Directing cellular information flow via CRISPR signal conductors

Nature Methods

Volumn 13, Issue 11, 2016, Pages 938-944

  Liu, Yuchen ^a   Zhan, Yonghao ^a   Chen, Zhicong ^a   He, Anbang ^a   Li, Jianfa ^a   Wu, Hanwei ^a   Liu, Li ^a   Zhuang, Chengle ^a   Lin, Junhao ^a   Guo, Xiaoqiang ^a   Zhang, Qiaoxia ^a   Huang, Weiren ^a   Cai, Zhiming ^a  

^a THE FIRST AFFILIATED HOSPITAL OF SHENZHEN UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN BCL 2; PROTEIN P53; GUIDE RNA; VASCULOTROPIN A; VEGFA PROTEIN, HUMAN;

ARTICLE; ARTIFICIAL NEURAL NETWORK; CANCER CELL; CELL FATE; CELL FUNCTION; CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC REPEAT; CONDUCTOR; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; DNA SEQUENCE; GENE ACTIVATION; GENE CONTROL; GENE EXPRESSION; GENE REPRESSION; GENETIC TRANSCRIPTION; HUMAN; HUMAN CELL; NUCLEAR REPROGRAMMING; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN EXPRESSION; SIGNAL CONDUCTOR; SIGNAL TRANSDUCTION; TUMOR SUPPRESSOR GENE; ANIMAL; APOPTOSIS; CELL MOTION; CELL PROLIFERATION; CRISPR CAS SYSTEM; DRUG EFFECTS; EXPERIMENTAL NEOPLASM; GENE REGULATORY NETWORK; GENETICS; HEK293 CELL LINE; METABOLISM; NUDE MOUSE; PLASMID; REAL TIME POLYMERASE CHAIN REACTION; SURFACE PLASMON RESONANCE; TRANSCRIPTION INITIATION; TUMOR CELL LINE;

ANIMALS; APOPTOSIS; CELL LINE, TUMOR; CELL MOVEMENT; CELL PROLIFERATION; CELLULAR REPROGRAMMING; CRISPR-CAS SYSTEMS; GENE REGULATORY NETWORKS; HEK293 CELLS; HUMANS; MICE, NUDE; NEOPLASMS, EXPERIMENTAL; PLASMIDS; REAL-TIME POLYMERASE CHAIN REACTION; RNA, GUIDE; SIGNAL TRANSDUCTION; SURFACE PLASMON RESONANCE; TRANSCRIPTIONAL ACTIVATION; VASCULAR ENDOTHELIAL GROWTH FACTOR A;

EID: 84991662130     PISSN: 15487091     EISSN: 15487105     Source Type: Journal    
DOI: 10.1038/nmeth.3994     Document Type: Article

References (41)

1. Scott, J.D., & Pawson, T. Cell signaling in space and time: where proteins come together and when they're apart. Science 326, 1220-1224 (2009).
2. Riento, K., & Ridley, A.J. Rocks: multifunctional kinases in cell behaviour. Nat. Rev. Mol. Cell Biol. 4, 446-456 (2003).
3. Bhattacharyya, R.P., Reményi, A., Yeh, B.J., & Lim, W.A. Domains, motifs, and scaffolds: the role of modular interactions in the evolution and wiring of cell signaling circuits. Annu. Rev. Biochem. 75, 655-680 (2006).
4. Slusarczyk, A.L., Lin, A., & Weiss, R. Foundations for the design and implementation of synthetic genetic circuits. Nat. Rev. Genet. 13, 406-420 (2012).
5. Youk, H., & Lim, W.A. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science 343, 1242782 (2014).
6. Townshend, B., Kennedy, A.B., Xiang, J.S., & Smolke, C.D. High-Throughput cellular RNA device engineering. Nat. Methods 12, 989-994 (2015).
7. Chau, A.H., Walter, J.M., Gerardin, J., Tang, C., & Lim, W.A. Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151, 320-332 (2012).
8. Galloway, K.E., Franco, E., & Smolke, C.D. Dynamically reshaping signaling networks to program cell fate via genetic controllers. Science 341, 1235005 (2013).
9. Hsu, P.D., Lander, E.S., & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014).
10. Qi, L.S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183 (2013).
11. Maeder, M.L. et al. CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10, 977-979 (2013).
12. Mali, P. et al. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31, 833-838 (2013).
13. Zalatan, J.G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350 (2015).
14. Polstein, L.R., & Gersbach, C.A. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 11, 198-200 (2015).
15. Nihongaki, Y., Yamamoto, S., Kawano, F., Suzuki, H., & Sato, M. CRISPR-Cas9-based photoactivatable transcription system. Chem. Biol. 22, 169-174 (2015).
16. Boerneke, M.A., & Hermann, T. Ligand-responsive RNA mechanical switches. RNA Biol. 12, 780-786 (2015).
17. Bayer, T.S., & Smolke, C.D. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol. 23, 337-343 (2005).
18. Culler, S.J., Hoff, K.G., & Smolke, C.D. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330, 1251-1255 (2010).
19. Moon, T.S., Lou, C., Tamsir, A., Stanton, B.C., & Voigt, C.A. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249-253 (2012).
20. Green, C. Restore Wild-Type Functions to P53 Mutants Using an RNA-Based Combinatorial Approach. Report No. DAMD17-97-1-7036 (SRI International, 2000).
21. Zhao, X. et al. An RNA aptamer that interferes with the DNA binding of the HSF transcription activator. Nucleic Acids Res. 34, 3755-3761 (2006).
22. Jian, Y. et al. RNA aptamers interfering with nucleophosmin oligomerization induce apoptosis of cancer cells. Oncogene 28, 4201-4211 (2009).
23. Tsui, K.H., Cheng, A.J., Chang, Pe., Pan, T.L., & Yung, B.Y. Association of nucleophosmin/B23 mRNA expression with clinical outcome in patients with bladder carcinoma. Urology 64, 839-844 (2004).
24. Kaur, J., & Tikoo, K. Ets1 identified as a novel molecular target of RNA aptamer selected against metastatic cells for targeted delivery of nano-formulation. Oncogene 34, 5216-5228 (2015).
25. Xu, W., & Ellington, A.D. Anti-peptide aptamers recognize amino acid sequence and bind a protein epitope. Proc. Natl. Acad. Sci. USA 93, 7475-7480 (1996).
26. Lee, Y.J., & Lee, S.W. Regression of hepatocarcinoma cells using RNA aptamer specific to alpha-fetoprotein. Biochem. Biophys. Res. Commun. 417, 521-527 (2012).
27. Luo, X., Budihardjo, I., Zou, H., Slaughter, C., & Wang, X. Bid, a Bcl2 interacting protein, mediates cytochrome c release from mitochondria in response to activation of cell surface death receptors. Cell 94, 481-490 (1998).
28. Beisel, C.L., Bayer, T.S., Hoff, K.G., & Smolke, C.D. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol. Syst. Biol. 4, 224 (2008).
29. An, C.I., Trinh, V.B., & Yokobayashi, Y. Artificial control of gene expression in mammalian cells by modulating RNA interference through aptamer-small molecule interaction. RNA 12, 710-716 (2006).
30. Wittmann, A., & Suess, B. Engineered riboswitches: expanding researchers toolbox with synthetic RNA regulators. FEBS Lett. 586, 2076-2083 (2012).
31. Winkler, W., Nahvi, A., & Breaker, R.R. Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression. Nature 419, 952-956 (2002).
32. Yen, L. et al. Exogenous control of mammalian gene expression through modulation of RNA self-cleavage. Nature 431, 471-476 (2004).
33. Chen, Y.Y., Jensen, M.C., & Smolke, C.D. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA 107, 8531-8536 (2010).
34. Shechner, D.M., Hacisuleyman, E., Younger, S.T., & Rinn, J.L. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat. Methods 12, 664-670 (2015).
35. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949 (2014).
36. Fu, Y., Sander, J.D., Reyon, D., Cascio, V.M., & Joung, J.K. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279-284 (2014).
37. Doench, J.G. et al. Optimized sgRNA design to maximize activity and minimize off-Target effects of CRISPR-Cas9. Nat. Biotechnol. 34, 184-191 (2016).
38. Slaymaker, I.M. et al. Rationally engineered Cas9 nucleases with improved specificity. Science 351, 84-88 (2016).
39. Thakore, P.I. et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12, 1143-1149 (2015).
40. Hilton, I.B. et al. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33, 510-517 (2015).
41. Gilbert, L.A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647-661 (2014).