Biology subjects

Lecompte, L.

Publications and source records attributed to Lecompte, L..

6 recordsLinked to original sources

bioRxiv2026

Transposable Element insertions Repurpose Immune Endonucleases as Drivers of Reproductive Isolation in Mice

The emergence of reproductive barriers between closely related populations is a fundamental step in speciation, yet the underlying genetic mechanisms remain poorly understood in mammals. Here we resolve the DDK syndrome, a long-standing model of hybrid incompatibility in mice, by showing that two independent retrotransposon insertions rewire immune Schlafen endoribonuclease genes expression, causing hybrid embryo death. A DDK-private MERVL element drives ectopic oocyte expression of Slfn1, while an intragenic ETn/MusD insertion in incompatible strains is associated with zygotic Slfn15 expression. SLFN1-SLFN15 heterodimerization constitutively activates tRNA ribonuclease activity, leading to global translation inhibition, and integrated stress response activation. Abolishing SLFN1 catalytic activity or SLFN15 expression rescues syndromic embryo development. Our findings uncover a previously unrecognized speciation mechanism in which transposable elements repurpose immune effectors as drivers of postzygotic reproductive isolation.

developmental biology↗

bioRxiv2024

Estimation of the Achilles tendon twist in vivo by individual triceps surae muscle stimulation

The Achilles tendon (AT) is comprised of three distinct subtendons, each arising from the one of the three heads of the triceps surae muscles: gastrocnemius medialis (GM), gastrocnemius lateralis (GL) and soleus (SOL). These subtendons exhibit a twisted structure, classified as low (Type I), medium (Type II), and high (Type III) twist, based on cadaveric studies. Nevertheless, the in-vivo investigation of AT twist is notably scarce, resulting in a limited understanding of its functional significance. The aim of this study was to give insights into the complex 3D AT structure in vivo. 30 healthy participants underwent individual stimulation of each of the triceps surae muscles at rest with the foot attached to the pedal of an isokinetic dynamometer. Ultrasound images were captured to concomitantly examine the displacement of the superficial, middle and deep AT layers. SOL stimulation resulted in the highest AT displacement followed by GM and GL stimulation. Independent of the muscle stimulated, non-uniformity within the AT was observed with the deep layer exhibiting more displacement compared to the middle and superficial layers, hence important inter-individual differences in AT displacement were noticeable. By leveraging these individual displacement patterns during targeted stimulations in conjunction with cadaveric twist classifications providing insights into the area of each specific subtendon, our classification identified 19 subjects with a low and 11 subjects with a high AT twist. More research is needed to understand the complexity of the AT twisted structure in vivo to further understand its effect on AT properties and behaviour.

physiology↗

bioRxiv2024

Reduced intra-tendinous sliding in Achilles tendinopathy during active plantarflexion regardless of horizontal foot position

The Achilles tendon consists of three subtendons with the ability to slide relative to each other. As optimal intra-tendinous sliding is thought to reduce the overall stress in the tendon, alterations in sliding behavior could potentially play a role in the development of Achilles tendinopathy. The aims of this study were to investigate the difference in intra-tendinous sliding within the Achilles tendon during isometric contractions between asymptomatic controls and patients with Achilles tendinopathy and the effect of changing the horizontal foot position on intra-tendinous sliding in both groups. 29 participants (13 Achilles tendinopathy, 16 controls) performed isometric plantarflexion contractions at 60% of their maximal voluntary contraction (MVC), in toes-neutral, and at 30% MVC in toes-neutral, toes-in and toes-out positions during which ultrasound images were recorded. Intra-tendinous sliding was estimated as the superficial-to-middle and middle-to-deep relative displacement. Our results indicate that patients with Achilles tendinopathy present lower intra-tendinous sliding compared to asymptomatic controls. Regarding the horizontal foot position in both groups, the toes-out foot position resulted in increased sliding compared to both toes-neutral and toes-out foot position. We provided evidence that patients with Achilles tendinopathy show lower intra-tendinous sliding compared to asymptomatic controls. Since intra-tendinous sliding is a physiological feature of the Achilles tendon, the external foot position holds promise to increase sliding in patients with Achilles tendinopathy and promote healthy tendon behavior. Future research should investigate if implementing this external foot position in rehabilitation programs stimulates sliding within the Achilles tendon and improves clinical outcome.

pathology↗

bioRxiv2019

SVJedi: Genotyping structural variations with long reads

MotivationStudies on structural variants (SV) are expanding rapidly. As a result, and thanks to third generation sequencing technologies, the number of discovered SVs is increasing, especially in the human genome. At the same time, for several applications such as clinical diagnoses, it is important to genotype newly sequenced individuals on well defined and characterized SVs. Whereas several SV genotypers have been developed for short read data, there is a lack of such dedicated tool to assess whether known SVs are present or not in a new long read sequenced sample, such as the one produced by Pacific Biosciences or Oxford Nanopore Technologies. ResultsWe present a novel method to genotype known SVs from long read sequencing data. The method is based on the generation of a set of reference sequences that represent the two alleles of each structural variant. Long reads are aligned to these reference sequences. Alignments are then analyzed and filtered out to keep only informative ones, to quantify and estimate the presence of each SV allele and the allele frequencies. We provide an implementation of the method, SVJedi, to genotype insertions and deletions with long reads. The tool has been applied to both simulated and real human datasets and achieves high genotyping accuracy. We also demonstrate that SV genotyping is considerably improved with SVJedi compared to other approaches, namely SV discovery and short read SV genotyping approaches. Availabilityhttps://github.com/llecompte/SVJedi.git Contactlolita.lecompte@inria.fr

bioinformatics↗

bioRxiv2019

ELECTOR: Evaluator for long reads correction methods

MotivationIn the last few years, the error rates of third generation sequencing data have been capped above 5%, including many insertions and deletions. Thereby, an increasing number of long reads correction methods have been proposed to reduce the noise in these sequences. Whether hybrid or self-correction methods, there exist multiple approaches to correct long reads. As the quality of the error correction has huge impacts on downstream processes, developing methods allowing to evaluate error correction tools with precise and reliable statistics is therefore a crucial need. Since error correction is often a resource bottleneck in long reads pipelines, a key feature of assessment methods is therefore to be efficient, in order to allow the fast comparison of different tools. ResultsWe propose ELECTOR, a reliable and efficient tool to evaluate long reads correction, that enables the evaluation of hybrid and self-correction methods. Our tool provides a complete and relevant set of metrics to assess the read quality improvement after correction and scales to large datasets. ELECTOR is directly compatible with a wide range of state-of-the-art error correction tools, using whether simulated or real long reads. We show that ELECTOR displays a wider range of metrics than the state-of-the-art tool, LRCstats, and additionally importantly decreases the runtime needed for assessment on all the studied datasets. AvailabilityELECTOR is available at https://github.com/kamimrcht/ELECTOR. Contactcamille.marchet@univ-lille.fr or pierre.morisse2@univ-rouen.fr

bioinformatics↗

bioRxiv2017

De novo Clustering Nanopore Long Reads of Transcriptomics Data by Gene

Long-read sequencing currently provides sequences of several thousand base pairs. This allows to obtain complete transcripts, which offers an un-precedented vision of the cellular transcriptome.\n\nHowever the literature is lacking tools to cluster such data de novo, in particular for Oxford Nanopore Technologies reads, because of the inherent high error rate compared to short reads.\n\nOur goal is to process reads from whole transcriptome sequencing data accurately and without a reference genome in order to reliably group reads coming from the same gene. This de novo approach is therefore particularly suitable for non-model species, but can also serve as a useful pre-processing step to improve read mapping. Our contribution is both to propose a new algorithm adapted to clustering of reads by gene and a practical and free access tool that permits to scale the complete processing of eukaryotic transcriptomes.\n\nWe sequenced a mouse RNA sample using the MinION device, this dataset is used to compare our solution to other algorithms used in the context of biological clustering. We demonstrate its is better-suited for transcriptomics long reads. When a reference is available thus mapping possible, we show that it stands as an alternative method that predicts complementary clusters.

bioinformatics↗