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Volumn 46, Issue , 2017, Pages 134-140

System-level perturbations of cell metabolism using CRISPR/Cas9

Author keywords

[No Author keywords available]

Indexed keywords

COST EFFECTIVENESS; COST ENGINEERING; GENES; METABOLISM;

EID: 85016416431     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2017.03.014     Document Type: Review
Times cited : (22)

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    • Among the first ones to perform genome-wide knock-out screen in mammalian cells by using CRISPR/Cas9. The screen identified 27 known and 4 unknown genes that play a role in resistance to  Clostridium septicum alpha-toxin or 6-thioguanine.
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    • Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design
    • This paper determines rules for choosing efficient guiding gRNAs. Employing dCas9 and modelling approach authors identify that guides targeting low nucleosome occupancy regions and regions between the transcription start site (TSS) and 200 bp upstream of the TSS are most effective.
    • 43•• Smith, J.D., Suresh, S., Schlecht, U., Wu, M., Wagih, O., Peltz, G., Davis, R.W., Steinmetz, L.M., Parts, L., St. Onge, R.P., et al. Quantitative CRISPR interference screens in yeast identify chemical-genetic interactions and new rules for guide RNA design. Genome Biol, 17, 2016, 45 This paper determines rules for choosing efficient guiding gRNAs. Employing dCas9 and modelling approach authors identify that guides targeting low nucleosome occupancy regions and regions between the transcription start site (TSS) and 200 bp upstream of the TSS are most effective.
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    • Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli
    • CRISPR array system based on dCas9 for down regulation of genes in  E.coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
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    • Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq
    • Has developed a method called CRISP-seq, which integrates single-cell RNA sequencing and CRISPR-pooled screens.
    • 46•• Jaitin, D.A., Weiner, A., Yofe, I., Lara-Astiaso, D., Keren-Shaul, H., David, E., Salame, T.M., Tanay, A., Oudenaarden van, A., Amit, I., Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-Seq. Cell 167 (2016), 1883–1896 Has developed a method called CRISP-seq, which integrates single-cell RNA sequencing and CRISPR-pooled screens.
    • (2016) Cell , vol.167 , pp. 1883-1896
    • Jaitin, D.A.1    Weiner, A.2    Yofe, I.3    Lara-Astiaso, D.4    Keren-Shaul, H.5    David, E.6    Salame, T.M.7    Tanay, A.8    Oudenaarden van, A.9    Amit, I.10
  • 48
    • 85011034228 scopus 로고    scopus 로고
    • Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering
    • Has developed CRISPR based method for trackable genome engineering (CREATE) and reverse engineered all 645 nonsynonymous mutations identified in an evolved thermotolerant  E. coli strain.
    • 48•• Garst, A.D., Bassalo, M.C., Pines, G., Lynch, S.A., Halweg-Edwards, A.L., Liu, R., Liang, L., Wang, Z., Zeitoun, R., Alexander, W.G., et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering. Nat Biotechnol 35 (2016), 48–55 Has developed CRISPR based method for trackable genome engineering (CREATE) and reverse engineered all 645 nonsynonymous mutations identified in an evolved thermotolerant  E. coli strain.
    • (2016) Nat Biotechnol , vol.35 , pp. 48-55
    • Garst, A.D.1    Bassalo, M.C.2    Pines, G.3    Lynch, S.A.4    Halweg-Edwards, A.L.5    Liu, R.6    Liang, L.7    Wang, Z.8    Zeitoun, R.9    Alexander, W.G.10
  • 50
    • 84988911466 scopus 로고    scopus 로고
    • Enhanced protein and biochemical production using CRISPRi-based growth switches
    • Have showed that CRISPR/Cas9 can be used to regulate expression of genes that are responsible for groth and by slowing the groth increase production proteins and chemicals.
    • 50• Li, S., Jendresen, C.B., Grünberger, A., Ronda, C., Jensen, S.I., Noack, S., Nielsen, A.T., Enhanced protein and biochemical production using CRISPRi-based growth switches. Metab Eng 38 (2016), 274–284 Have showed that CRISPR/Cas9 can be used to regulate expression of genes that are responsible for groth and by slowing the groth increase production proteins and chemicals.
    • (2016) Metab Eng , vol.38 , pp. 274-284
    • Li, S.1    Jendresen, C.B.2    Grünberger, A.3    Ronda, C.4    Jensen, S.I.5    Noack, S.6    Nielsen, A.T.7
  • 51
    • 85013830067 scopus 로고    scopus 로고
    • Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae
    • This paper describes a method for systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in  Saccharomyces cerevisiae.
    • 51• Deaner, M., Alper, H.S., Systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in Saccharomyces cerevisiae. Metab Eng 40 (2017), 14–22, 10.1016/j.ymben.2017.01.012 This paper describes a method for systematic testing of enzyme perturbation sensitivities via graded dCas9 modulation in  Saccharomyces cerevisiae.
    • (2017) Metab Eng , vol.40 , pp. 14-22
    • Deaner, M.1    Alper, H.S.2
  • 52
    • 77954590959 scopus 로고    scopus 로고
    • OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions
    • 52 Ranganathan, S., Suthers, P.F., Maranas, C.D., OptForce: an optimization procedure for identifying all genetic manipulations leading to targeted overproductions. PLoS Comput Biol, 6, 2010, e1000744.
    • (2010) PLoS Comput Biol , vol.6 , pp. e1000744
    • Ranganathan, S.1    Suthers, P.F.2    Maranas, C.D.3
  • 53
    • 84930971149 scopus 로고    scopus 로고
    • CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli
    • CRISPR array system based on dCas9 for down regulation of genes in  E. coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
    • 53•• Cress, B.F., Toparlak ÖD, Guleria, S., Lebovich, M., Stieglitz, J.T., Englaender, J.A., Jones, J.A., Linhardt, R.J., Koffas, M.A.G., CRISPathBrick: modular combinatorial assembly of type II-A CRISPR arrays for dCas9-mediated multiplex transcriptional repression in E. coli. ACS Synth Biol 4 (2015), 987–1000 CRISPR array system based on dCas9 for down regulation of genes in  E. coli. Authors show that down-regulating novel and computationally predicted metabolic engineering targets can improve the yield of certain compound.
    • (2015) ACS Synth Biol , vol.4 , pp. 987-1000
    • Cress, B.F.1    Toparlak ÖD2    Guleria, S.3    Lebovich, M.4    Stieglitz, J.T.5    Englaender, J.A.6    Jones, J.A.7    Linhardt, R.J.8    Koffas, M.A.G.9
  • 55
    • 84961794371 scopus 로고    scopus 로고
    • Multiple gene repression in Cyanobacteria using CRISPRi
    • 55 Yao, L., Cengic, I., Anfelt, J., Hudson, E.P., Multiple gene repression in Cyanobacteria using CRISPRi. ACS Synth Biol 5 (2016), 207–212.
    • (2016) ACS Synth Biol , vol.5 , pp. 207-212
    • Yao, L.1    Cengic, I.2    Anfelt, J.3    Hudson, E.P.4
  • 56
    • 84982860066 scopus 로고    scopus 로고
    • CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002
    • This study shows usability of dCas9 for gene repression in cyanobacteria to increase central carbon flux. Such experimental design provides 2-fold increase in lactate production.
    • 56• Gordon, G.C., Korosh, T.C., Cameron, J.C., Markley, A.L., Begemann, M.B., Pfleger, B.F., CRISPR interference as a titratable, trans-acting regulatory tool for metabolic engineering in the cyanobacterium Synechococcus sp. strain PCC 7002. Metab Eng 38 (2016), 170–179 This study shows usability of dCas9 for gene repression in cyanobacteria to increase central carbon flux. Such experimental design provides 2-fold increase in lactate production.
    • (2016) Metab Eng , vol.38 , pp. 170-179
    • Gordon, G.C.1    Korosh, T.C.2    Cameron, J.C.3    Markley, A.L.4    Begemann, M.B.5    Pfleger, B.F.6
  • 57
    • 85027956141 scopus 로고    scopus 로고
    • CRISPRi engineering E. coli for morphology diversification
    • 57 Elhadi, D., Lv, L., Jiang, X.-R., Wu, H., Chen, G.-Q., CRISPRi engineering E. coli for morphology diversification. Metab Eng 38 (2016), 358–369.
    • (2016) Metab Eng , vol.38 , pp. 358-369
    • Elhadi, D.1    Lv, L.2    Jiang, X.-R.3    Wu, H.4    Chen, G.-Q.5
  • 58
    • 84962052932 scopus 로고    scopus 로고
    • Stability of ensemble models predicts productivity of enzymatic systems
    • 58 Theisen, M.K., Lafontaine Rivera, J.G., Liao, J.C., Stability of ensemble models predicts productivity of enzymatic systems. PLOS Comput Biol, 12, 2016, e1004800.
    • (2016) PLOS Comput Biol , vol.12 , pp. e1004800
    • Theisen, M.K.1    Lafontaine Rivera, J.G.2    Liao, J.C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.