Biology subjects

Dupuy, D.

Publications and source records attributed to Dupuy, D..

7 recordsLinked to original sources

bioRxiv2026

Quantitative Description of C. elegans mRNA Landscapes From High Coverage Single Cell Transcriptomes

Single-cell RNA sequencing technology dramatically changed the way we investigate transcriptomes. However, the amount and complexity of data generated by such methods poses new challenges for biologists who are trying to extract detailed insights into the genetic programs that drive cellular functions and differentiation. To provide a more intuitive understanding of cell specific gene expression programs, we developed a novel approach for exploiting scRNA-seq data that detects individual gene expression levels in each cell, by avoiding dimensional reduction methods. This was achieved by focusing our analysis on individual cells with a high sequencing coverage (above 15000 Unique Molecular Identifiers (UMIs)). Such High Coverage Cells (HCC), were found in all five C. elegans scRNA-seq datasets we investigated and constitute direct quantitative experimental observations of the mRNA content of individual cells. Clustering the complete gene expression matrix for these cells, we identified gene sets specific for most C. elegans tissues. Among each set we found genes that are dominating cell specific transcriptomes as well as genes that are restricted to particular cell types but are a thousand fold less expressed. For each cell type or subtype we characterized, we identified a set of genes with expression restricted to those cells that were not previously associated with the corresponding tissue. Our results demonstrate that by focusing on HCCs, we can provide high-resolution quantitative descriptions of cellular expression landscapes that are immediately exploitable for researchers to generate new biological hypotheses. Overall, we demonstrate that HCCs represent a powerful and largely unexplored source of biological insights and suggest that future scRNA-seq experiments could benefit from focusing on HCC enrichment to capture and exploit the full complexity of cellular transcriptomes.

systems biology↗

bioRxiv2026

A Spinal Muscular Atrophy Model Reveals Both Developmental and Degenerative Neuronal Defects in C. elegans

Spinal muscular atrophy (SMA) is a neuromuscular disorder primarily caused by mutations in the Survival of Motor Neuron 1 (SMN1) gene. SMN1 is ubiquitously expressed and encodes a protein essential for the assembly of small nuclear ribonucleoproteins (snRNPs), key components of pre-mRNA splicing. Beyond this canonical role, SMN participates in several other fundamental cellular processes, including RNA transport, regulation of actin dynamics, transcription, and translation. While multiple hypotheses have been put forward to explain selective motor neuron (MN) vulnerability to SMN deficiency, the precise mechanisms involved remain incompletely understood. In this study, we used a simple and tractable C. elegans model to investigate the molecular mechanisms underlying neuronal degeneration in SMA. Silencing of the smn-1 in targeted neurons resulted in defects in the birth and development of both motor neurons and touch receptor neurons (TRNs). In TRNs SMN-1 depletion caused distinct defects in neuronal process morphology. Our results provide evidence that key aspects of SMA pathology are conserved in C. elegans, which may offer new opportunities to elucidate the molecular mechanisms underlying neuronal degeneration in SMA.

genetics↗

bioRxiv2024

Reticulon dependent ER-phagy mediates adaptation to heat stress in Caenorhabditis elegans

The selective degradation of ER by autophagy, named ER-phagy, promotes the recovery of ER homeostasis after a stress. Depending on the ER stress, different types of ER-phagy involve various selective autophagy receptors. In this study, we report a macroER-phagy induced by the fragmentation of tubular ER in response to acute heat stress. We identified a novel ER-phagy receptor encoded by the reticulon long isoform RET-1d. RET-1d is mainly expressed in the nervous system and the epidermis and colocalize with the ubiquitin-like autophagy protein LGG-1/GABARAP during heat stress induced autophagy. Two LIR motifs in the long intrinsically disordered region of RET-1d mediate its interaction with LGG-1 protein. The specific depletion of RET-1d isoform resulted in a delay in autophagosome biogenesis and a decrease in the capacity of animals to adapt to heat stress. Our data revealed a RET-1d dependent ER-phagy mechanism that takes place in neurons and epidermis and participates to the adaptation of C. elegans to heat stress.

cell biology↗

bioRxiv2022

Two RhoGEF isoforms with distinct localisation act in concert to control asymmetric cell division

Cytokinesis is essential for the partitioning of cellular contents into daughter cells. It relies on the formation of an acto-myosin contractile ring, whose constriction induces the ingression of the cleavage furrow between the segregated chromatids. Rho1 GTPase and its RhoGEF (Pbl) are essential for this process as they drive the assembly and constriction of the contractile ring. However, how Rho1 is regulated to sustain efficient furrow ingression while maintaining correct furrow position remains poorly defined. Here, we show that during asymmetric division of Drosophila neuroblasts, Rho1 is controlled by two Pbl isoforms with distinct localisation. Spindle midzone- and furrow-enriched Pbl-A focuses Rho1 at the furrow to sustain efficient ingression, while Pbl-B pan-plasma membrane localization promotes the broadening of Rho1 activity and the subsequent enrichment of cortical myosin. This enlarged zone of Rho1 activity becomes essential to adjust furrow position during ingression, thereby preserving correct daughter cell size asymmetry. Our work highlights how the use of isoforms with distinct localisation patterns provides robustness to an essential process.

cell biology↗

bioRxiv2022

Quantitative analysis of C. elegans transcripts by Nanopore direct-cDNA sequencing reveals terminal hairpins in non trans-spliced mRNAs

Nematode mRNA processing involves a trans-splicing step through which a 21nt sequence from a snRNP replaces the original 5 end of the primary transcript. It has long been held that 70% of C. elegans mRNAs are submitted to trans-splicing. Our recent work suggested that the mechanism is more pervasive but not fully captured by mainstream transcriptome sequencing methods. In this study, we used Oxford Nanopores long-read amplification-free sequencing technology to perform a comprehensive analysis of trans-splicing in worms. We demonstrated that spliced leader (SL) sequences presence at the 5 end of the messengers affected library preparation and generated sequencing artefacts due to their self-complementarity. Consistent with our previous observations, we found evidence of trans-splicing for most genes. However, a subset of genes appears to be only marginally trans-spliced. These messengers all share the capacity to generate a 5 terminal hairpin structure mimicking the SL structure providing a mechanistic explanation for their non conformity. Altogether, our data provides the most comprehensive quantitative analysis of SL usage to date in C. elegans.

genomics↗

bioRxiv2018

Inverse toeprinting: a new tool to decipher the translational arrest code

It has recently become clear that various antibiotics block the translation of bacterial proteins in a sequence-specific manner. In order to understand how this specificity contributes to antibiotic potency and select better antimicrobial leads, new high-throughput tools are needed. Here, we present inverse toeprinting, a new method to map the position of ribosomes arrested on messenger RNAs during in vitro translation. Unlike ribosome profiling, our method protects the entire coding region upstream of a stalled ribosome, making it possible to work with transcript libraries that randomly sample the sequence space. We used inverse toeprinting to characterize the pausing landscape of free and drug-bound bacterial ribosomes engaged in translation. We obtained a comprehensive list of arrest motifs that could be validated in vivo, along with a quantitative measure of their pause strength. Thus, our method provides a highly parallel and scalable means to characterize the sequence specificity of translation inhibitors.

molecular biology↗

bioRxiv2017

Quantitative RNAseq Meta Analysis Of Alternative Exon Usage In C. elegans

Almost twenty years after the completion of the C. elegans genome sequence, gene structure annotation is still an ongoing process with new evidence for gene variants still being regularly uncovered by additional in-depth transcriptome studies. While alternative splice forms can allow a single gene to encode several functional isoforms the question of how much spurious splicing is tolerated is still heavily debated.\n\nHere we gathered a compendium of 1,682 publicly available C. elegans RNA-seq datasets to increase the dynamic range of detection of RNA isoforms and obtained robust measurements of the relative abundance of each splicing event. While most of the splicing reads come from reproducibly detected splicing events, a large fraction of purported junctions are only supported by a very low number of reads. We devised an automated curation method that takes into account the expression level of each gene to discriminate robust splicing events from potential biological noise. We found that rarely used splice sites disproportionately come from highly expressed genes and are significantly less conserved in other nematode genomes than splice sites with a higher usage frequency.\n\nOur increased detection power confirmed trans-splicing for at least 84% of C. elegans protein coding genes. The genes for which trans-splicing was not observed are overwhelmingly low expression genes, suggesting that the mechanism is pervasive but not full captured by organism-wide RNA-Seq.\n\nWe generated annotated gene models including quantitative exon usage information for the entire C. elegans genome. This allows users to visualize at a glance the relative expression of each isoform for their gene of interest.

genomics↗