Study of the interplay between CRISPR interference and DNA repair pathways towards the development of novel CRISPR tools

Publications

Peer reviewed articles (16)

The impact of genetic diversity on gene essentiality within the Escherichia coli species

Author(s): François Rousset, Jose Cabezas-Caballero, Florence Piastra-Facon, Jesús Fernández-Rodríguez, Olivier Clermont, Erick Denamur, Eduardo P. C. Rocha, David Bikard
Published in: Nature Microbiology, 20585276, 2021, ISSN 2058-5276
Publisher: Nature Microbiology
DOI: 10.1038/s41564-020-00839-y

CRISPR Tools To Control Gene Expression in Bacteria

Author(s): Antoine Vigouroux, David Bikard
Published in: Microbiology and Molecular Biology Reviews, 84/2, 2020, ISSN 1092-2172
Publisher: American Society for Microbiology
DOI: 10.1128/mmbr.00077-19

Class-A penicillin binding proteins do not contribute to cell shape but repair cell-wall defects

Author(s): Antoine Vigouroux, Baptiste Cordier, Andrey Aristov, Laura Alvarez, Gizem Özbaykal, Thibault Chaze, Enno Rainer Oldewurtel, Mariette Matondo, Felipe Cava, David Bikard, Sven van Teeffelen
Published in: eLife, 9, 2020, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/eLife.51998

Lipoprotein DolP supports proper folding of BamA in the bacterial outer membrane, promoting fitness upon envelope stress.

Author(s): David Ranava; Yiying Yang; Luis Orenday-Tapia; François Rousset; Catherine Turlan; Violette Morales; Lun Cui; Cyril Moulin; Carine Froment; Gladys Munoz; Jérôme Rech; Julien Marcoux; Anne Caumont-Sarcos; Cécile Albenne; David Bikard; Raffaele Ieva
Published in: Elife, 2050084X, 2021, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.67817

Gene silencing with CRISPRi in bacteria and optimization of dCas9 expression levels

Author(s): Florence Depardieu, David Bikard
Published in: Methods, 172, 2020, Page(s) 61-75, ISSN 1046-2023
Publisher: Academic Press
DOI: 10.1016/j.ymeth.2019.07.024

A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9

Author(s): Lun Cui, Antoine Vigouroux, François Rousset, Hugo Varet, Varun Khanna, David Bikard
Published in: Nature Communications, 9/1, 2018, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-018-04209-5

Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

Author(s): Antoine Vigouroux, Enno Oldewurtel, Lun Cui, David Bikard, Sven van Teeffelen
Published in: Molecular Systems Biology, 14/3, 2018, Page(s) e7899, ISSN 1744-4292
Publisher: Nature Publishing Group
DOI: 10.15252/msb.20177899

Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria

Author(s): Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard
Published in: Nature Communications, 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-02350-1

Using CRISPR-Cas systems as antimicrobials

Author(s): David Bikard, Rodolphe Barrangou
Published in: Current Opinion in Microbiology, 37, 2017, Page(s) 155-160, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2017.08.005

Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors

Author(s): François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard
Published in: PLOS Genetics, 14/11, 2018, Page(s) e1007749, ISSN 1553-7404
Publisher: PLOS
DOI: 10.1371/journal.pgen.1007749

Editing the microbiome the CRISPR way

Author(s): Gayetri Ramachandran, David Bikard
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, 374/1772, 2019, Page(s) 20180103, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2018.0103

A matter of background: DNA repair pathways as a possible cause for the sparse distribution of CRISPR-Cas systems in bacteria

Author(s): Aude Bernheim, David Bikard, Marie Touchon, Eduardo P. C. Rocha
Published in: Philosophical Transactions of the Royal Society B: Biological Sciences, 374/1772, 2019, Page(s) 20180088, ISSN 0962-8436
Publisher: Royal Society of London
DOI: 10.1098/rstb.2018.0088

CRISPR screens in the era of microbiomes

Author(s): François Rousset, David Bikard
Published in: Current Opinion in Microbiology, 57, 2020, Page(s) 70-77, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2020.07.009

On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria

Author(s): Alicia Calvo-Villamañán, Jérome Wong Ng, Rémi Planel, Hervé Ménager, Arthur Chen, Lun Cui, David Bikard
Published in: Nucleic Acids Research, 48/11, 2020, Page(s) e64-e64, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkaa294

Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements

Author(s): Aude Bernheim, David Bikard, Marie Touchon, Eduardo P C Rocha
Published in: Nucleic Acids Research, 2019, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gkz1091

Phages and their satellites encode hotspots of antiviral systems

Author(s): Rousset F., Depardieu F., Miele S., Dowding J., Laval A.-L., Lieberman E., Garry D., Rocha E.P.C., Bernheim A., Bikard D.
Published in: Cell Host & Microbe, 19313128, 2022, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2022.02.018