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

Project Information

CRISPAIR

Grant agreement ID: 677823

DOI 10.3030/677823

Project closed

EC signature date 14 January 2016

Start date 1 March 2016

End date 31 August 2022

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 499 763,00

EU contribution € 1 499 763,00

Coordinated by

INSTITUT PASTEUR
France

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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 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, Issue 19313128, 2022, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2022.02.018

Intellectual Property Rights

Patent (3)

IMPROVING SEQUENCE-SPECIFIC ANTIMICROBIALS BY BLOCKING DNA REPAIR

Application/Publication number: EP 16741899
Date: 2016-07-13

IMPROVING SEQUENCE-SPECIFIC ANTIMICROBIALS BY BLOCKING DNA REPAIR

Application/Publication number: EP 16741899
Date: 2016-07-13

IMPROVING SEQUENCE-SPECIFIC ANTIMICROBIALS BY BLOCKING DNA REPAIR

Application/Publication number: EP 16741899
Date: 2016-07-13
Applicant(s): INSTITUT PASTEUR