Biology subjects

Charton, F.

Publications and source records attributed to Charton, F..

4 recordsLinked to original sources

bioRxiv2026

A quick and efficient method enabling lncRNA functional studies in the marine diatom Phaeodactylum tricornutum using a multiplexed CRISPR-Cas9 editing approach

Background: Long non protein coding (lnc)RNAs are ubiquitous transcripts known to be major regulators of cellular processes in eukaryotes. In diatoms, specific lncRNA expression is tightly correlated to nutrient fluctuations, which suggests function, but their biological relevance remains to be established. In order to fill this knowledge gap, we sought to design a protocol to generate diatom lncRNA knockout mutants by CRISPR-Cas9 enabling subsequent functional studies to shed light into their mechanistic roles. Since lncRNAs do not contain open reading frames that can be targeted by point mutations for the generation of functional knockouts, we designed a multiplexed CRISPR-Cas9 plasmid harboring two independent gRNA for the specific ablation of lncRNA loci in P. tricornutum. As proof of concept, we used our plasmid-based system to target three phosphate depletion responsive lncRNAs. Results: Using the golden gate based uLoop system, we assembled a single plasmid containing all the necessary components to generate CRISPR-Cas9 large genomic ablations of lncRNAs in P. tricornutum using bacterial conjugation. Three intergenic lncRNAs (Linc91, Linc77 and Linc24) responsive to phosphate fluctuations were selected and independently targeted. Around 32% of the exconjugants presented a monoallelic ablation of the targeted loci and 11% presented a biallelic ablation on the first PCR-screening round. Mutated lines, harboring biallelic lncRNAs ablations for each lncRNA targeted, were successfully generated for each of the targeted lncRNAs. Additionally, a first line of phenotypic analysis revealed significant growth rate differences for one of the mutants ({Delta}Lnc24) under both full and phosphate depleted conditions, suggesting its involvement in cell division regulation under nutrient fluctuations. Conclusions: This work provides a simple and efficient method for the generation of lncRNA knock-out mutants in P. tricornutum. Furthermore, this approach can be easily adapted to other microalgae amenable to transformation, enabling the enhancement of our understanding of these important cellular regulatory transcripts in the marine environment.

molecular biology↗

bioRxiv2024

Pangenome-Informed Language Models for Privacy-Preserving Synthetic Genome Sequence Generation

Language Models (LM) have been extensively utilized for learning DNA sequence patterns and generating synthetic sequences. In this paper, we present a novel approach for the generation of synthetic DNA data using pangenomes in combination with LM. We introduce three innovative pangenome-based tokenization schemes that enhance DNA sequence generation. Our experimental results demonstrate the superiority of pangenome-based tokenization over classical methods in generating high-utility synthetic DNA sequences, highlighting significant improvements in training efficiency and sequence quality.

bioinformatics↗

bioRxiv2021

Dynamic Cell Imaging: application to the diatom Phaeodactylum tricornutum under environmental stresses

The dynamic movement of cell organelles is an important and poorly understood component of cellular organisation and metabolism. In this work we present a non-invasive non-destructive method (Dynamic Cell Imaging, DCI) based on light scattering and interferometry to monitor dynamic events within photosynthetic cells using the diatom Phaeodactylum tricornutum as a model system. For this monitoring we acquire few seconds movies of the signals that are related to the motion of dynamic structures within the cell (denoted scatterers), followed by a statistical analysis of each pixel time series. Illuminating P.tricornutum with LEDs of different wavelengths associated to short pulsed or continuous-wave modes of illumination revealed that dynamic movements depend on chloroplast activity, in agreement with the reduction in the number of pixels with dynamic behaviour after addition of photosystemII inhibitors. We studied P. tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. The major dynamic sites were located within lipid droplets and chloroplast envelope membranes. By comparing standard deviation and cumulative sum analysis of the time series, we showed that within the droplets two types of scatterer movement could be observed: random motions (Brownian type) but also anomalous movements corresponding to a drift which may relate to molecular fluxes within a cell. The method appears valuable for studying the effects of various environments on a large variety of microalgae in the laboratory as well as in natural aquatic environments. HIGHLIGHTsLight scattering an alternative to fluorescence to rapidly evidence dynamic processes. Lipid droplets the major metabolic active sites under stress A non-destructive visualisation method for laboratory microalgae and aquatic samples.. SIGNIFICANCE STATEMENTLight scattering could be an alternative to fluorescence techniques to study dynamic processes within photosynthetic cells. We used a method combining light scattering and interferometry to analyse movements of intracellular scatterers in the marine diatom Phaedactylum tricornutum under two environmentally relevant stresses, iron and phosphate deficiency. Lipid droplets were the major active sites under stress. The method which is rapid and non destructive can be broadly expanded to study other microalgae and their stress responses, in the laboratory and in aquatic environments.

microbiology↗

bioRxiv2020

Discriminating the Influence of Correlated Factors from Multivariate Observations: the Back-to-Back Regression

Identifying causes solely from observations can be particularly challenging when i) potential factors are difficult to manipulate independently and ii) observations are multi-dimensional. To address this issue, we introduce "Back-to-Back" regression (B2B), a linear method designed to efficiently measure, from a set of correlated factors, those that most plausibly account for multidimensional observations. First, we prove the consistency of B2B, its links to other linear approaches, and show how it provides a robust, unbiased and interpretable scalar estimate for each factor. Second, we use a variety of simulated data to show that B2B outperforms least-squares regression and cross-decomposition techniques (e.g. canonical correlation analysis and partial least squares) on causal identification when the factors and the observations are partially collinear. Finally, we apply B2B to magneto-encephalography of 102 subjects recorded during a reading task to test whether our method appropriately disentangles the respective contribution of word length and word frequency - two correlated factors known to cause early and late brain responses respectively. The results show that these two factors are better disentangled with B2B than with other standard techniques.

neuroscience↗