Biology subjects

Le Crom, S.

Publications and source records attributed to Le Crom, S..

7 recordsLinked to original sources

bioRxiv2026

Shining a light on the dark Nt-acetylome by integrating omics data

N-terminal acetylation, catalysed by N-terminal acetyltransferases (Nats), is one of the most prevalent protein modifications and is implicated in human diseases. Yet, despite extensive COFRADIC-based proteomics, only [~]5-10% of the proteome has been interrogated, leaving the majority of the Nt-acetylome unexplored. Here, we combined all major COFRADIC datasets with sel-TRAP, a high-sensitivity, orthogonal approach for profiling co-translational Nat targets via selective ribosome purification. This integrated analysis refined the substrate specificities of NatA, NatB, and NatC/E/F and provided the most comprehensive view to date of the canonical human and yeast Nt-acetylomes. Importantly, we also uncovered hundreds of cryptic Nat substrates arising from alternative translation initiation, with unexpected Nt-proteoforms constituting a previously underappreciated source of Nat targets. Collectively, our results revealed the complex landscape of a "dark" Nt-acetylome, the characterization of which, including its functional roles in regulating protein function and in disease, remains a major challenge for future research.

genomics↗

bioRxiv2022

Functional mapping of N-terminal residues in the yeast proteome uncovers novel determinants for mitochondrial protein import.

N-terminal ends of polypeptides are critical for the selective co-translational recruitment of N-terminal modification enzymes. However, it is unknown whether specific N-terminal signatures differentially regulate protein fate according to their cellular functions. In this work, we developed an in-silico approach to detect functional preferences in cellular N-terminomes, and identified in S. cerevisiae more than 200 Gene Ontology terms with specific N-terminal signatures. In particular, we discovered that Mitochondrial Targeting Sequences (MTS) show a strong and specific over-representation at position 2 of hydrophobic residues known to define potential substrates of the N-terminal acetyltransferase NatC. We validated mitochondrial precursors as co-translational targets of NatC by selective purification of translating ribosomes, and found that their N-terminal signature is conserved in Saccharomycotina yeasts. Finally, systematic mutagenesis of the position 2 in a prototypal yeast mitochondrial protein confirmed its critical role in mitochondrial protein import. Our work highlights the hydrophobicity of MTS N-terminal residues and their modification by NatC as critical features for the definition of the mitochondrial proteome, providing a molecular explanation for mitochondrial defects observed in yeast or human NatC-depleted cells. Functional mapping of N-terminal residues thus has the potential to support the discovery of novel mechanisms of protein regulation or targeting.

genomics↗

bioRxiv2021

Eoulsan 2: an efficient workflow manager for reproducible bulk, long-read and single-cell transcriptomics analyses

AO_SCPLOWBSTRACTC_SCPLOWO_ST_ABSMotivationC_ST_ABSCore sequencing facilities produce huge amounts of sequencing data that need to be analysed with automated workflows to ensure reproducibility and traceability. Eoulsan is a versatile open-source workflow engine meeting the needs of core facilities, by automating the analysis of a large number of samples. Its core design separates the description of the workflow from the actual commands to be run. This originality simplifies its usage as the user does not need to handle code, while ensuring reproducibility. Eoulsan was initially developed for bulk RNA-seq data, but the transcriptomics applications have recently widened with the advent of long-read sequencing and single-cell technologies, calling for the development of new workflows. ResultWe present Eoulsan 2, a major update that (i) enhances the workflow manager itself, (ii) facilitates the development of new modules, and (iii) expands its applications to long reads RNA-seq (Oxford Nanopore Technologies) and scRNA-seq (Smart-seq2 and 10x Genomics). The workflow manager has been rewritten, with support for execution on a larger choice of computational infrastructure (workstations, Hadoop clusters, and various job schedulers for cluster usage). Eoulsan now facilitates the development of new modules, by reusing wrappers developed for the Galaxy platform, with support for container images (Docker or Singularity) packaging tools to execute. Finally, Eoulsan natively integrates novel modules for bulk RNA-seq, as well as others specifically designed for processing long read RNA-seq and scRNA-seq. Eoulsan 2 is distributed with ready-to-use workflows and companion tutorials. Availability and implementationEoulsan is implemented in Java, supported on Linux systems and distributed under the LGPL and CeCILL-C licenses at: http://outils.genomique.biologie.ens.fr/eoulsan/. The source code and sample workflows are available on GitHub: https://github.com/GenomicParisCentre/eoulsan. A GitHub repository for modules using the Galaxy tool XML syntax is further provided at: https://github.com/GenomicParisCentre/eoulsan-tools Contacteoulsan@bio.ens.psl.eu

bioinformatics↗

bioRxiv2020

Local translation in perisynaptic astrocytic processes is specific and regulated by fear conditioning

Local translation is a conserved molecular mechanism conferring cells the ability to quickly respond to local stimuli. It not only permits cells with complex morphology to bypass somatic protein synthesis and transport, but also contributes locally to the establishment of molecular and functional polarity. In the brain, local translation has been extensively studied in neurons and has only been recently reported in astrocytes, whose fine processes contact both blood vessels and synapses. Yet the specificity and regulation of astrocyte local translation remain unknown. Here, we studied hippocampal perisynaptic astrocytic processes (PAPs) and show that they contain all the machinery for translation. Using our recently refined polysome immunoprecipitation technique, we then characterized the pool of polysomal mRNAs in PAPs, referred to as the PAPome, and compared it to the one found in the whole astrocyte. We found that the PAPome encoded an unexpected molecular repertoire, mostly composed of cytoplasmic proteins and of proteins involved in iron homeostasis, translation, cell cycle and cytoskeleton. Among them, ezrin (Ezr), ferritin heavy chain 1 (Fth1) and 60S acidic ribosomal protein1 (Rplp1) were enriched in PAPs compared to perivascular astrocytic processes, indicating that local translation differs at these two interfaces. Remarkably, PAPs were also enriched in transcripts coding for proteins involved in learning and memory, such as ferritin (Ftl1 and Fth1), G1/S-specific cyclin-D2 (Ccnd2), E3 ubiquitin-protein ligase (Mdm2), Receptor of activated protein C kinase 1 (Gnb2l1) and Elongation factor 1-alpha 1 (Eef1a1). To address their regulation in a physiological context, we assessed their local translation after fear conditioning. We found alterations in their density and/or distribution in astrocytes as well as a drop in their translation specifically in PAPs. In all, our results reveal an unexpected molecular repertoire of hippocampal PAPs, which is regulated by local translation during learning and memory processes.

neuroscience↗

bioRxiv2017

A de novo approach to disentangle partner identity and function in holobiont systems

BackgroundStudy of meta-transcriptomic datasets involving non-model organisms represents bioinformatic challenges. The production of chimeric sequences and our inability to distinguish the taxonomic origins of the sequences produced are inherent and recurrent difficulties in de novo assembly analyses. The study of holobiont transcriptomes shares similarities with meta-transcriptomic, and hence, is also affected by challenges invoked above. Here we propose an innovative approach to tackle such difficulties which was applied to the study of marine holobiont models as a proof of concept.\n\nResultsWe considered three holobionts models, of which two transcriptomes were previously assembled and published, and a yet unpublished transcriptome, to analyze their raw reads and assign them to the host and/or to the symbiont(s) using Short Read Connector, a k-mer based similarity method. We were able to define four distinct categories of reads for each holobiont transcriptome: host reads, symbiont reads, shared reads and unassigned reads. The result of the independent assemblies for each category within a transcriptome led to a significant diminution of de novo assembled chimeras compared to classical assembly methods. Combining independent functional and taxonomic annotations of each partners transcriptome is particularly convenient to explore the functional diversity of an holobiont. Finally, our strategy allowed to propose new functional annotations for two well-studied holobionts and a first transcriptome from a planktonic Radiolaria-Dinophyta system forming widespread symbiotic association for which our knowledge is limited. Conclusions\n\nIn contrast to classical assembly approaches, our bioinformatic strategy not only allows biologists to studying separately host and symbiont data from a holobiont mixture, but also generates improved transcriptome assemblies. The use of Short Read Connector has proven to be an effective way to tackle meta-transcriptomic challenges to study holobiont systems composed of either well-studied or poorly characterized symbiotic lineages such as the newly sequenced marine plankton Radiolaria-Dinophyta symbiosis and ultimately expand our knowledge about these marine symbiotic associations.

genomics↗

bioRxiv2017

Analysis Of The Genomic Basis Of Functional Diversity In Dinoflagellates Using A Transcriptome-Based Sequence Similarity Network

Dinoflagellates are one of the most abundant and functionally diverse groups of eukaryotes. Despite an overall scarcity of genomic information for dinoflagellates, constantly emerging high-throughput sequencing resources can be used to characterize and compare these organisms. We assembled de novo and processed 46 dinoflagellate transcriptomes and used a sequence similarity network (SSN) to compare the underlying genomic basis of functional features within the group. This approach constitutes the most comprehensive picture to date of the genomic potential of dinoflagellates. A core proteome composed of 252 connected components (CCs) of putative conserved protein domains (pCDs) was identified. Of these, 206 were novel and 16 lacked any functional annotation in public databases. Integration of functional information in our network analyses allowed investigation of pCDs specifically associated to functional traits. With respect to toxicity, sequences homologous to those of proteins involved in toxin biosynthesis pathways (e.g. sxtA1-4 and sxtG) were not specific to known toxin-producing species. Although not fully specific to symbiosis, the most represented functions associated with proteins involved in the symbiotic trait were related to membrane processes and ion transport. Overall, our SSN approach led to identification of 45,207 and 90,794 specific and constitutive pCDs of respectively the toxic and symbiotic species represented in our analyses. Of these, 56% and 57% respectively (i.e. 25,393 and 52,193 pCDs) completely lacked annotation in public databases. This stresses the extent of our lack of knowledge, while emphasizing the potential of SSNs to identify candidate pCDs for further functional genomic characterization.

genomics↗

bioRxiv2017

Cyclin G And The Polycomb Repressive Complexes PRC1 And PR-DUB Cooperate For Developmental Stability

In Drosophila, ubiquitous expression of a short Cyclin G isoform generates extreme developmental noise estimated by fluctuating asymmetry (FA), providing a model to tackle developmental stability. This transcriptional cyclin interacts with chromatin regulators of the Enhancer of Trithorax and Polycomb (ETP) and Polycomb families. We investigate here the importance of these interactions in developmental stability. Deregulation of Cyclin G highlights an organ intrinsic control of developmental noise, linked to the ETP-interacting domain, and enhanced by mutations in genes encoding members of the Polycomb Repressive complexes PRC1 and PR-DUB. Deep-sequencing of wing imaginal discs deregulating CycG reveals that high developmental noise correlates with up-regulation of genes involved in translation and down-regulation of genes involved in energy production. Most Cyclin G direct transcriptional targets are also direct targets of PRC1, ASX and RNAPolII in the developing wing. Altogether, our results suggest that Cyclin G, PRC1 and PR-DUB cooperate for developmental stability.

developmental biology↗