High-throughput retrieval of target sequences from complex clone libraries using CRISPRi

Wang, J.Y., Pausch, P. & Doudna, J.A. Structural biology of CRISPR–Cas immunity and genome editing enzymes. Nat. Rev. Microbiol. 20, 641–656 (2022).

Xu, X. & Qi, L. S. A CRISPR–dCas toolbox for genetic engineering and synthetic biology. J. Mol. Biol. 431, 34–47 (2019).

Article  CAS  PubMed  Google Scholar 

Adli, M. The CRISPR tool kit for genome editing and beyond. Nat. Commun. 9, 1911 (2018).

Article  PubMed  PubMed Central  Google Scholar 

Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816–821 (2012).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bikard, D. et al. Programmable repression and activation of bacterial gene expression using an engineered CRISPR–Cas system. Nucleic Acids Res. 41, 7429–7437 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Schultzhaus, Z., Wang, Z. & Stenger, D. CRISPR-based enrichment strategies for targeted sequencing. Biotechnol. Adv. 46, 107672 (2021).

Article  CAS  PubMed  Google Scholar 

Feldman, D. et al. CloneSifter: enrichment of rare clones from heterogeneous cell populations. BMC Biol. 18, 177 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, S. et al. CRISPRi chemical genetics and comparative genomics identify genes mediating drug potency in Mycobacterium tuberculosis. Nat. Microbiol. 7, 766–779 (2022).

Article  PubMed  PubMed Central  Google Scholar 

Jost, M. et al. Combined CRISPRi/a-based chemical genetic screens reveal that rigosertib is a microtubule-destabilizing agent. Mol. Cell 68, 210–223 (2017).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Owen, J. G. et al. Multiplexed metagenome mining using short DNA sequence tags facilitates targeted discovery of epoxyketone proteasome inhibitors. Proc. Natl Acad. Sci. USA 112, 4221–4226 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang, W. et al. Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters. Nat. Commun. 6, 8101 (2015).

Article  PubMed  Google Scholar 

Lee, N. C., Larionov, V. & Kouprina, N. Highly efficient CRISPR/Cas9-mediated TAR cloning of genes and chromosomal loci from complex genomes in yeast. Nucleic Acids Res. 43, e55 (2015).

Article  PubMed  PubMed Central  Google Scholar 

Wang, H. et al. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res. 46, e28 (2018).

Article  PubMed  Google Scholar 

Eid, J. et al. Real-time DNA sequencing from single polymerase molecules. Science 323, 133–138 (2009).

Article  CAS  PubMed  Google Scholar 

Burian, J. & Thompson, C. J. Regulatory genes coordinating antibiotic-induced changes in promoter activity and early transcriptional termination of the mycobacterial intrinsic resistance gene whiB7. Mol. Microbiol. 107, 402–415 (2018).

Article  CAS  PubMed  Google Scholar 

Pierce, J. C., Sauer, B. & Sternberg, N. A positive selection vector for cloning high molecular weight DNA by the bacteriophage P1 system: improved cloning efficacy. Proc. Natl Acad. Sci. USA 89, 2056–2060 (1992).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gay, P., Le Coq, D., Steinmetz, M., Berkelman, T. & Kado, C. I. Positive selection procedure for entrapment of insertion sequence elements in gram-negative bacteria. J. Bacteriol. 164, 918–921 (1985).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brady, S. F. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat. Protoc. 2, 1297–1305 (2007).

Article  CAS  PubMed  Google Scholar 

Haley, J. D. in New Nucleic Acid Techniques (ed Walker, J. M.) 257–283 (Humana Press, 1988).

Blin, K. et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res. 49, W29–W35 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tesson, F. et al. Systematic and quantitative view of the antiviral arsenal of prokaryotes. Nat. Commun. 13, 2561 (2022).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Calvo-Villamanan, A. et al. On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria. Nucleic Acids Res. 48, e64 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang, W., Zheng, G. & Lu, Y. Recent advances in strategies for the cloning of natural product biosynthetic gene clusters. Front. Bioeng. Biotechnol. 9, 692797 (2021).

Article  PubMed  PubMed Central  Google Scholar 

Picelli, S. et al. Tn5 transposase and tagmentation procedures for massively scaled sequencing projects. Genome Res. 24, 2033–2040 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Athanasopoulou, K., Boti, M. A., Adamopoulos, P. G., Skourou, P. C. & Scorilas, A. Third-generation sequencing: the spearhead towards the radical transformation of modern genomics. Life (Basel) 12, 30 (2021).

Google Scholar 

Sternberg, N., Ruether, J. & deRiel, K. Generation of a 50,000-member human DNA library with an average DNA insert size of 75-100 kbp in a bacteriophage P1 cloning vector. New Biol. 2, 151–162 (1990).

CAS  PubMed  Google Scholar 

Zaburannyi, N., Rabyk, M., Ostash, B., Fedorenko, V. & Luzhetskyy, A. Insights into naturally minimised Streptomyces albus J1074 genome. BMC Genomics 15, 97 (2014).

Article  PubMed  PubMed Central  Google Scholar 

Wu, C., Shang, Z., Lemetre, C., Ternei, M. A. & Brady, S. F. Cadasides, Calcium-dependent acidic lipopeptides from the soil metagenome that are active against multidrug-resistant bacteria. J. Am. Chem. Soc. 141, 3910–3919 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jiang, Y. et al. Multigene editing in the Escherichia coli genome via the CRISPR–Cas9 system. Appl. Environ. Microbiol. 81, 2506–2514 (2015).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chang, A. C. & Cohen, S. N. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134, 1141–1156 (1978).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173–1183 (2013).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Cohen, S. N., Chang, A. C., Boyer, H. W. & Helling, R. B. Construction of biologically functional bacterial plasmids in vitro. Proc. Natl Acad. Sci. USA 70, 3240–3244 (1973).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Doench, J. G. et al. Rational design of highly active sgRNAs for CRISPR–Cas9-mediated gene inactivation. Nat. Biotechnol. 32, 1262–1267 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chan, W. T., Verma, C. S., Lane, D. P. & Gan, S. K. A comparison and optimization of methods and factors affecting the transformation of Escherichia coli. Biosci. Rep. 33, e00086 (2013).

Article  PubMed  PubMed Central  Google Scholar 

Kolmogorov, M. et al. metaFlye: scalable long-read metagenome assembly using repeat graphs. Nat. Methods 17, 1103–1110 (2020).

Article  CAS  PubMed  Google Scholar 

Blin, K. et al. antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47, W81–W87 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Shen, W., Le, S., Li, Y. & Hu, F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS ONE 11, e0163962 (2016).

Article  PubMed  PubMed Central  Google Scholar 

Rognes, T., Flouri, T., Nichols, B., Quince, C. & Mahe, F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 4, e2584 (2016).

Article  PubMed 

留言 (0)

沒有登入
gif