Multi-input CRISPR/Cas genetic circuits that interface host regulatory networks

Molecular Systems Biology

Volumn 10, Issue 11, 2014, Pages

  Nielsen, Alec Ak ^a   Voigt, Christopher A ^a  

^a USA   (United States)

Author keywords

CRISPR; genetic compiler; synthetic biology; TALE; TetR homologue

Indexed keywords

GUIDE RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MALT; UNCLASSIFIED DRUG; UNTRANSLATED RNA; ESCHERICHIA COLI PROTEIN;

ARTICLE; BASE PAIRING; CRISPR CAS SYSTEM; DNA RNA HYBRIDIZATION; DNA SEQUENCE; ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI K 12; FLOW CYTOMETRY; GENE INTERACTION; GENE LOCUS; GENE REGULATORY NETWORK; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL; PROMOTER REGION; REPRESSOR GENE; RNA PROCESSING; SIGNAL PROCESSING; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; BIOLOGICAL MODEL; ESCHERICHIA COLI; GENETICS;

ESCHERICHIA COLI;

BASE PAIRING; CRISPR-CAS SYSTEMS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE REGULATORY NETWORKS; MODELS, BIOLOGICAL;

EID: 84934936070     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20145735     Document Type: Article

References (62)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410
2. Beerli RR, Barbas CF, (2002) Engineering polydactyl zinc-finger transcription factors. Nat Biotechnol 20: 135-141
3. Bikard D, Jiang W, Samai P, Hochschild A, Zhang F, Marraffini LA, (2013) Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41: 7429-7437
4. Blattner FR, Plunkett G, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y, (1997) The complete genome sequence of Escherichia coli K-12. Science 277: 1453-1462
5. Boos W, Böhm A, (2000) Learning new tricks from an old dog: MalT of the Escherichia coli maltose system is part of a complex regulatory network. Trends Genet 16: 404-409
6. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S, (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34: 5402-5415
7. Campbell RE, Tour O, Palmer AE, Steinbach PA, Baird GS, Zacharias DA, Tsien RY, (2002) A monomeric red fluorescent protein. Proc Natl Acad Sci USA 99: 7877-7882
8. Chen Y-J, Liu P, Nielsen AAK, Brophy JAN, Clancy K, Peterson T, Voigt CA, (2013) Characterization of 582 natural and synthetic terminators and quantification of their design constraints. Nat Methods 10: 659-664
9. Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F, (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819-823
10. Cormack BP, Valdivia RH, Falkow S, (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173: 33-38
11. Cradick TJ, Fine EJ, Antico CJ, Bao G, (2013) CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity. Nucleic Acids Res 41: 9584-9592
12. Durfee T, Nelson R, Baldwin S, Plunkett G, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csörg B, Põsfai G, Weinstock GM, Blattner FR, (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol 190: 2597-2606
13. Engler C, Gruetzner R, Kandzia R, Marillonnet S, (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS ONE 4: e5553
14. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM, (2013) Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat Methods 10: 1116-1121
15. Farzadfard F, Perli SD, Lu TK, (2013) Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth Biol 2: 604-613
16. Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD, (2013) High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31: 822-826
17. Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK, (2014) Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat Biotechnol 32: 279-284
18. Gao Y, Zhao Y, (2014) Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J Integr Plant Biol 56: 343-349
19. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA, Torres SE, Stern-Ginossar N, Brandman O, Whitehead EH, Doudna JA, Lim WA, Weissman JS, Qi LS, (2013) CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154: 442-451
20. Guilinger JP, Thompson DB, Liu DR, (2014) Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification. Nat Biotechnol 32: 577-582
21. Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F, (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol 31: 827-832
22. Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA, (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31: 233-239
23. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E, (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816-821
24. Kang Z, Wang X, Li Y, Wang Q, Qi Q, (2012) Small RNA RyhB as a potential tool used for metabolic engineering in Escherichia coli. Biotechnol Lett 34: 527-531
25. Katz RH, Boriello G, (2004) Contemporary Logic Design
26. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R, (2014) CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat Methods 11: 723-726
27. Kimelman A, Levy A, Sberro H, Kidron S, Leavitt A, Amitai G, Yoder-Himes DR, Wurtzel O, Zhu Y, Rubin EM, Sorek R, (2012) A vast collection of microbial genes that are toxic to bacteria. Genome Res 22: 802-809
28. Kosuri S, Goodman DB, Cambray G, Mutalik VK, Gao Y, Arkin AP, Endy D, Church GM, (2013) Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc Natl Acad Sci USA 110: 14024-14029
29. Kuscu C, Arslan S, Singh R, Thorpe J, Adli M, (2014) Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease. Nat Biotechnol 32: 677-683
30. Larson MH, Gilbert LA, Wang X, Lim WA, Weissman JS, Qi LS, (2013) CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat Protoc 8: 2180-2196
31. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM, (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol 31: 833-838
32. Man S, Cheng R, Miao C, Gong Q, Gu Y, Lu X, Han F, Yu W, (2011) Artificial trans-encoded small non-coding RNAs specifically silence the selected gene expression in bacteria. Nucleic Acids Res 39: e50.
33. Marraffini LA, Sontheimer EJ, (2010) CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea. Nat Rev Genet 11: 181-190
34. Miller JC, Holmes MC, Wang J, Guschin DY, Lee Y-L, Rupniewski I, Beausejour CM, Waite AJ, Wang NS, Kim KA, Gregory PD, Pabo CO, Rebar EJ, (2007) An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25: 778-785
35. Miller JC, Tan S, Qiao G, Barlow KA, Wang J, Xia DF, Meng X, Paschon DE, Leung E, Hinkley SJ, Dulay GP, Hua KL, Ankoudinova I, Cost GJ, Urnov FD, Zhang HS, Holmes MC, Zhang L, Gregory PD, Rebar EJ, (2011) A TALE nuclease architecture for efficient genome editing. Nat Biotechnol 29: 143-148
36. Moon TS, Lou C, Tamsir A, Stanton BC, Voigt CA, (2012) Genetic programs constructed from layered logic gates in single cells. Nature 491: 249-253
37. Morbitzer R, Römer P, Boch J, Lahaye T, (2010) Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors. Proc Natl Acad Sci USA 107: 21617-21622
38. Na D, Yoo SM, Chung H, Park H, Park JH, Lee SY, (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 31: 170-174
39. Nielsen AA, Segall-Shapiro TH, Voigt CA, (2013) Advances in genetic circuit design: novel biochemistries, deep part mining, and precision gene expression. Curr Opin Chem Biol 17: 878-892
40. Nielsen J, Fussenegger M, Keasling J, Lee SY, Liao JC, Prather K, Palsson B, (2014) Engineering synergy in biotechnology. Nat Chem Biol 10: 319-322
41. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK, (2014) Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol Cell 54: 698-710
42. Pattanayak V, Lin S, Guilinger JP, Ma E, Doudna JA, Liu DR, (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol 31: 839-843
43. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA, (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 1173-1183
44. Qi LS, Arkin AP, (2014) A versatile framework for microbial engineering using synthetic non-coding RNAs. Nat Rev Microbiol 12: 341-354
45. Ran FA, Hsu PD, Lin C-Y, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F, (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154: 1380-1389
46. Rhodius VA, Segall-Shapiro TH, Sharon BD, Ghodasara A, Orlova E, Tabakh H, Burkhardt DH, Clancy K, Peterson TC, Gross CA, Voigt CA, (2013) Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol Syst Biol 9: 702
47. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F, (2013) Genome-scale CRISPR-Cas9 knockout screening in human cells. Science 343: 84-87
48. Sharma V, Yamamura A, Yokobayashi Y, (2012) Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth Biol 1: 6-13
49. Sharma V, Sakai Y, Smythe KA, Yokobayashi Y, (2013) Knockdown of recA gene expression by artificial small RNAs in Escherichia coli. Biochem Biophys Res Commun 430: 256-259
50. Sleight SC, Bartley BA, Lieviant JA, Sauro HM, (2010) Designing and engineering evolutionary robust genetic circuits. J Biol Eng 4: 1-20
51. Sleight SC, Sauro HM, (2013) Visualization of evolutionary stability dynamics and competitive fitness of Escherichia coli engineered with randomized multigene circuits. ACS Synth Biol 2: 519-528
52. Stanton BC, Nielsen AAK, Tamsir A, Clancy K, Peterson T, Voigt CA, (2014) Genomic mining of prokaryotic repressors for orthogonal logic gates. Nat Chem Biol 10: 99-105
53. Tamsir A, Tabor JJ, Voigt CA, (2011) Robust multicellular computing using genetically encoded NOR gates and chemical/wires/'. Nature 469: 212-215
54. Tchetina E, Newman EB, (1995) Identification of Lrp-regulated genes by inverse PCR and sequencing: regulation of two mal operons of Escherichia coli by leucine-responsive regulatory protein. J Bacteriol 177: 2679-2683
55. Thirion JP, Hofnung M, (1972) On some genetic aspects of phage A resistance in E. coli K12. Genetics 71: 207-216
56. Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK, (2014) Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing. Nat Biotechnol 32: 569-576
57. Tummala SB, Welker NE, Papoutsakis ET, (2003) Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J Bacteriol 185: 1923-1934
58. Wang HH, Isaacs FJ, Carr PA, Sun ZZ, Xu G, Forest CR, Church GM, (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460: 894-898
59. Wang T, Wei JJ, Sabatini DM, Lander ES, (2013) Genetic screens in human cells using the CRISPR/Cas9 system. Science 343: 80-84
60. Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA, (2014) Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nat Biotechnol 32: 670-676
61. Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P, (2011) Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat Biotechnol 29: 149-153
62. Zhou Y, Zhu S, Cai C, Yuan P, Li C, Huang Y, Wei W, (2014) High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells. Nature 509: 487-491