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

Total Cost €


EC-Contrib. €






Project "CRISPAIR" data sheet

The following table provides information about the project.


Organization address
address: RUE DU DOCTEUR ROUX 25-28
city: PARIS CEDEX 15
postcode: 75724

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country France [FR]
 Total cost 1˙499˙763 €
 EC max contribution 1˙499˙763 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2015-STG
 Funding Scheme ERC-STG
 Starting year 2016
 Duration (year-month-day) from 2016-03-01   to  2021-11-30


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    INSTITUT PASTEUR FR (PARIS CEDEX 15) coordinator 1˙499˙763.00


 Project objective

CRISPR-Cas loci are the adaptive immune system of archaea and bacteria. They can capture pieces of invading DNA and use this information to degrade target DNA through the action of RNA-guided nucleases. The consequences of DNA cleavage by Cas nucleases, i.e. how breaks are processed and whether they can be repaired, remains to be investigated. A better understanding of the interplay between DNA repair and CRISPR-Cas is critical both to shed light on the evolution and biology of these fascinating systems and for the development of biotechnological tools based on Cas nucleases. CRISPR systems have indeed become a popular tool to edit Eukaryotic genomes. The strategies employed take advantage of different DNA repair pathways to introduce mutations upon DNA cleavage. In bacteria however, the introduction of breaks by Cas nucleases in the chromosome has been described to kill the cell. Preliminary data indicates that this might not always be the case and that some DNA repair pathways could compete with CRISPR immunity allowing cells to survive. Using a combination of bioinformatics and genetics approaches we will investigate the interplay between CRISPR and DNA repair in bacteria with a particular focus on the widely used CRISPR-Cas9 system. The knowledge gained from this study will then help us develop novel tools for bacterial genome engineering. In particular we will introduce a NHEJ pathway in E.coli making it possible to perform CRISPR knockout screens. Finally using CRISPR libraries and multiplexed targeting, we will generate for the first time all combinations of pair-wise gene knockouts in an organism, a task that for now remains elusive, even for large consortiums and with the use of automation. This will enable to decipher genome-scale genetic interaction networks, an important step for our understanding of bacteria as a system.


year authors and title journal last update
List of publications.
2017 David Bikard, Rodolphe Barrangou
Using CRISPR-Cas systems as antimicrobials
published pages: 155-160, ISSN: 1369-5274, DOI: 10.1016/j.mib.2017.08.005
Current Opinion in Microbiology 37 2020-01-21
2018 François Rousset, Lun Cui, Elise Siouve, Christophe Becavin, Florence Depardieu, David Bikard
Genome-wide CRISPR-dCas9 screens in E. coli identify essential genes and phage host factors
published pages: e1007749, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1007749
PLOS Genetics 14/11 2020-01-21
2018 Lun Cui, Antoine Vigouroux, François Rousset, Hugo Varet, Varun Khanna, David Bikard
A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-018-04209-5
Nature Communications 9/1 2020-01-21
2017 Aude Bernheim, Alicia Calvo-Villamañán, Clovis Basier, Lun Cui, Eduardo P. C. Rocha, Marie Touchon, David Bikard
Inhibition of NHEJ repair by type II-A CRISPR-Cas systems in bacteria
published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-02350-1
Nature Communications 8/1 2020-01-21
2018 Antoine Vigouroux, Enno Oldewurtel, Lun Cui, David Bikard, Sven van Teeffelen
Tuning dCas9\'s ability to block transcription enables robust, noiseless knockdown of bacterial genes
published pages: e7899, ISSN: 1744-4292, DOI: 10.15252/msb.20177899
Molecular Systems Biology 14/3 2020-01-21

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