| Literature DB >> 33868193 |
Riyu Zhang1, Wensheng Xu2, Shuai Shao1, Qiyao Wang1,3,4.
Abstract
Functional genetic screening is an important method that has been widely used to explore the biological processes and functional annotation of genetic elements. CRISPR/Cas (Clustered regularly interspaced short palindromic repeat sequences/CRISPR-associated protein) is the newest tool in the geneticist's toolbox, allowing researchers to edit a genome with unprecedented ease, accuracy, and high-throughput. Most recently, CRISPR interference (CRISPRi) has been developed as an emerging technology that exploits the catalytically inactive Cas9 (dCas9) and single-guide RNA (sgRNA) to repress sequence-specific genes. In this review, we summarized the characteristics of the CRISPRi system, such as programmable, highly efficient, and specific. Moreover, we demonstrated its applications in functional genetic screening and highlighted its potential to dissect the underlying mechanism of pathogenesis. The recent development of the CRISPRi system will provide a high-throughput, practical, and efficient tool for the discovery of functionally important genes in bacteria.Entities:
Keywords: CRISPR/Cas; CRISPRi screen; Tn-seq; essential genes; gene silencing
Year: 2021 PMID: 33868193 PMCID: PMC8044314 DOI: 10.3389/fmicb.2021.635227
Source DB: PubMed Journal: Front Microbiol ISSN: 1664-302X Impact factor: 5.640
FIGURE 1Schematic of the CRISPRi approach. Left, Cartoon representation of the CRISPR-mediated regulation of gene expression. The wild-type Cas9 protein binds to the sgRNA and forms a protein–RNA complex. Once Cas9–sgRNA complex binds to specific DNA target adjacent to PAM, it leads to the cleavage of the target DNA due to the nuclease activity of the Cas9 protein. Right, Cartoon depicting the CRISPRi-mediated interference of gene expression caused by nuclease-deficient dCas9. The nuclease-deficient dCas9 contains two substitutions in the nuclease domains (D10A and H840A, blue dots), and thus lose the endonuclease activity. If the target DNA sequence locates inside an open reading frame, the dCas9–sgRNA–DNA complex will block the movement of RNAP and subsequent transcription elongation, resulting in transcription inhibition of the target gene.
The advantages and disadvantages of CRISPRi.
| Advantages | Disadvantages |
| Tunable knockdown | Off-target |
| Inducible knockdown | Bad-seed effect |
| Reversible knockdown | Polar effect and reverse polar effect |
| Controlling multiple genes | Toxicity of dCas9 |
Comparison of sRNA-mediated gene silencing and CRISPRi.
| Characteristic | sRNA-mediated gene silencing | CRISPR interference |
| Silence type | post-transcriptional inhibition | transcription inhibition |
| Target | 5′ UTR of mRNA | promoter or the ORF of interested genes |
| Required tools | sRNA and chaperone protein (Hfq, etc.) | sgRNA and dCas9 |
| Common characteristics | silencing through base pairing of RNA and target, silence simultaneously multiple genes, programmable, off-target | |
Comparison of Tn-seq and CRISPRi screen.
| Characteristic | Tn-seq | CRISPRi screen |
| Mutation type | insertion mutation | knock-down |
| Required tools | transposon | sgRNA, dCas9 |
| Gene selection | random insertion | random design or specific design |
| Gene type | non-essential gene | non-essential gene or essential gene |
| Library size | genome-wide library | genome-wide library or tiling library |
| Advantages | suitable for operon genes | adjustable library size, suitable for essential gene, and short genes |
| Disadvantages | unsuitable for essential gene and short genes, transposon insertion prefers TA site, which results in insertion sites uneven distribution. | off-target, polar and reverse polar effect, bad-seed effect, dCas9-specific toxicity |
FIGURE 2The CRISPRi screening procedure in bacteria. Firstly, oligos designed on a large scale by the software are synthesized through a chip and then, the sgRNA plasmids library is constructed. Mix sgRNA plasmids are co-transformed into recipient strains in which dCas9 is integrated into genomic DNA. Competitive growth culture is performed in selective condition and control conditions. The mixed plasmids are isolated from pooled colonized strain and subsequently used for high-throughput sequencing. Finally, data analysis of the relative fitness contribution of each gene is performed.