W. Jiang, D. Bikard, D. Cox, F. Zhang, and L. A. Marraffini, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat. Biotechnol, vol.31, pp.233-239, 2013.

Y. Jiang, Multigene editing in the Escherichia coli genome via the CRISPR-Cas9 system, Appl. Environ. Microbiol, vol.81, pp.2506-2514, 2015.

M. E. Pyne, M. Moo-young, D. A. Chung, and C. P. Chou, Coupling the CRISPR/Cas9 system with lambda red recombineering enables simplified chromosomal gene replacement in Escherichia coli, Appl. Environ. Microbiol, vol.81, pp.5103-5114, 2015.

Y. Li, Metabolic engineering of Escherichia coli using CRISPR-Cas9 meditated genome editing, Metab. Eng, vol.31, pp.13-21, 2015.

A. D. Garst, Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering, Nat. Biotechnol, vol.35, pp.48-55, 2016.

J. M. Vento, N. Crook, and C. L. Beisel, Barriers to genome editing with CRISPR in bacteria, J. Ind. Microbiol. Biotechnol, vol.46, pp.1327-1341, 2019.

B. L. Oakes, Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch, Nat. Biotechnol, vol.34, pp.646-651, 2016.

K. Kundert, Controlling CRISPR-Cas9 with ligand-activated and liganddeactivated sgRNAs, Nat. Commun, vol.10, p.2127, 2019.

Y. Liu, Directing cellular information flow via CRISPR signal conductors, Nat. Methods, vol.13, pp.938-944, 2016.

Q. R. Ferry, R. Lyutova, and T. A. Fulga, Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs, Nat. Commun, vol.8, p.14633, 2017.

W. Tang, J. H. Hu, and D. R. Liu, Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation, Nat. Commun, vol.8, p.15939, 2017.

J. C. Rose, Rapidly inducible Cas9 and DSB-ddPCR to probe editing kinetics, Nat. Methods, vol.14, pp.891-896, 2017.

K. I. Liu, A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing, Nat. Chem. Biol, vol.12, pp.980-987, 2016.

B. Zetsche, S. E. Volz, and F. Zhang, A split-Cas9 architecture for inducible genome editing and transcription modulation, Nat. Biotechnol, vol.33, pp.139-142, 2015.

Y. Nihongaki, F. Kawano, T. Nakajima, and M. Sato, Photoactivatable CRISPR-Cas9 for optogenetic genome editing, Nat. Biotechnol, vol.33, pp.755-760, 2015.

J. Hemphill, E. K. Borchardt, K. Brown, A. Asokan, and A. Deiters, Optical control of CRISPR/Cas9 gene editing, J. Am. Chem. Soc, vol.137, pp.5642-5645, 2015.

F. Richter, Engineering of temperature-and light-switchable Cas9 variants, Nucleic Acids Res. gkw930, 2016.

B. Maji, Multidimensional chemical control of CRISPR-Cas9, Nat. Chem. Biol, vol.13, pp.9-11, 2017.

K. Siu and W. Chen, Riboregulated toehold-gated gRNA for programmable CRISPR-Cas9 function, Nat. Chem. Biol, 2018.

L. Cui and D. Bikard, Consequences of Cas9 cleavage in the chromosome of Escherichia coli, Nucleic Acids Res, vol.44, pp.4243-4251, 2016.
URL : https://hal.archives-ouvertes.fr/pasteur-01967442

M. Jinek, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, vol.337, pp.816-821, 2012.

D. M. Shechner, E. Hacisuleyman, S. T. Younger, J. L. Rinn, and . Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display, Nat. Methods, vol.12, pp.664-670, 2015.

A. E. Briner, Guide RNA functional modules direct Cas9 activity and orthogonality, Mol. Cell, vol.56, pp.333-339, 2014.

H. Nishimasu, Crystal structure of Cas9 in complex with guide RNA and target DNA, Cell, vol.156, pp.935-949, 2014.

S. Warming, Simple and highly efficient BAC recombineering using galK selection, Nucleic Acids Res, vol.33, pp.36-36, 2005.

S. Datta, N. Costantino, and D. L. Court, A set of recombineering plasmids for gram-negative bacteria, Gene, vol.379, pp.109-115, 2006.

M. C. Bassalo, Rapid and efficient one-step metabolic pathway integration in E. coli, ACS Synth. Biol, vol.5, pp.561-568, 2016.

J. A. Sawitzke, Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering, J. Mol. Biol, vol.407, pp.45-59, 2011.

L. Clarke and J. Carbon, Selection of specific clones from colony banks by suppression or complementation tests, Method Enzymol, vol.68, pp.396-408, 1979.

C. M. Armstrong, D. J. Meyers, L. S. Imlay, C. Meyers, and A. R. Odom, Resistance to the antimicrobial agent Fosmidomycin and an FR900098 prodrug through mutations in the deoxyxylulose phosphate reductoisomerase gene (dxr), Antimicrob. Agents Chemother, vol.59, pp.5511-5519, 2015.

G. Pines, Genomic deoxyxylulose phosphate reductoisomerase (DXR) mutations conferring resistance to the antimalarial drug, Fosmidomycin in E. coli. ACS Synth. Biol, vol.7, pp.2824-2832, 2018.

R. D. Jenison, C. G. Stanley, A. Pardi, and B. Polisky, High-resolution molecular discrimination by RNA, Science, vol.263, pp.1425-1429, 1994.

A. D. Garst, A. L. Edwards, and R. T. Batey, Riboswitches: structures and mechanisms, Cold Spring Harb. Perspect. Biol, vol.3, p.3533, 2011.

C. Berens, F. Groher, and B. Suess, RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression, Biotechnol. J, vol.10, pp.246-257, 2015.

G. A. Soukup, G. A. Emilsson, and R. R. Breaker, Altering molecular recognition of RNA aptamers by allosteric selection, J. Mol. Biol, vol.298, pp.623-632, 2000.

J. Quan and J. Tian, Circular polymerase extension cloning for high-throughput cloning of complex and combinatorial DNA libraries, Nat. Protoc, vol.6, pp.242-251, 2011.

D. G. Gibson, Enzymatic assembly of DNA molecules up to several hundred kilobases, Nat. Methods, vol.6, pp.343-345, 2009.

S. Lin, B. T. Staahl, R. K. Alla, and J. A. Doudna, Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery, vol.3, p.4766, 2014.

R. R. Burgess, Use of polyethyleneimine in purification of DNA-binding proteins, Methods Enzymol, vol.208, pp.3-10, 1991.

A. L. Edwards, A. D. Garst, and R. Batey, Nucleic Acids and Peptide Aptamers, pp.135-163, 2009.