An updated evolutionary classification of CRISPR???Cas systems, Nature Reviews Microbiology, vol.41, issue.11, pp.722-736, 2015. ,
DOI : 10.1038/nrmicro3569
Evolution and classification of the CRISPR???Cas systems, Nature Reviews Microbiology, vol.35, issue.6, pp.467-477, 2011. ,
DOI : 10.1038/nrmicro2577
Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements, Journal of Molecular Evolution, vol.2, issue.2, pp.174-182, 2005. ,
DOI : 10.1007/s00239-004-0046-3
Unravelling the structural and mechanistic basis of CRISPR???Cas systems, Nature Reviews Microbiology, vol.41, issue.7, pp.479-492, 2014. ,
DOI : 10.1093/nar/gku120
CRISPR-Cas Systems: Prokaryotes Upgrade to Adaptive Immunity, Molecular Cell, vol.54, issue.2, pp.234-244, 2014. ,
DOI : 10.1016/j.molcel.2014.03.011
Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes, Biological Chemistry, vol.392, issue.4, pp.277-289, 2011. ,
DOI : 10.1515/bc.2011.042
CRISPR-Cas immunity in prokaryotes, Nature, vol.232, issue.7571, pp.55-61, 2015. ,
DOI : 10.1038/nature15386
Biogenesis pathways of RNA guides in archaeal and bacterial CRISPR-Cas adaptive immunity, FEMS Microbiology Reviews, vol.39, issue.3, pp.428-441, 2015. ,
DOI : 10.1093/femsre/fuv023
CRISPR ??? a widespread system that provides acquired resistance against phages in bacteria and archaea, Nature Reviews Microbiology, vol.7, issue.3, pp.181-186, 2008. ,
DOI : 10.1038/nrmicro1793
Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product., Journal of Bacteriology, vol.169, issue.12, pp.5429-5433, 1987. ,
DOI : 10.1128/jb.169.12.5429-5433.1987
Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli, Nucleic Acids Research, vol.40, issue.12, pp.5569-5576, 2012. ,
DOI : 10.1093/nar/gks216
Cas9 specifies functional viral targets during CRISPR???Cas adaptation, Nature, vol.41, issue.7542, pp.199-202, 2015. ,
DOI : 10.1038/nature14245
Cas9 function and host genome sampling in Type II-A CRISPR???Cas adaptation, Genes & Development, vol.29, issue.4, pp.356-361, 2015. ,
DOI : 10.1101/gad.257550.114
Characterization of the CRISPR/Cas Subtype I-A System of the Hyperthermophilic Crenarchaeon Thermoproteus tenax, Journal of Bacteriology, vol.194, issue.10, pp.2491-2500, 2012. ,
DOI : 10.1128/JB.00206-12
Foreign DNA acquisition by the I-F??CRISPR???Cas system requires all components of the interference machinery, Nucleic Acids Research, vol.43, issue.22, pp.10848-10860, 2015. ,
DOI : 10.1093/nar/gkv1261
CRISPR???Cas adaptation: insights into the mechanism of action, Nature Reviews Microbiology, vol.4, issue.2, pp.67-76, 2016. ,
DOI : 10.1038/nrmicro.2015.14
Adaptation in CRISPR-Cas Systems, Molecular Cell, vol.61, issue.6, pp.61-797, 2016. ,
DOI : 10.1016/j.molcel.2016.01.030
Integrase-mediated spacer acquisition during CRISPR???Cas adaptive immunity, Nature, vol.14, issue.7542, pp.193-198, 2015. ,
DOI : 10.1038/nature14237
CRISPR Immunological Memory Requires a Host Factor for Specificity, Molecular Cell, vol.62, issue.6, pp.824-833, 2016. ,
DOI : 10.1016/j.molcel.2016.04.027
Foreign DNA capture during CRISPR???Cas adaptive immunity, Nature, vol.30, issue.7579, pp.535-538, 2015. ,
DOI : 10.1038/nature15760
Detection and characterization of spacer integration intermediates in type I-E CRISPR???Cas system, Nucleic Acids Research, vol.42, issue.12, pp.7884-7893, 2014. ,
DOI : 10.1093/nar/gku510
Sequences spanning the leader-repeat junction mediate CRISPR adaptation to phage in Streptococcus thermophilus, Nucleic Acids Research, vol.43, issue.3, pp.1749-1758, 2015. ,
DOI : 10.1093/nar/gku1407
Casposons: a new superfamily of self-synthesizing DNA transposons at the origin of prokaryotic CRISPR-Cas immunity, BMC Biology, vol.12, issue.1, p.36, 2014. ,
DOI : 10.1093/molbev/mst197
URL : https://hal.archives-ouvertes.fr/pasteur-01001796
The basic building blocks and evolution of CRISPR???Cas systems, Biochemical Society Transactions, vol.41, issue.6, pp.1392-1400, 2013. ,
DOI : 10.1042/BST20130038
Mechanisms of DNA Transposition, Microbiology Spectrum, vol.3, issue.2, pp.3-0034, 2015. ,
DOI : 10.1128/microbiolspec.MDNA3-0034-2014
Everyman's Guide to Bacterial Insertion Sequences, Microbiology Spectrum, vol.3, issue.2, pp.10-1128, 2015. ,
DOI : 10.1128/microbiolspec.MDNA3-0030-2014
Insertion sequences, Microbiol. Mol. Biol. Rev, vol.62, pp.725-774, 1998. ,
URL : https://hal.archives-ouvertes.fr/hal-00021179
Evolution of adaptive immunity from transposable elements combined with innate immune systems, Nature Reviews Genetics, vol.4, issue.3, pp.184-192, 2015. ,
DOI : 10.1038/nature13011
Self-synthesizing transposons: unexpected key players in the evolution of viruses and defense systems, Current Opinion in Microbiology, vol.31, pp.25-33, 2016. ,
DOI : 10.1016/j.mib.2016.01.006
is a DNA integrase that generates target site duplications, Nucleic Acids Research, vol.43, issue.22, pp.10576-10587, 2015. ,
DOI : 10.1093/nar/gkv1180
Molecular memory of prior infections activates the CRISPR/Cas adaptive bacterial immunity system, Nature Communications, vol.3, p.945, 2012. ,
DOI : 10.1073/pnas.120163297
Recent Mobility of Casposons, Self-Synthesizing Transposons at the Origin of the CRISPR-Cas Immunity, Genome Biology and Evolution, vol.8, issue.2, pp.375-386, 2016. ,
DOI : 10.1093/gbe/evw006
URL : https://hal.archives-ouvertes.fr/hal-01443928
Isolation and characterization of catalytic and calmodulin-binding domains of Bordetella pertussis adenylate cyclase, European Journal of Biochemistry, vol.215, issue.2, pp.469-474, 1991. ,
DOI : 10.1016/0968-0004(90)90177-D
URL : https://hal.archives-ouvertes.fr/pasteur-00167100
Construction of T-vectors, a rapid and general system for direct cloning of unmodified PCR products, Nucleic Acids Research, vol.19, issue.5, p.1154, 1991. ,
DOI : 10.1093/nar/19.5.1154
Mechanisms of Site-Specific Recombination, Annual Review of Biochemistry, vol.75, issue.1, pp.567-605, 2006. ,
DOI : 10.1146/annurev.biochem.73.011303.073908
Resolving integral questions in site-specific recombination, Nature Structural & Molecular Biology, vol.13, issue.8, pp.641-643, 2005. ,
DOI : 10.1016/j.jmb.2004.05.027
A dual function of the CRISPR-Cas system in bacterial antivirus immunity and DNA repair, Molecular Microbiology, vol.9, issue.2, pp.484-502, 2011. ,
DOI : 10.1111/j.1365-2958.2010.07465.x
Structural Basis for DNase Activity of a Conserved Protein Implicated in CRISPR-Mediated Genome Defense, Structure, vol.17, issue.6, pp.904-912, 2009. ,
DOI : 10.1016/j.str.2009.03.019
Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003. ,
DOI : 10.1093/nar/gkg595
Memory of viral infections by CRISPR-Cas adaptive immune systems: Acquisition of new information, Virology, vol.434, issue.2, pp.202-209, 2012. ,
DOI : 10.1016/j.virol.2012.10.003
Short motif sequences determine the targets of the prokaryotic CRISPR defence system, Microbiology, vol.155, pp.733-740, 2009. ,
Cas1???Cas2 complex formation mediates spacer acquisition during CRISPR???Cas adaptive immunity, Nature Structural & Molecular Biology, vol.25, issue.6, pp.528-534, 2014. ,
DOI : 10.1038/nsmb.2820
Structural and Mechanistic Basis of PAM-Dependent Spacer Acquisition in CRISPR-Cas Systems, Cell, vol.163, issue.4, pp.840-853, 2015. ,
DOI : 10.1016/j.cell.2015.10.008
The tRNAscan-SE, snoscan and snoGPS web servers for the detection of tRNAs and snoRNAs, Nucleic Acids Research, vol.33, issue.Web Server, pp.686-689, 2005. ,
DOI : 10.1093/nar/gki366