Biology subjects

Carre, C.

Publications and source records attributed to Carre, C..

9 recordsLinked to original sources

bioRxiv2026

A single H2A variant prevents genome instability through piRNAs biogenesis and replication stress control.

Transposable elements (TEs) pose a major threat to genome integrity in the germline, where the piRNA pathway ensures heritable TEs silencing. How the chromatin environment that enables piRNA biogenesis is first established during oogenesis remains unclear. Here, we identify the histone variant His2Av, the single H2A variant in Drosophila combining H2A.Z (transcriptional) and H2A.X (DNA repair) features, as a critical regulator of the earliest steps of piRNA pathway activation. Germline-specific depletion of His2Av disrupts transcription of piRNA pathway genes, abolishes dual-strand piRNA cluster transcription, and triggers strong TEs derepression. These defects are associated with loss of Rhino recruitment despite intact H3K9me3, suggesting that His2Av contributes to the establishment of a specialized heterochromatin permissive for noncanonical piRNA cluster transcription. His2Av depletion also causes DNA damage, replication stress, and activation of Chk2- and Claspin-dependent checkpoints, leading to oogenesis arrest. Remarkably, overexpression of RNase H, but not a catalytic-dead variant, robustly rescues oocyte development, suggesting that replication stress is a major source of DNA damage in His2Av mutants. Finally, using a separation-of-function approach with a C-terminal truncation inhibiting H2A.X-like activity, we show that the essential germline role of His2Av is transcriptional (H2A.Z-like). Together, our findings reveal that His2Av primes germline chromatin for piRNA pathway initiation while limiting transcription-replication conflicts during early oogenesis.

developmental biology↗

bioRxiv2025

A Combined Chemo-Enzymatic Treatment for the Oxidation of Epoxy-Based Carbon Fiber-Reinforced Polymers (CFRPs)

Carbon fiber-reinforced polymers (CFRPs), particularly epoxy-based composites, have become essential in the aerospace, automotive, and wind energy industries due to their robust mechanical properties, and lightweight nature. However, there is a lack of recycling technologies that are environmentally sustainable while also ensuring the recovery of carbon fibers in their original state. Although certain bacterial and fungal strains can colonize epoxy polymers, enzymes capable of efficiently degrading these materials have not yet been reported. Consequently, there is an urgent need for an effective, sustainable, and biologically inspired solution for CFRP recycling. Here, a chemo-enzymatic two-step oxidation process was developed. A chemical pre-treatment with propionic acid and hydrogen peroxide was used to recover imbedded carbon fibers. Additionally, three novel bacterial laccases isolated from the European spruce bark beetle (Ips typographus) demonstrated the ability to degrade three epoxy resin scaffolds from Hexflow(R) RTM6, used in aircraft applications. The sequential combination of both oxidative steps enabled the retrieval of clean carbon fibers and partial modification of epoxy functional groups, with the release of defined products over time. This bio-inspired approach renders the process more environmentally friendly and marks an initial step toward developing a bio-based recycling method for epoxy CFRPs.

biochemistry↗

bioRxiv2024

Classification and Regression Trees to predict Transcription Factor Combinatorial Interaction in scRNA-seq data.

Understanding the regulatory mechanisms that govern gene expression is crucial for deciphering cellular functions. Transcription factors (TFs) play a key role in regulating gene expression. In particular TF combinatorial interactions (TFCI) are now thought to largely shape genomic transcriptional responses, but predicting TFCI per se is still a difficult task. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool providing a whole new readout of gene regulatory effects. In this study, we propose a machine learning approach utilizing Classification and Regression Trees (CART) for predicting TFCI in >110k scRNA-seq data points yielded from Arabidopsis thaliana root. The proposed methodology provides a valuable tool for pointing to new TFCI mechanisms and could advance our understanding of Gene Regulatory Networks functioning.

bioinformatics↗

bioRxiv2022

PeTriBERT : Augmenting BERT withtridimensional encoding for inverse protein foldingand design

Protein is biology workhorse. Since the recent break-through of novel folding methods, the amount of available structural data is increasing, closing the gap between data-driven sequence-based and structure-based methods. In this work, we focus on the inverse folding problem that consists in predicting an amino-acid primary sequence from protein 3D structure. For this purpose, we introduce a simple Transformer model from Natural Language Processing augmented 3D-structural data. We call the resulting model PeTriBERT: Proteins embedded in tridimensional representation in a BERT model. We train this small 40-million parameters model on more than 350 000 proteins sequences retrieved from the newly available AlphaFoldDB database. Using PetriBert, we are able to in silico generate totally new proteins with a GFP-like structure. These 9 of 10 of these GFP structural homologues have no ressemblance when blasted on the whole entry proteome database. This shows that PetriBert indeed capture protein folding rules and become a valuable tool for de novo protein design.

bioinformatics↗

bioRxiv2022

Full epistatic interaction maps retrieve part of missing heritability and improve phenotypic prediction

The first Genome Wide Association Studies (GWAS) shed light on the concept of missing heritability. It constitutes a mystery with transcending consequences from plant to human genetics. This mystery lies in the fact that a large proportion of phenotypes are not explained by unique or simple genomic modifications. One has to invoke genetic interactions among different loci, also known as epistasis, to partly account for it. However, current GWAS statistical models are moderately scalable, very sensitive to False Discovery Rate (FDR) corrections and, even combined with High Performance Computing (HPC), they can take years to evaluate for a full combinatorial epistatic space for a single phenotype. Here we propose a modeling approach, named Next-Gen GWAS (NGG) that evaluates, within hours, >60 billions of single nucleotide polymorphism (SNP) combinatorial first-order interactions, on a reasonable computer power. We first benchmark NGG on state of the art GWAS model results, and applied this to Arabidopsis thaliana providing 2D epistatic maps at gene resolution. We demonstrate on several phenotypes that a large proportion of the missing heritability can i) be retrieved with this modeling approach, ii) indeed lies in epistatic interactions and iii) can be used to improve phenotype prediction.

genetics↗

bioRxiv2022

The histone demethylase KDM3 prevents auto-immune piRNAs production in Drosophila

In animals, genome integrity of the germ line is protected from transposable element (TE) activity by small, non-coding, dedicated RNAs acting as an immune system against TEs, and called PIWI-interacting RNAs (piRNAs) 1,2. In Drosophila, the production of piRNAs is initiated from heterochromatic loci containing remnants of TEs and enriched in histone H3 trimethylated on lysine 9 (H3K9me3) 3-5. These loci, called piRNA clusters, constitute a memory of past TE invasions. Little is known about how piRNA clusters are genetically defined. Using a genetic screen combined with a bimodal epigenetic state piRNA cluster (BX2), we identified the splicing factor Half pint (Hfp) and the histone demethylase KDM3 as being able to prevent BX2 piRNA production. Furthermore, we showed that Hfp is needed to splice Kdm3 transcripts. Germline expression of Kdm3 coding sequence (splicing-independent) rescued the hfp germline knock-down (GLKD) effect demonstrating that Kdm3 is sufficient to prevent BX2 piRNA production. Our data revealed that in the absence of Kdm3, dozens of gene-containing regions become bona fide germinal dual strand piRNA clusters. Indeed, they produce piRNAs originating from both DNA strands, become transcribed in a Moonshiner-dependent manner and enriched in di-and tri-methylation of lysine 9 of histone H3 (H3K9me2/3) and in Rhino, an HP1-like protein. Eggs laid by Kdm3 GLKD females do not hatch and show developmental defects phenocopying loss of function of genes included into the new piRNA clusters, suggesting an inheritance of functional ovarian "auto-immune" piRNAs. Our results demonstrate that some gene-containing regions are actively prevented for piRNA production by proteins that counteract piRNA cluster emergence. Hence, a non-piRNA-producing state is therefore not a "by default" state but rather a cellular lock that is actively controlled for some genomic loci. KEY FACTSO_LIHfp regulates the expression of Kdm3 via its splicing C_LIO_LIKdm3 prevents genomic regions containing coding genes from becoming piRNA clusters C_LIO_LIEmbryos from Kdm3 mutant females show developmental phenotypes suggesting that auto-immune piRNAs are functional and alter the expression of genes embedded in newly established piRNA clusters C_LI

genetics↗

bioRxiv2019

tRNA fragments (tRFs) populations analysis in mutants affecting tRNAs processing and tRNA methylation

tRNA fragments (tRFs) are a class of small non-coding RNAs (sncRNAs) derived from tRNAs. tRFs are highly abundant in many cell types including stem cells and cancer cells, and are found in all domains of life. Beyond translation control, tRFs have several functions ranging from transposon silencing to cell proliferation control. However, the analysis of tRFs presents specific challenges and their biogenesis is not well understood. They are very heterogeneous and highly modified by numerous post-transcriptional modifications. Here we describe a bioinformatic pipeline to study tRFs populations and shed light onto tRNA fragments biogenesis. Indeed, we used small RNAs Illumina sequencing datasets extracted from wild type and mutant Drosophila ovaries affecting two different highly conserved steps of tRNA biogenesis: 5pre-tRNA processing (RNase-P subunit Rpp30) and tRNA 2-O-methylation (CG7009 and CG5220). Using our pipeline, we show how defects in tRNA biogenesis affect nuclear and mitochondrial tRFs populations and other small non-coding RNAs biogenesis, such as small nucleolar RNAs (snoRNAs). This tRF analysis workflow will advance the current understanding of tRFs biogenesis, which is crucial to better comprehend tRFs roles and their implication in human pathology.

bioinformatics↗

bioRxiv2019

tRNA 2-O-methylation modulates small RNA silencing and life span in Drosophila.

2-O-methylation (Nm) represents one of the most common RNA modifications. Nm affects RNA structure and function with crucial roles in various RNA-mediated processes ranging from RNA silencing, translation, self versus non-self recognition to viral defense mechanisms. Here, we identify two novel Nm methyltransferases (Nm-MTases) in Drosophila melanogaster (CG7009 and CG5220) as functional orthologs of yeast TRM7 and human FTSJ1, respectively. Genetic knockout studies together with MALDI-TOF mass spectrometry and RiboMethSeq mapping revealed that CG7009 is responsible for methylating the wobble position in tRNAPhe, tRNATrp and tRNALeu, while subsequently, CG5220 methylates position C32 in the same tRNAs and targets also additional tRNAs. CG7009 or CG5220 mutant animals were viable and fertile but exhibited various phenotypes such as life span reduction, small RNA pathways dysfunction and increased sensitivity to RNA virus infections. Our results provide the first detailed characterization of two TRM7 family members in Drosophila and uncover a molecular link between enzymes catalysing Nm at specific tRNAs and small RNA-induced gene silencing pathways.

molecular biology↗

bioRxiv2018

Dual-layer transposon repression in heads of Drosophila melanogaster

piRNA-mediated repression of transposable elements (TE) in the germline limits the accumulation of heritable mutations caused by their transposition in the genome. It is not clear whether the piRNA pathway plays a functional role in adult, non-gonadal tissues in Drosophila melanogaster. To address this question, we first analyzed the small RNA content of adult Drosophila melanogaster heads. We found that varying amount of piRNA-sized, ping-pong positive molecules in heads correlates with contamination by gonadal tissue during RNA extraction, suggesting that most of piRNAs detected in head sequencing libraries originate from gonads. We next sequenced the heads of wild type and piwi mutants to address whether piwi loss of function would affect the low amount of piRNA-sized, ping-pong negative molecules that are still detected in heads hand-checked to avoid gonadal contamination. We find that loss of piwi does not affect significantly these 24-28 RNA molecules. Instead, we observe increased siRNA levels against the majority of Drosophila transposable element families. To determine the effect of this siRNA level change on transposon expression, we sequenced the transcriptome of wild type, piwi, dicer-2 and piwi, dicer-2 double-mutant fly heads. We find that RNA expression levels of the majority of TE families in piwi or dicer-2 mutants remain unchanged and that TE transcript abundance increases significantly only in piwi, dicer-2 double-mutants. These results lead us to suggest a dual-layer model for TE repression in adult somatic tissues. Piwi-mediated transcriptional gene silencing (TGS) established during embryogenesis constitutes the first layer of TE repression whereas Dicer-2-dependent siRNA-mediated post-transcriptional gene silencing (PTGS) provide a backup mechanism to repress TEs that escape silencing by piwi-mediated TGS.

genetics↗