Biology subjects

Chauvin, L.

Publications and source records attributed to Chauvin, L..

4 recordsLinked to original sources

bioRxiv2020

CRISPR-induced indels and base editing using the Staphylococcus aureus Cas9 in potato

Genome editing is now widely used in plant science for both fundamental research and molecular crop breeding. The clustered regularly interspaced short palindromic repeats (CRISPR) technology, through its precision, high efficiency and versatility, allows to edit many sites in plant genomes. This system has been highly successful to produce of knock-out mutants through the introduction of frameshift mutations due to error-prone repair pathways. Nevertheless, recent new CRISPR-based technologies such as base editing and prime editing can generate precise and on request nucleotide conversion, allowing to fine-tune protein function and generate gain-of-function mutants. However, genome editing through CRISPR systems still have some drawbacks and limitations, such as the PAM restriction and the need for more diversity in CRISPR tools to simultaneously mediate different catalytic activities. In this study, we successfully used the CRISPR-Cas9 system from Staphylococcus aureus (SaCas9) for the introduction of frameshift mutations in the tetraploid genome of the cultivated potato (Solanum tuberosum). We also developed a S. aureus-cytosine base editor that mediate nucleotide conversions, allowing to precisely modify specific residues or regulatory elements in potato. Our proof-of-concept results in potato expand the plant dicot CRISPR toolbox for biotechnology and precision breeding applications.View Full Text

plant biology↗

bioRxiv2020

Prime editing is achievable in the tetraploid potato, but needs improvement

Since its discovery and first applications for genome editing in plants, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology has revolutionized plant research and precision crop breeding. Although the classical CRISPR-Cas9 system is highly useful for the introduction of targeted small mutations for knock-out applications, this system is mostly inefficient for the introduction of precise and predictable nucleotide substitutions. Recently, the prime editing (PE) technology has been developed in human cells, allowing the introduction of all kinds of mutations, including the simultaneous generation of nucleotide transitions and transversions. Therefore, this system holds great promises for the production of gain-of-function mutants and for the improvement of precision breeding in crops. In this study, we report on the successful use of prime editing in the tetraploid and highly heterozygous potato (Solanum tuberosum) with the introduction of simultaneous nucleotide transitions and transversions in the StALS1 gene.

plant biology↗

bioRxiv2019

The Solanum tuberosum GBSSI gene: a target for assessing gene and base editing in tetraploid potato

Genome editing has recently become a method of choice for basic research and functional genomics, and holds great potential for molecular plant breeding applications. The powerful CRISPR-Cas9 system that typically produces double-strand DNA breaks is mainly used to generate knockout mutants. Recently, the development of base editors has broadened the scope of genome editing, allowing precise and efficient nucleotide substitutions. In this study, we produced mutants in two cultivated elite cultivars of the tetraploid potato (Solanum tuberosum) using stable or transient expression of the CRISPR-Cas9 components to knockout the amylose-producing StGBSSI gene. We set up a rapid, highly sensitive and cost-effective screening strategy based on high-resolution melting analysis followed by direct Sanger sequencing and trace chromatogram analysis. Most mutations consisted of small indels, but unwanted insertions of plasmid DNA were also observed. We successfully created tetra-allelic mutants with impaired amylose biosynthesis, confirming the loss-of-function of the StGBSSI protein. The second main objective of this work was to demonstrate the proof of concept of CRISPR-Cas9 base editing in the tetraploid potato by targeting two loci encoding catalytic motifs of the StGBSSI enzyme. Using a cytidine base editor (CBE), we efficiently and precisely induced DNA substitutions in the KTGGL-encoding locus, leading to discrete variation in the amino acid sequence and generating a loss-of-function allele. The successful application of base editing in the tetraploid potato opens up new avenues for genome engineering in this species.\n\nKey MessageThe StGBSSI gene was successfully and precisely edited in the tetraploid potato using gene and base editing strategies, leading to plants with impaired amylose biosynthesis.

plant biology↗

bioRxiv2017

Multi-modal brain fingerprinting: a manifold approximation based framework

This work presents an efficient framework, based on manifold approximation, for generating brain fingerprints from multi-modal data. The proposed framework represents images as bags of local features, which are used to build a subject proximity graph. Compact fingerprints are obtained by projecting this graph in a low-dimensional manifold, using spectral embedding. Experiments using the T1/T2-weighted MRI, diffusion MRI, and resting state fMRI data of 945 Human Connectome Project subjects demonstrate the benefit of combining multiple modalities, with multi-modal fingerprints more discriminative than those generated from individual modalities. Results also highlight the link between fingerprint similarity and genetic proximity, monozygotic twins having more similar fingerprints than dizygotic or non-twin siblings. This link is also reflected in the differences of feature correspondences between twin/sibling pairs, occurring in major brain structures and across hemispheres. The robustness of the proposed framework to factors like image alignment and scan resolution, as well as the reproducibility of results on retest scans, suggest the potential of multi-modal brain fingerprinting for characterizing individuals in a large cohort analysis. In addition, taking inspiration from the computer vision community, the proposed rank retrieval evaluation based on the task of twin/sibling identification and using Mean Average Precision (MAP) can be used for a standardized comparison of future brain fingerprints.

neuroscience↗