a double-helix. Later on, other structures of DNA were discovered and shown to play important roles in the cell, in particular G-quadruplex (G4). Following genome sequencing, several bioinformatic algorithms were developed to map G4s in vitro based on a canonical sequence motif, G-richness and G-skewness or alternatively sequence features including k-mers, and more recently machine/deep learning. Here, we propose a novel convolutional neural network (DeepG4) to map active G4s (forming both in vitro and in vivo). DeepG4 is very accurate to predict active G4s, while most state-of-the-art algorithms fail. Moreover, DeepG4 identifies key DNA motifs that are predictive of G4 activity. We found that active G4 motifs do not follow a very flexible sequence pattern as current algorithms seek for. Instead, active G4s are determined by numerous specific motifs. Moreover, among those motifs, we identified known transcription factors (TFs) which could play important roles in G4 activity by contributing either directly to G4 structures themselves or indirectly by participating in G4 formation in the vicinity. Moreover, we showed that specific TFs might explain G4 activity depending on cell type. Lastly, variant analysis suggests that SNPs altering predicted G4 activity could affect transcription and chromatin, e.g. gene expression, H3K4me3 mark and DNA methylation. Thus, DeepG4 paves the way for future studies assessing the impact of known disease-associated variants on DNA secondary structure by providing a mechanistic interpretation of SNP impact on transcription and chromatin. Availability: https://github.com/morphos30/DeepG4. Author summaryDNA is a molecule carrying genetic information and found in all living cells. In 1953, Watson and Crick found that DNA has a double helix structure. However, other DNA structures were later identified, and most notably, G-quadruplex (G4). In 2000, the Human Genome Project revealed the widespread presence of G4s in the genome using algorithms. To date, all G4 mapping algorithms were developed to map G4s on naked DNA, without knowing if they could be formed in the cell. Here, we designed a novel artificial intelligence algorithm that could map G4s active in the cell from the DNA sequence. We showed its better accuracy compared to existing algorithms. Moreover, we identified key transcriptional factor motifs that could explain G4 activity depending on cell type. Lastly, we demonstrated the existence of mutations that could alter G4 activity and therefore impact molecular processes, such as transcription, in the cell. Such results could provide a novel mechanistic interpretation of known disease-associated mutations.

bioinformatics↗

bioRxiv2020

BLM-dependent Break-Induced Replication handles DSBs in transcribed chromatin upon impaired RNA:DNA hybrids dissolution.

Transcriptionally active loci are particularly prone to breakage and mounting evidence suggest that DNA Double-Strand Breaks arising in genes are handled by a dedicated repair pathway, Transcription-Coupled DSB Repair (TC-DSBR), that entails R-loops accumulation and dissolution. Here, we uncovered a critical function of the Bloom RecQ DNA helicase (BLM) in TC-DSBR in human cells. BLM is recruited in a transcription dependent-manner at DSBs where it fosters resection, RAD51 binding and accurate Homologous Recombination repair. However, in a R-loop dissolution-deficient background BLM switches from promoting Homologous Recombination to promoting Break-Induced Replication (BIR), which strongly impairs cell viability. Altogether our work unveils a role for BLM in BIR at DSBs in active chromatin, and highlights the toxic potential of RNA:DNA hybrids that accumulate at these transcription-associated DSBs.

molecular biology↗

bioRxiv2020

Loop extrusion as a mechanism for DNA Double-Strand Breaks repair foci formation

DNA Double-Strand Breaks (DSBs) repair is essential to safeguard genome integrity. Upon DSBs, the ATM PI3K kinase rapidly triggers the establishment of megabase-sized, {gamma}H2AX-decorated chromatin domains which further act as seeds for the formation of DNA Damage Response (DDR) foci1. How these foci are rapidly assembled in order to establish a "repair-prone" environment within the nucleus is yet unclear. Topologically Associating Domains (TADs) are a key feature of 3D genome organization that regulate transcription and replication, but little is known about their contribution to DNA repair processes2,3. Here we found that TADs are functional units of the DDR, instrumental for the correct establishment of {gamma}H2AX/53BP1 chromatin domains in a manner that involves one-sided cohesin-mediated loop extrusion on both sides of the DSB. We propose a model whereby H2AX-containing nucleosomes are rapidly phosphorylated as they actively pass by DSB-anchored cohesin. Our work highlights the critical impact of chromosome conformation in the maintenance of genome integrity and provides the first example of a chromatin modification established by loop extrusion.

molecular biology↗

bioRxiv2017

The fitness cost of mis-splicing is the main determinant of alternative splicing patterns

Most eukaryotic genes are subject to alternative splicing (AS), which may contribute to the production of functional protein variants or to the regulation of gene expression, notably via nonsense-mediated mRNA decay (NMD). However, a fraction of splice variants might correspond to spurious transcripts, and the question of the relative proportion of splicing errors vs. functional splice variants remains highly debated. We propose here a test to quantify the fraction of AS events corresponding to errors. This test is based on the fact that the fitness cost of splicing errors increases with the number of introns in a gene and with expression level. We first analyzed the transcriptome of the intron-rich unicellular eukaryote Paramecium tetraurelia. We show that both in normal and in NMD-deficient cells, AS rates (intron retention, alternative splice site usage or cryptic intron splicing) strongly decrease with increasing expression level and with increasing number of introns. This relationship is observed both for AS events that are detectable by NMD or not, which invalidates the hypothesis of a possible link with the regulation of gene expression. Our results indicate that in genes with a median expression level, 92%-98% of observed splice variants correspond to errors. Interestingly, we observed the same patterns in human transcriptomes. These results are consistent with the mutation-selection-drift theory, which predicts that genes under weaker selective pressure should accumulate more maladaptive substitutions, and therefore should be more prone to errors of gene expression.

genomics↗