메뉴 건너뛰기




Volumn 8, Issue , 2017, Pages

Rational design of inducible CRISPR guide RNAs for de novo assembly of transcriptional programs

Author keywords

[No Author keywords available]

Indexed keywords

CRISPR ASSOCIATED PROTEIN; GUIDE RNA; RIBOZYME; SINGLE GUIDE RNA; SINGLE STRANDED DNA; SYNTHETIC DNA; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG; LIGAND;

EID: 85014514373     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/ncomms14633     Document Type: Article
Times cited : (64)

References (41)
  • 1
    • 84894534641 scopus 로고    scopus 로고
    • Synthetic biology in mammalian cells: Next generation research tools and therapeutics
    • Lienert, F., Lohmueller, J. J., Garg, A. & Silver, P. A. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15, 95-107 (2014).
    • (2014) Nat. Rev. Mol. Cell Biol. , vol.15 , pp. 95-107
    • Lienert, F.1    Lohmueller, J.J.2    Garg, A.3    Silver, P.A.4
  • 2
    • 84977589267 scopus 로고    scopus 로고
    • Engineering gene circuits for mammalian cell-based applications
    • Auslander, S. & Fussenegger, M. Engineering gene circuits for mammalian cell-based applications. Cold Spring Harb. Perspect. Biol. http://dx. doi. org/ 10. 1101/cshperspect. a023895 (2016).
    • (2016) Cold Spring Harb. Perspect. Biol.
    • Auslander, S.1    Fussenegger, M.2
  • 3
    • 84899694320 scopus 로고    scopus 로고
    • Principles of genetic circuit design
    • Brophy, J. A. & Voigt, C. A. Principles of genetic circuit design. Nat. Methods 11, 508-520 (2014).
    • (2014) Nat. Methods , vol.11 , pp. 508-520
    • Brophy, J.A.1    Voigt, C.A.2
  • 4
    • 84969791285 scopus 로고    scopus 로고
    • Comparison of Cas9 activators in multiple species
    • Chavez, A. et al. Comparison of Cas9 activators in multiple species. Nat. Methods 13, 563-567 (2016).
    • (2016) Nat. Methods , vol.13 , pp. 563-567
    • Chavez, A.1
  • 5
    • 84956857435 scopus 로고    scopus 로고
    • Engineering synthetic gene circuits in living cells with CRISPR technology
    • Jusiak, B., Cleto, S., Perez-Pinera, P. & Lu, T. K. Engineering synthetic gene circuits in living cells with CRISPR technology. Trends Biotechnol. 34, 535-547 (2016).
    • (2016) Trends Biotechnol. , vol.34 , pp. 535-547
    • Jusiak, B.1    Cleto, S.2    Perez-Pinera, P.3    Lu, T.K.4
  • 6
    • 84923096541 scopus 로고    scopus 로고
    • Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
    • Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588 (2015).
    • (2015) Nature , vol.517 , pp. 583-588
    • Konermann, S.1
  • 7
    • 84961782000 scopus 로고    scopus 로고
    • Chemical and biophysical modulation of Cas9 for tunable genome engineering
    • Nunez, J. K., Harrington, L. B. & Doudna, J. A. Chemical and biophysical modulation of Cas9 for tunable genome engineering. ACS Chem. Biol. 11, 681-688 (2016).
    • (2016) ACS Chem. Biol. , vol.11 , pp. 681-688
    • Nunez, J.K.1    Harrington, L.B.2    Doudna, J.A.3
  • 8
    • 84887104139 scopus 로고    scopus 로고
    • Orthogonal Cas9 proteins for RNA-guided gene regulation and editing
    • Esvelt, K. M. et al. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10, 1116-1121 (2013).
    • (2013) Nat. Methods , vol.10 , pp. 1116-1121
    • Esvelt, K.M.1
  • 9
    • 84865070369 scopus 로고    scopus 로고
    • A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    • Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
    • (2012) Science , vol.337 , pp. 816-821
    • Jinek, M.1
  • 10
    • 84922322005 scopus 로고    scopus 로고
    • Guide RNA functional modules direct Cas9 activity and orthogonality
    • Briner, A. E. et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell 56, 333-339 (2014).
    • (2014) Mol. Cell , vol.56 , pp. 333-339
    • Briner, A.E.1
  • 11
    • 84908508061 scopus 로고    scopus 로고
    • Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease
    • Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569-573 (2014).
    • (2014) Nature , vol.513 , pp. 569-573
    • Anders, C.1    Niewoehner, O.2    Duerst, A.3    Jinek, M.4
  • 12
    • 84901195977 scopus 로고    scopus 로고
    • Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells
    • Nissim, L., Perli, S. D., Fridkin, A., Perez-Pinera, P. & Lu, T. K. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol. Cell 54, 698-710 (2014).
    • (2014) Mol. Cell , vol.54 , pp. 698-710
    • Nissim, L.1    Perli, S.D.2    Fridkin, A.3    Perez-Pinera, P.4    Lu, T.K.5
  • 13
    • 77956498326 scopus 로고    scopus 로고
    • Sequenceand structure-specific RNA processing by a CRISPR endonuclease
    • Haurwitz, R. E., Jinek, M., Wiedenheft, B., Zhou, K. & Doudna, J. A. Sequenceand structure-specific RNA processing by a CRISPR endonuclease. Science 329, 1355-1358 (2010).
    • (2010) Science , vol.329 , pp. 1355-1358
    • Haurwitz, R.E.1    Jinek, M.2    Wiedenheft, B.3    Zhou, K.4    Doudna, J.A.5
  • 14
    • 84947225411 scopus 로고    scopus 로고
    • Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease
    • Dahlman, J. E. et al. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat. Biotechnol. 33, 1159-1161 (2015).
    • (2015) Nat. Biotechnol. , vol.33 , pp. 1159-1161
    • Dahlman, J.E.1
  • 15
    • 0024041180 scopus 로고
    • Role of RNase H in hybrid-arrested translation by antisense oligonucleotides
    • Walder, R. Y. & Walder, J. A. Role of RNase H in hybrid-arrested translation by antisense oligonucleotides. Proc. Natl Acad. Sci. USA 85, 5011-5015 (1988).
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 5011-5015
    • Walder, R.Y.1    Walder, J.A.2
  • 16
    • 77949512140 scopus 로고    scopus 로고
    • RNA targeting therapeutics: Molecular mechanisms of antisense oligonucleotides as a therapeutic platform
    • Bennett, C. F. & Swayze, E. E. RNA targeting therapeutics: molecular mechanisms of antisense oligonucleotides as a therapeutic platform. Annu. Rev. Pharmacol. Toxicol. 50, 259-293 (2010).
    • (2010) Annu. Rev. Pharmacol. Toxicol. , vol.50 , pp. 259-293
    • Bennett, C.F.1    Swayze, E.E.2
  • 17
    • 84981294965 scopus 로고    scopus 로고
    • Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames
    • Liang, X. H. et al. Translation efficiency of mRNAs is increased by antisense oligonucleotides targeting upstream open reading frames. Nat. Biotechnol. 34, 875-880 (2016).
    • (2016) Nat. Biotechnol. , vol.34 , pp. 875-880
    • Liang, X.H.1
  • 18
    • 0034234550 scopus 로고    scopus 로고
    • RNA accessibility prediction: A theoretical approach is consistent with experimental studies in cell extracts
    • Scherr, M., Rossi, J. J., Sczakiel, G. & Patzel, V. RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts. Nucleic Acids Res. 28, 2455-2461 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 2455-2461
    • Scherr, M.1    Rossi, J.J.2    Sczakiel, G.3    Patzel, V.4
  • 19
    • 0035283171 scopus 로고    scopus 로고
    • Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
    • Ding, Y. & Lawrence, C. E. Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res. 29, 1034-1046 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 1034-1046
    • Ding, Y.1    Lawrence, C.E.2
  • 20
    • 84893230222 scopus 로고    scopus 로고
    • Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases
    • Niewoehner, O., Jinek, M. & Doudna, J. A. Evolution of CRISPR RNA recognition and processing by Cas6 endonucleases. Nucleic Acids Res. 42, 1341-1353 (2014).
    • (2014) Nucleic Acids Res. , vol.42 , pp. 1341-1353
    • Niewoehner, O.1    Jinek, M.2    Doudna, J.A.3
  • 21
    • 78149355812 scopus 로고    scopus 로고
    • NUPACK: Analysis and design of nucleic acid systems
    • Zadeh, J. N. et al. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170-173 (2011).
    • (2011) J. Comput. Chem. , vol.32 , pp. 170-173
    • Zadeh, J.N.1
  • 22
    • 54249113318 scopus 로고    scopus 로고
    • Higher-order cellular information processing with synthetic RNA devices
    • Win, M. N. & Smolke, C. D. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-460 (2008).
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 23
    • 35448990907 scopus 로고    scopus 로고
    • A modular and extensible RNA-based generegulatory platform for engineering cellular function
    • Win, M. N. & Smolke, C. D. A modular and extensible RNA-based generegulatory platform for engineering cellular function. Proc. Natl Acad. Sci. USA 104, 14283-14288 (2007).
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 14283-14288
    • Win, M.N.1    Smolke, C.D.2
  • 24
    • 77952330657 scopus 로고    scopus 로고
    • A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression
    • Auslander, S., Ketzer, P. & Hartig, J. S. A ligand-dependent hammerhead ribozyme switch for controlling mammalian gene expression. Mol. Biosyst. 6, 807-814 (2010).
    • (2010) Mol. Biosyst. , vol.6 , pp. 807-814
    • Auslander, S.1    Ketzer, P.2    Hartig, J.S.3
  • 25
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • Tuerk, C. & Gold, L. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510 (1990).
    • (1990) Science , vol.249 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 26
    • 0025074907 scopus 로고
    • In vitro selection of RNA molecules that bind specific ligands
    • Ellington, A. D. & Szostak, J. W. In vitro selection of RNA molecules that bind specific ligands. Nature 346, 818-822 (1990).
    • (1990) Nature , vol.346 , pp. 818-822
    • Ellington, A.D.1    Szostak, J.W.2
  • 27
    • 41949098095 scopus 로고    scopus 로고
    • Improved aptazyme design and in vivo screening enable riboswitching in bacteria
    • Wieland, M. & Hartig, J. S. Improved aptazyme design and in vivo screening enable riboswitching in bacteria. Angew. Chem. 47, 2604-2607 (2008).
    • (2008) Angew. Chem. , vol.47 , pp. 2604-2607
    • Wieland, M.1    Hartig, J.S.2
  • 28
    • 84860489398 scopus 로고    scopus 로고
    • Engineering of ribozyme-based riboswitches for mammalian cells
    • Wieland, M., Auslander, D. & Fussenegger, M. Engineering of ribozyme-based riboswitches for mammalian cells. Methods 56, 351-357 (2012).
    • (2012) Methods , vol.56 , pp. 351-357
    • Wieland, M.1    Auslander, D.2    Fussenegger, M.3
  • 29
    • 84991662130 scopus 로고    scopus 로고
    • Directing cellular information flow via CRISPR signal conductors
    • Liu, Y. et al. Directing cellular information flow via CRISPR signal conductors. Nat. Methods 13, 938-944 (2016).
    • (2016) Nat. Methods , vol.13 , pp. 938-944
    • Liu, Y.1
  • 30
    • 84902096048 scopus 로고    scopus 로고
    • Development and applications of CRISPRCas9 for genome engineering
    • Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPRCas9 for genome engineering. Cell 157, 1262-1278 (2014).
    • (2014) Cell , vol.157 , pp. 1262-1278
    • Hsu, P.D.1    Lander, E.S.2    Zhang, F.3
  • 31
    • 84952639685 scopus 로고    scopus 로고
    • Beyond editing: Repurposing CRISPRCas9 for precision genome regulation and interrogation
    • Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPRCas9 for precision genome regulation and interrogation. Nat. Rev. Mol. Cell Biol. 17, 5-15 (2016).
    • (2016) Nat. Rev. Mol. Cell Biol. , vol.17 , pp. 5-15
    • Dominguez, A.A.1    Lim, W.A.2    Qi, L.S.3
  • 32
    • 84971006562 scopus 로고    scopus 로고
    • Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage
    • Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420-424 (2016).
    • (2016) Nature , vol.533 , pp. 420-424
    • Komor, A.C.1    Kim, Y.B.2    Packer, M.S.3    Zuris, J.A.4    Liu, D.R.5
  • 33
    • 84894063115 scopus 로고    scopus 로고
    • Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system
    • Chen, B. et al. Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system. Cell 155, 1479-1491 (2013).
    • (2013) Cell , vol.155 , pp. 1479-1491
    • Chen, B.1
  • 34
    • 84884160273 scopus 로고    scopus 로고
    • CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
    • Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838 (2013).
    • (2013) Nat. Biotechnol. , vol.31 , pp. 833-838
    • Mali, P.1
  • 35
    • 84920992414 scopus 로고    scopus 로고
    • Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds
    • Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350 (2015).
    • (2015) Cell , vol.160 , pp. 339-350
    • Zalatan, J.G.1
  • 36
    • 84974576984 scopus 로고    scopus 로고
    • Whole organism lineage tracing by combinatorial and cumulative genome editing
    • McKenna, A. et al. Whole organism lineage tracing by combinatorial and cumulative genome editing. Science 353, aaf7907 (2016).
    • (2016) Science , vol.353 , pp. aaf7907
    • McKenna, A.1
  • 37
    • 77952944052 scopus 로고    scopus 로고
    • Designing customized cell signalling circuits
    • Lim, W. A. Designing customized cell signalling circuits. Nat. Rev. Mol. Cell Biol. 11, 393-403 (2010).
    • (2010) Nat. Rev. Mol. Cell Biol. , vol.11 , pp. 393-403
    • Lim, W.A.1
  • 38
    • 84887010498 scopus 로고    scopus 로고
    • Genome engineering using the CRISPR-Cas9 system
    • Ran, F. A. et al. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8, 2281-2308 (2013).
    • (2013) Nat. Protoc. , vol.8 , pp. 2281-2308
    • Ran, F.A.1
  • 39
    • 84929574689 scopus 로고    scopus 로고
    • Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S
    • Klauser, B., Atanasov, J., Siewert, L. K. & Hartig, J. S. Ribozyme-based aminoglycoside switches of gene expression engineered by genetic selection in S. cerevisiae. ACS Synth. Biol. 4, 516-525 (2015).
    • (2015) Cerevisiae. ACS Synth. Biol. , vol.4 , pp. 516-525
    • Klauser, B.1    Atanasov, J.2    Siewert, L.K.3    Hartig, J.S.4
  • 40
    • 33745912405 scopus 로고    scopus 로고
    • A time-and cost-efficient system for high-level protein production in mammalian cells
    • Aricescu, A. R., Lu, W. & Jones, E. Y. A time-and cost-efficient system for high-level protein production in mammalian cells. Acta Crystallogr. D Biol. Crystallogr. 62, 1243-1250 (2006).
    • (2006) Acta Crystallogr. D Biol. Crystallogr. , vol.62 , pp. 1243-1250
    • Aricescu, A.R.1    Lu, W.2    Jones, E.Y.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.