, Papers of particular interest, published within the period of review, have been highlighted as: of special interest of outstanding interest
Current understanding of the human microbiome, Nat Med, vol.24, pp.392-400, 2018. ,
CRISPR provides acquired resistance against viruses in prokaryotes, Science, vol.80, pp.1709-1712, 2007. ,
Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants, Nat Rev Microbiol, vol.18, pp.67-83, 2019. ,
A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, vol.337, pp.816-821, 2012. ,
RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat Biotechnol, vol.31, pp.233-239, 2013. ,
CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, vol.154, pp.442-451, 2013. ,
Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system, Nucleic Acids Res, vol.41, pp.7429-7437, 2013. ,
Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, vol.152, pp.1173-1183, 2013. ,
Multiplex genome engineering using CRISPR/Cas systems, Science, p.339 ,
RNA-guided human genome engineering via Cas9, Science, vol.339, pp.823-826 ,
A benchmark of computational CRISPR-Cas9 guide design methods, PLoS Comput Biol, vol.15, p.1007274, 2019. ,
Improving CRISPR guide design with consensus approaches, BMC Genomics, vol.20, p.931, 2019. ,
Genome-scale CRISPR-Cas9 knockout screening in human cells, Science, vol.343, pp.84-87, 2014. ,
Genetic screens in human cells using the CRISPR-Cas9 system, Science, vol.343, pp.80-84, 2014. ,
Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library, Nat Biotechnol, vol.32, pp.267-273, 2014. ,
CRISPR screen reveals that EHEC's T3SS and Shiga toxin rely on shared host factors for infection, vol.9, pp.1003-1021, 2018. ,
, authors identify human genes required for the toxicity of enterohemorragic E. coli in intestinal epithelial cells. Interestingly, a common route for the toxicity of the shiga-toxin and the type-3 secretion system is unveiled
A FACS-based genome-wide CRISPR screen reveals a requirement for COPI in Chlamydia trachomatis invasion, vol.11, pp.71-84, 2019. ,
Genome-scale CRISPR-mediated control of gene repression and activation, Cell, vol.159, pp.647-661, 2014. ,
Highthroughput screening of a CRISPR/Cas9 library for functional genomics in human cells, Nature, vol.509, pp.487-491, 2014. ,
Frizzled proteins are colonic epithelial receptors for C. difficile toxin B, Nature, vol.538, pp.350-355, 2016. ,
CRISPR/Cas9 screens reveal requirements for host cell sulfation and fucosylation in bacterial Type III secretion system-mediated cytotoxicity, Cell Host Microbe, vol.20, pp.226-237, 2016. ,
A comprehensive, CRISPR-based functional analysis of essential genes in bacteria, Cell, vol.165, pp.1493-1506, 2016. ,
, High-throughput CRISPRi phenotyping identifies new essential genes in Streptococcus pneumoniae, vol.13, p.931, 2017.
Arrayed CRISPRi and quantitative imaging describe the morphotypic landscape of essential mycobacterial genes, 2020. ,
Analysis of lipoprotein transport depletion in Vibrio cholerae using CRISPRi, Proc Natl Acad Sci, vol.116, pp.17013-17022, 2019. ,
Genome-wide screening identifies promiscuous phosphatases impairing terpenoid biosynthesis in Escherichia coli, Appl Microbiol Biotechnol, vol.102, pp.9771-9780, 2018. ,
Systematic genome-wide querying of coding and non-coding functional elements in E. coli using CRISPRi, 2020. ,
The impact of genetic diversity on gene essentiality within the E. coli species, 2020. ,
Pooled CRISPRi screening of the cyanobacterium Synechocystis sp. PCC 6803 for enhanced industrial phenotypes, Nat Commun, vol.2020, p.1666 ,
, A nice application of CRISPRi screens in a biotechnological context. In particular, the authors combine droplet-based cell sorting with a chemical assay to identify knockdowns that produce higher titers of L-lactate
CRISPRi-Seq for the identification and characterisation of essential mycobacterial genes and transcriptional units, 2018. ,
, Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi, vol.4, pp.1105-1113, 2019.
, This study uses CRISPRi to identify the essential genes of V. natriegens, a species of biotechnological interest for which Tn-seq was unsuccessfull
Selective enrichment of slow-growing bacteria in a metabolism-wide CRISPRi library with a TIMER protein, ACS Synth Biol, vol.7, pp.2775-2782, 2018. ,
Genome-wide CRISPRi-based identification of targets for decoupling growth from production, ACS Synth Biol, vol.2020, pp.1030-1040 ,
accessing certain phenotypes is challenging with pooled CRISPRi screens, the authors provide an ingenious solution by combining timelapse microscopy of a pooled library with in situ genotyping by sequential FISH, Nat Methods, vol.17, pp.86-92, 2019. ,
Comprehensive genomewide perturbations via CRISPR adaptation reveal complex genetics of antibiotic sensitivity, Cell, vol.2020, p.0 ,
Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi, Nat Microbiol, vol.4, pp.244-250, 2019. ,
Modulating pathogenesis with mobile-CRISPRi, J Bacteriol, 0201. ,
A decade of advances in transposon-insertion sequencing, Nat Rev Genet, 2020. ,
Exploration of bacterial bottlenecks and Streptococcus pneumoniae pathogenesis by CRISPRi-seq, 2020. ,
, This preprint describes the first CRISPRi screen employed in vivo in bacteria, investigating the population bottlenecks during pneumococcal infection in mice and identifying pneumococcal genes required for pathogenicity
CRISPathBrick: modular combinatorial assembly of Type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli, ACS Synth Biol, vol.4, pp.987-1000, 2015. ,
CRISPR RNA-guided activation of endogenous human genes, Nat Methods, vol.10, pp.977-979, 2013. ,
Synthetic CRISPR-Cas gene activators for transcriptional reprogramming in bacteria, Nat Commun, vol.9, p.2489, 2018. ,
Engineered CRISPRa enables programmable eukaryote-like gene activation in bacteria, Nat Commun, vol.10, p.3693, 2019. ,
Effective CRISPRa-mediated control of gene expression in bacteria must overcome strict target site requirements, Nat Commun, vol.11, pp.1-11, 2020. ,
Programmable and portable CRISPR-Cas transcriptional activation in bacteria, 2020. ,
Programmable editing of a target base in genomic DNA without doublestranded DNA cleavage, Nature, vol.533, pp.420-424, 2016. ,
Programmable base editing of T to G C in genomic DNA without DNA cleavage, Nature, vol.551, pp.464-471, 2017. ,
Highly efficient base editing in: Staphylococcus aureus using an engineered CRISPR RNA-guided cytidine deaminase, Chem Sci, vol.9, pp.3248-3253, 2018. ,
Programmable adenine deamination in bacteria using a Cas9-adenine-deaminase fusion, Chem Sci, vol.11, pp.1657-1664, 2020. ,
CRISPRCas9 and CRISPR-assisted cytidine deaminase enable precise and efficient genome editing in Klebsiella pneumoniae, Appl Environ Microbiol, p.84, 2018. ,
A highly efficient CRISPR-Cas9-based genome engineering platform in Acinetobacter baumannii to understand the H 2 O 2 -sensing mechanism of OxyR, Cell Chem Biol, vol.26, pp.1732-1742, 2019. ,
CRISPR/Cas9-based genome editing in Pseudomonas aeruginosa and cytidine deaminase-mediated base editing in Pseudomonas species, vol.6, pp.222-231, 2018. ,
, Highly efficient DSB-free base editing for streptomycetes with CRISPR-BEST
, Proc Natl Acad Sci, vol.116, pp.20366-20375, 2019.
Deaminase-mediated multiplex genome editing in Escherichia coli, Nat Microbiol, vol.3, pp.423-429, 2018. ,
Functional genetic variants revealed by massively parallel precise genome editing, Cell, vol.175, pp.544-557, 2018. ,
Multiplex generation, tracking, and functional screening of substitution mutants using a crispr/retron system, ACS Synth Biol, vol.2020, pp.1003-1009 ,
Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, vol.576, pp.149-157, 2019. ,
RNA-guided DNA insertion with CRISPRassociated transposases, Science, vol.364, pp.48-53 ,
Transposon-encoded CRISPR-Cas systems direct RNAguided DNA integration, Nature, vol.571, pp.219-225, 2019. ,