The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution. These tools have been critical for the expansion of synthetic biology techniques from prokaryotic and lower eukaryotic hosts to mammalian systems. Recent progress in the development of genome and epigenome editing tools and in the engineering of designer cells with programmable genetic circuits is expanding approaches to prevent, diagnose, and treat disease and to establish personalized theranostic strategies for next-generation medicines. This review summarizes the development of these enabling technologies and their application to transforming mammalian synthetic biology into a distinct field in research and medicine.


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Literature Cited

  1. Benner SA, Sismour AM. 2.  2005. Synthetic biology. Nat. Rev. Genet. 6:533–43 [Google Scholar]
  2. Elowitz MB, Leibler S. 3.  2000. A synthetic oscillatory network of transcriptional regulators. Nature 403:335–38 [Google Scholar]
  3. Gardner TS, Cantor CR, Collins JJ. 4.  2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403:339–42 [Google Scholar]
  4. Hasty J, McMillen D, Collins JJ. 5.  2002. Engineered gene circuits. Nature 420:224–30 [Google Scholar]
  5. Khalil AS, Collins JJ. 6.  2010. Synthetic biology: Applications come of age. Nat. Rev. Genet. 11:367–79 [Google Scholar]
  6. Purnick PE, Weiss R. 7.  2009. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10:410–22 [Google Scholar]
  7. Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F. 8.  2013. Genome engineering using the CRISPR-Cas9 system. Nat. Protoc. 8:2281–308 [Google Scholar]
  8. Keung AJ, Joung JK, Khalil AS, Collins JJ. 9.  2015. Chromatin regulation at the frontier of synthetic biology. Nat. Rev. Genet. 16:159–71 [Google Scholar]
  9. Hilton IB, Gersbach CA. 10.  2015. Enabling functional genomics with genome engineering. Genome Res 25:1442–55 [Google Scholar]
  10. Thakore PI, Black JB, Hilton IB, Gersbach CA. 11.  2016. Editing the epigenome: technologies for programmable transcription and epigenetic modulation. Nat. Methods 13:127–37 [Google Scholar]
  11. Nissim L, Perli SD, Fridkin A, Perez-Pinera P, Lu TK. 1.  2014. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Mol. Cell 54:698–710 [Google Scholar]
  12. Li Y, Jiang Y, Chen H, Liao W, Li Z. 12.  et al. 2015. Modular construction of mammalian gene circuits using TALE transcriptional repressors. Nat. Chem. Biol. 11:207–13 [Google Scholar]
  13. Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM. 13.  et al. 2016. Engineering customized cell sensing and response behaviors using synthetic Notch receptors. Cell 164:780–91 [Google Scholar]
  14. Guye P, Ebrahimkhani MR, Kipniss N, Velazquez JJ, Schoenfeld E. 14.  et al. 2016. Genetically engineering self-organization of human pluripotent stem cells into a liver bud–like tissue using Gata6. Nat. Commun. 7:10243 [Google Scholar]
  15. Bernstein BE, Meissner A, Lander ES. 15.  2007. The mammalian epigenome. Cell 128:669–81 [Google Scholar]
  16. 16. ENCODE Proj. Consort 2012. An integrated encyclopedia of DNA elements in the human genome. Nature 489:57–74 [Google Scholar]
  17. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A. 17.  et al. (Roadmap Epigenom. Consort.) 2015. Integrative analysis of 111 reference human epigenomes. Nature 518:317–30 [Google Scholar]
  18. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A. 18.  et al. 2010. The NIH Roadmap Epigenomics Mapping Consortium. Nat. Biotechnol. 28:1045–48 [Google Scholar]
  19. Hawkins RD, Hon GC, Ren B. 19.  2010. Next-generation genomics: an integrative approach. Nat. Rev. Genet. 11:476–86 [Google Scholar]
  20. Ernst J, Kellis M. 20.  2012. ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9:215–16 [Google Scholar]
  21. Tian J, Gong H, Sheng N, Zhou X, Gulari E. 21.  et al. 2004. Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432:1050–54 [Google Scholar]
  22. Kosuri S, Church GM. 22.  2014. Large-scale de novo DNA synthesis: technologies and applications. Nat. Methods 11:499–507 [Google Scholar]
  23. Engler C, Gruetzner R, Kandzia R, Marillonnet S. 23.  2009. Golden gate shuffling: a one-pot DNA shuffling method based on type IIS restriction enzymes. PLOS ONE 4:e5553 [Google Scholar]
  24. Gibson DG, Young L, Chuang RY, Venter JC, 3rd Hutchison CA, Smith HO. 24.  2009. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6:343–45 [Google Scholar]
  25. Guye P, Li Y, Wroblewska L, Duportet X, Weiss R. 25.  2013. Rapid, modular and reliable construction of complex mammalian gene circuits. Nucleic Acids Res 41:e156 [Google Scholar]
  26. Patwardhan RP, Lee C, Litvin O, Young DL, Pe'er D, Shendure J. 26.  2009. High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol. 27:1173–75 [Google Scholar]
  27. Arnold CD, Gerlach D, Stelzer C, Boryn LM, Rath M, Stark A. 27.  2013. Genome-wide quantitative enhancer activity maps identified by STARR-seq. Science 339:1074–77 [Google Scholar]
  28. Patwardhan RP, Hiatt JB, Witten DM, Kim MJ, Smith RP. 28.  et al. 2012. Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol. 30:265–70 [Google Scholar]
  29. Melnikov A, Murugan A, Zhang X, Tesileanu T, Wang L. 29.  et al. 2012. Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay. Nat. Biotechnol. 30:271–77 [Google Scholar]
  30. Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A. 30.  et al. 2016. Direct GR binding sites potentiate clusters of TF binding across the human genome. Cell 166:1269–81 [Google Scholar]
  31. Murtha M, Tokcaer-Keskin Z, Tang Z, Strino F, Chen X. 31.  et al. 2014. FIREWACh: high-throughput functional detection of transcriptional regulatory modules in mammalian cells. Nat. Methods 11:559–65 [Google Scholar]
  32. Akhtar W, de Jong J, Pindyurin AV, Pagie L, Meuleman W. 32.  et al. 2013. Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154:914–27 [Google Scholar]
  33. Gaj T, Gersbach CA, 3rd Barbas CF. 33.  2013. ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31:397–405 [Google Scholar]
  34. Kim YG, Cha J, Chandrasegaran S. 34.  1996. Hybrid restriction enzymes: zinc finger fusions to Fok I cleavage domain. PNAS 93:1156–60 [Google Scholar]
  35. Smith J, Bibikova M, Whitby FG, Reddy AR, Chandrasegaran S, Carroll D. 35.  2000. Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28:3361–69 [Google Scholar]
  36. Christian M, Cermak T, Doyle EL, Schmidt C, Zhang F. 36.  et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–61 [Google Scholar]
  37. Miller JC, Tan S, Qiao G, Barlow KA, Wang J. 37.  et al. 2011. A TALE nuclease architecture for efficient genome editing. Nat. Biotechnol. 29:143–48 [Google Scholar]
  38. Cong L, Ran FA, Cox D, Lin S, Barretto R. 38.  et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–23 [Google Scholar]
  39. Mali P, Yang L, Esvelt KM, Aach J, Guell M. 39.  et al. 2013. RNA-guided human genome engineering via Cas9. Science 339:823–26 [Google Scholar]
  40. Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna JA, Charpentier E. 40.  2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–21 [Google Scholar]
  41. Maeder ML, Gersbach CA. 41.  2016. Genome-editing technologies for gene and cell therapy. Mol. Ther. 24:430–46 [Google Scholar]
  42. Shalem O, Sanjana NE, Zhang F. 42.  2015. High-throughput functional genomics using CRISPR–Cas9. Nat. Rev. Genet. 16:299–311 [Google Scholar]
  43. Beerli RR, Segal DJ, Dreier B, 3rd Barbas CF. 43.  1998. Toward controlling gene expression at will: specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks. PNAS 95:14628–33 [Google Scholar]
  44. Liu Q, Segal DJ, Ghiara JB, 3rd Barbas CF. 44.  1997. Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. PNAS 94:5525–30 [Google Scholar]
  45. Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS. 45.  et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–83 [Google Scholar]
  46. Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P. 46.  2011. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29:149–53 [Google Scholar]
  47. Gilbert LA, Larson MH, Morsut L, Liu Z, Brar GA. 47.  et al. 2013. CRISPR-mediated modular RNA–guided regulation of transcription in eukaryotes. Cell 154:442–51 [Google Scholar]
  48. Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK. 48.  2013. CRISPR RNA-guided activation of endogenous human genes. Nat. Methods 10:977–79 [Google Scholar]
  49. Perez-Pinera P, Kocak DD, Vockley CM, Adler A, Kabadi AM. 49.  et al. 2013. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat. Methods 10:973–76 [Google Scholar]
  50. Mali P, Aach J, Stranges PB, Esvelt KM, Moosburner M. 50.  et al. 2013. CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat. Biotechnol. 31:833–38 [Google Scholar]
  51. Brown M, Figge J, Hansen U, Wright C, Jeang KT. 51.  et al. 1987. lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells. Cell 49:603–12 [Google Scholar]
  52. Gossen M, Bujard H. 52.  1992. Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. PNAS 89:5547–51 [Google Scholar]
  53. Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y. 53.  et al. 2013. Robust, synergistic regulation of human gene expression using TALE activators. Nat. Methods 10:243–45 [Google Scholar]
  54. Perez-Pinera P, Ousterout DG, Brunger JM, Farin AM, Glass KA. 54.  et al. 2013. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat. Methods 10:239–42 [Google Scholar]
  55. Gilbert LA, Horlbeck MA, Adamson B, Villalta JE, Chen Y. 55.  et al. 2014. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159:647–61 [Google Scholar]
  56. Konermann S, Brigham MD, Trevino AE, Joung J, Abudayyeh OO. 56.  et al. 2015. Genome-scale transcriptional activation by an engineered CRISPR–Cas9 complex. Nature 517:583–88 [Google Scholar]
  57. Hilton IB, D'Ippolito AM, Vockley CM, Thakore PI, Crawford GE. 57.  et al. 2015. Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers. Nat. Biotechnol. 33:510–17 [Google Scholar]
  58. Deng W, Rupon JW, Krivega I, Breda L, Motta I. 58.  et al. 2014. Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158:849–60 [Google Scholar]
  59. Polstein L, Perez-Pinera P, Kocak D, Vockley C, Bledsoe P. 59.  et al. 2015. Genome-wide specificity of DNA-binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators. Genome Res 25:1158–69 [Google Scholar]
  60. Thakore PI, D'Ippolito AM, Song L, Safi A, Shivakumar NK. 60.  et al. 2015. Highly specific epigenome editing by CRISPR–Cas9 repressors for silencing of distal regulatory elements. Nat. Methods 12:1143–49 [Google Scholar]
  61. Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC. 61.  et al. 2012. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150:647–58 [Google Scholar]
  62. Esvelt KM, Mali P, Braff JL, Moosburner M, Yaung SJ, Church GM. 62.  2013. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing. Nat. Methods 10:1116–21 [Google Scholar]
  63. Zalatan JG, Lee ME, Almeida R, Gilbert LA, Whitehead EH. 63.  et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160:339–50 [Google Scholar]
  64. Kleinstiver BP, Prew MS, Tsai SQ, Topkar VV, Nguyen NT. 64.  et al. 2015. Engineered CRISPR–Cas9 nucleases with altered PAM specificities. Nature 523:481–85 [Google Scholar]
  65. Dahlman JE, Abudayyeh OO, Joung J, Gootenberg JS, Zhang F, Konermann S. 65.  2015. Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease. Nat. Biotechnol. 33:1159–61 [Google Scholar]
  66. Kiani S, Chavez A, Tuttle M, Hall RN, Chari R. 66.  et al. 2015. Cas9 gRNA engineering for genome editing, activation and repression. Nat. Methods 12:1051–54 [Google Scholar]
  67. Shechner DM, Hacisuleyman E, Younger ST, Rinn JL. 67.  2015. Multiplexable, locus-specific targeting of long RNAs with CRISPR display. Nat. Methods 12:664–70 [Google Scholar]
  68. Polstein LR, Gersbach CA. 68.  2012. Light-inducible spatiotemporal control of gene activation by customizable zinc finger transcription factors. J. Am. Chem. Soc. 134:16480–83 [Google Scholar]
  69. Konermann S, Brigham MD, Trevino AE, Hsu PD, Heidenreich M. 69.  et al. 2013. Optical control of mammalian endogenous transcription and epigenetic states. Nature 500:472–76 [Google Scholar]
  70. Polstein LR, Gersbach CA. 70.  2015. A light-inducible CRISPR-Cas9 system for control of endogenous gene activation. Nat. Chem. Biol. 11:198–200 [Google Scholar]
  71. Nihongaki Y, Yamamoto S, Kawano F, Suzuki H, Sato M. 71.  2015. CRISPR-Cas9-based photoactivatable transcription system. Chem. Biol. 22:169–74 [Google Scholar]
  72. Nihongaki Y, Kawano F, Nakajima T, Sato M. 72.  2015. Photoactivatable CRISPR–Cas9 for optogenetic genome editing. Nat. Biotechnol. 33:755–60 [Google Scholar]
  73. Hemphill J, Borchardt EK, Brown K, Asokan A, Deiters A. 73.  2015. Optical control of CRISPR/Cas9 gene editing. J. Am. Chem. Soc. 137:5642–45 [Google Scholar]
  74. Beerli RR, Schopfer U, Dreier B, 3rd Barbas CF. 74.  2000. Chemically regulated zinc finger transcription factors. J. Biol. Chem. 275:32617–27 [Google Scholar]
  75. Li Y, Moore R, Guinn M, Bleris L. 75.  2012. Transcription activator–like effector hybrids for conditional control and rewiring of chromosomal transgene expression. Sci. Rep. 2:897 [Google Scholar]
  76. Mercer AC, Gaj T, Sirk SJ, Lamb BM, 3rd Barbas CF. 76.  2014. Regulation of endogenous human gene expression by ligand-inducible TALE transcription factors. ACS Synth. Biol. 3:723–30 [Google Scholar]
  77. Zetsche B, Volz SE, Zhang F. 77.  2015. A split-Cas9 architecture for inducible genome editing and transcription modulation. Nat. Biotechnol. 33:139–42 [Google Scholar]
  78. Nguyen DP, Miyaoka Y, Gilbert LA, Mayerl SJ, Lee BH. 78.  et al. 2016. Ligand-binding domains of nuclear receptors facilitate tight control of split CRISPR activity. Nat. Commun. 7:12009 [Google Scholar]
  79. Davis KM, Pattanayak V, Thompson DB, Zuris JA, Liu DR. 79.  2015. Small molecule–triggered Cas9 protein with improved genome-editing specificity. Nat. Chem. Biol. 11:316–18 [Google Scholar]
  80. Gao Y, Xiong X, Wong S, Charles EJ, Lim WA, Qi LS. 80.  2016. Complex transcriptional modulation with orthogonal and inducible dCas9 regulators. Nat. Methods 13:1043–49 [Google Scholar]
  81. Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT. 81.  et al. 2016. Profiling of engineering hotspots identifies an allosteric CRISPR–Cas9 switch. Nat. Biotechnol. 34:646–51 [Google Scholar]
  82. Gao Y, Zhao Y. 82.  2014. Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. J. Integr. Plant Biol. 56:343–49 [Google Scholar]
  83. Liu Y, Zhan Y, Chen Z, He A, Li J. 83.  et al. 2016. Directing cellular information flow via CRISPR signal conductors. Nat. Methods 13:938–44 [Google Scholar]
  84. Kearns NA, Pham H, Tabak B, Genga RM, Silverstein NJ. 84.  et al. 2015. Functional annotation of native enhancers with a Cas9–histone demethylase fusion. Nat. Methods 12:401–3 [Google Scholar]
  85. Keung AJ, Bashor CJ, Kiriakov S, Collins JJ, Khalil AS. 85.  2014. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158:110–20 [Google Scholar]
  86. Stolzenburg S, Beltran AS, Swift-Scanlan T, Rivenbark AG, Rashwan R, Blancafort P. 86.  2015. Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer. Oncogene 34:5427–35 [Google Scholar]
  87. Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG. 87.  et al. 2012. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 7:350–60 [Google Scholar]
  88. Kungulovski G, Nunna S, Thomas M, Zanger UM, Reinhardt R, Jeltsch A. 88.  2015. Targeted epigenome editing of an endogenous locus with chromatin modifiers is not stably maintained. Epigenetics Chromatin 8:12 [Google Scholar]
  89. Vojta A, Dobrinic P, Tadic V, Bockor L, Korac P. 89.  et al. 2016. Repurposing the CRISPR–Cas9 system for targeted DNA methylation. Nucleic Acids Res 44:5615–28 [Google Scholar]
  90. Amabile A, Migliara A, Capasso P, Biffi M, Cittaro D. 90.  et al. 2016. Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167:219–32 [Google Scholar]
  91. Auslander S, Auslander D, Muller M, Wieland M, Fussenegger M. 91.  2012. Programmable single-cell mammalian biocomputers. Nature 487:123–27 [Google Scholar]
  92. Kramer BP, Fischer C, Fussenegger M. 92.  2004. Biologic gates enable logical transcription control in mammalian cells. Biotechnol. Bioeng. 87:478–84 [Google Scholar]
  93. Kramer BP, Viretta AU, Daoud-El-Baba M, Aubel D, Weber W, Fussenegger M. 93.  2004. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 22:867–70 [Google Scholar]
  94. Weber W, Stelling J, Rimann M, Keller B, Daoud-El Baba M. 94.  et al. 2007. A synthetic time-delay circuit in mammalian cells and mice. PNAS 104:2643–48 [Google Scholar]
  95. Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M. 95.  2009. A tunable synthetic mammalian oscillator. Nature 457:309–12 [Google Scholar]
  96. Auslander S, Fussenegger M. 96.  2013. From gene switches to mammalian designer cells: present and future prospects. Trends Biotechnol 31:155–68 [Google Scholar]
  97. Lienert F, Torella JP, Chen JH, Norsworthy M, Richardson RR, Silver PA. 97.  2013. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res 41:9967–75 [Google Scholar]
  98. Lohmueller JJ, Armel TZ, Silver PA. 98.  2012. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res 40:5180–87 [Google Scholar]
  99. Gaber R, Lebar T, Majerle A, Ster B, Dobnikar A. 99.  et al. 2014. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat. Chem. Biol. 10:203–8 [Google Scholar]
  100. Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN. 100.  et al. 2014. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat. Methods 11:723–26 [Google Scholar]
  101. Serganov A, Patel DJ. 101.  2007. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nat. Rev. Genet. 8:776–90 [Google Scholar]
  102. Liang JC, Bloom RJ, Smolke CD. 102.  2011. Engineering biological systems with synthetic RNA molecules. Mol. Cell 43:915–26 [Google Scholar]
  103. Tuerk C, Gold L. 103.  1990. Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249:505–10 [Google Scholar]
  104. Bloom RJ, Winkler SM, Smolke CD. 104.  2014. A quantitative framework for the forward design of synthetic miRNA circuits. Nat. Methods 11:1147–53 [Google Scholar]
  105. Townshend B, Kennedy AB, Xiang JS, Smolke CD. 105.  2015. High-throughput cellular RNA device engineering. Nat. Methods 12:989–94 [Google Scholar]
  106. Chang AL, Wolf JJ, Smolke CD. 106.  2012. Synthetic RNA switches as a tool for temporal and spatial control over gene expression. Curr. Opin. Biotechnol. 23:679–88 [Google Scholar]
  107. Chen YY, Jensen MC, Smolke CD. 107.  2010. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. PNAS 107:8531–36 [Google Scholar]
  108. Wei KY, Smolke CD. 108.  2015. Engineering dynamic cell cycle control with synthetic small molecule–responsive RNA devices. J. Biol. Eng. 9:21 [Google Scholar]
  109. Ketzer P, Haas SF, Engelhardt S, Hartig JS, Nettelbeck DM. 109.  2012. Synthetic riboswitches for external regulation of genes transferred by replication-deficient and oncolytic adenoviruses. Nucleic Acids Res 40:e167 [Google Scholar]
  110. Bell CL, Yu D, Smolke CD, Geall AJ, Beard CW, Mason PW. 110.  2015. Control of alphavirus-based gene expression using engineered riboswitches. Virology 483:302–11 [Google Scholar]
  111. Bloom RJ, Winkler SM, Smolke CD. 111.  2015. Synthetic feedback control using an RNAi-based gene-regulatory device. J. Biol. Eng. 9:5 [Google Scholar]
  112. Vogel V, Sheetz M. 112.  2006. Local force and geometry sensing regulate cell functions. Nat. Rev. Mol. Cell Biol. 7:265–75 [Google Scholar]
  113. Seo D, Southard KM, Kim JW, Lee HJ, Farlow J. 113.  et al. 2016. A mechanogenetic toolkit for interrogating cell signaling in space and time. Cell 165:1507–18 [Google Scholar]
  114. Liu Z, Liu Y, Chang Y, Seyf HR, Henry A. 114.  et al. 2016. Nanoscale optomechanical actuators for controlling mechanotransduction in living cells. Nat. Methods 13:143–46 [Google Scholar]
  115. Fan Z, Sun Y, Di C, Tay D, Chen W. 115.  et al. 2013. Acoustic tweezing cytometry for live-cell subcellular modulation of intracellular cytoskeleton contractility. Sci. Rep. 3:2176 [Google Scholar]
  116. Boyden ES, Zhang F, Bamberg E, Nagel G, Deisseroth K. 116.  2005. Millisecond-timescale, genetically targeted optical control of neural activity. Nat. Neurosci. 8:1263–68 [Google Scholar]
  117. Boyden ES. 117.  2015. Optogenetics and the future of neuroscience. Nat. Neurosci. 18:1200–1 [Google Scholar]
  118. Yazawa M, Sadaghiani AM, Hsueh B, Dolmetsch RE. 118.  2009. Induction of protein–protein interactions in live cells using light. Nat. Biotechnol. 27:941–45 [Google Scholar]
  119. Kennedy MJ, Hughes RM, Peteya LA, Schwartz JW, Ehlers MD, Tucker CL. 119.  2010. Rapid blue-light-mediated inductin of protein interactions in living cells. Nat. Methods 7:973–75 [Google Scholar]
  120. Wang X, Chen X, Yang Y. 120.  2012. Spatiotemporal control of gene expression by a light-switchable transgene system. Nat. Methods 9:266–69 [Google Scholar]
  121. Ye H, Daoud-El-Baba M, Peng RW, Fussenegger M. 121.  2011. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332:1565–68 [Google Scholar]
  122. Stanley SA, Sauer J, Kane RS, Dordick JS, Friedman JM. 122.  2015. Remote regulation of glucose homeostasis in mice using genetically encoded nanoparticles. Nat. Med. 21:92–98 [Google Scholar]
  123. Wheeler MA, Smith CJ, Ottolini M, Barker BS, Purohit AM. 123.  et al. 2016. Genetically targeted magnetic control of the nervous system. Nat. Neurosci. 19:756–61 [Google Scholar]
  124. Dong S, Rogan SC, Roth BL. 124.  2010. Directed molecular evolution of DREADDs: a generic approach to creating next-generation RASSLs. Nat. Protoc. 5:561–73 [Google Scholar]
  125. Urban DJ, Roth BL. 125.  2015. DREADDs (designer receptors exclusively activated by designer drugs): chemogenetic tools with therapeutic utility. Annu. Rev. Pharmacol. Toxicol. 55:399–417 [Google Scholar]
  126. Barnea G, Strapps W, Herrada G, Berman Y, Ong J. 126.  et al. 2008. The genetic design of signaling cascades to record receptor activation. PNAS 105:64–69 [Google Scholar]
  127. Schwarz KA, Daringer NM, Dolberg TB, Leonard JN. 127.  2017. Rewiring human cellular input–output using modular extracellular sensors. Nat. Chem. Biol. 13:202–9 [Google Scholar]
  128. Duportet X, Wroblewska L, Guye P, Li Y, Eyquem J. 128.  et al. 2014. A platform for rapid prototyping of synthetic gene networks in mammalian cells. Nucleic Acids Res 42:13440–51 [Google Scholar]
  129. Davidsohn N, Beal J, Kiani S, Adler A, Yaman F. 129.  et al. 2015. Accurate predictions of genetic circuit behavior from part characterization and modular composition. ACS Synth. Biol. 4:673–81 [Google Scholar]
  130. Stanton BC, Siciliano V, Ghodasara A, Wroblewska L, Clancy K. 130.  et al. 2014. Systematic transfer of prokaryotic sensors and circuits to mammalian cells. ACS Synth. Biol. 3:880–91 [Google Scholar]
  131. Slusarczyk AL, Lin A, Weiss R. 131.  2012. Foundations for the design and implementation of synthetic genetic circuits. Nat. Rev. Genet. 13:406–20 [Google Scholar]
  132. Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA. 132.  et al. 2013. Genome-scale CRISPR–Cas9 knockout screening in human cells. Nature 343:84–87 [Google Scholar]
  133. Wang T, Wei JJ, Sabatini DM, Lander ES. 133.  2013. Genetic screens in human cells using the CRISPR/Cas9 system. Science 343:80–84 [Google Scholar]
  134. Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O. 134.  et al. 2013. Locus-specific editing of histone modifications at endogenous enhancers. Nat. Biotechnol. 31:1133–36 [Google Scholar]
  135. Chen S, Sanjana NE, Zheng K, Shalem O, Lee K. 135.  et al. 2015. Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. Cell 160:1246–60 [Google Scholar]
  136. Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A. 136.  et al. 2015. A Genome-wide CRISPR screen in primary immune cells to dissect regulatory networks. Cell 162:675–86 [Google Scholar]
  137. Korkmaz G, Lopes R, Ugalde AP, Nevedomskaya E, Han R. 137.  et al. 2016. Functional genetic screens for enhancer elements in the human genome using CRISPR–Cas9. Nat. Biotechnol. 34:192–98 [Google Scholar]
  138. Rajagopal N, Srinivasan S, Kooshesh K, Guo Y, Edwards MD. 138.  et al. 2016. High-throughput mapping of regulatory DNA. Nat. Biotechnol. 34:167–74 [Google Scholar]
  139. Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE. 139.  et al. 2015. BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. Nature 527:192–97 [Google Scholar]
  140. Fulco CP, Munschauer M, Anyoha R, Munson G, Grossman SR. 140.  et al. 2016. Systematic mapping of functional enhancer–promoter connections with CRISPR interference. Science 354:769–73 [Google Scholar]
  141. Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P. 141.  et al. 2016. High-resolution interrogation of functional elements in the noncoding genome. Science 353:1545–49 [Google Scholar]
  142. Wong AS, Choi GC, Cheng AA, Purcell O, Lu TK. 142.  2015. Massively parallel high-order combinatorial genetics in human cells. Nat. Biotechnol. 33:952–61 [Google Scholar]
  143. Wong AS, Choi GC, Cui CH, Pregernig G, Milani P. 143.  et al. 2016. Multiplexed barcoded CRISPR–Cas9 screening enabled by CombiGEM. PNAS 113:2544–49 [Google Scholar]
  144. Dixit A, Parnas O, Li B, Chen J, Fulco CP. 144.  et al. 2016. Perturb-seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens. Cell 167:1853–66 [Google Scholar]
  145. Jaitin DA, Weiner A, Yofe I, Lara-Astiaso D, Keren-Shaul H. 145.  et al. 2016. Dissecting immune circuits by linking CRISPR-pooled screens with single-cell RNA-seq. Cell 167:1883–96 [Google Scholar]
  146. Chin JW. 146.  2014. Expanding and reprogramming the genetic code of cells and animals. Annu. Rev. Biochem. 83:379–408 [Google Scholar]
  147. Elsässer SJ, Ernst RJ, Walker OS, Chin JW. 147.  2016. Genetic code expansion in stable cell lines enables encoded chromatin modification. Nat. Methods 13:158–64 [Google Scholar]
  148. David Y, Vila-Perello M, Verma S, Muir TW. 148.  2015. Chemical tagging and customizing of cellular chromatin states using ultrafast trans-splicing inteins. Nat. Chem. 7:394–402 [Google Scholar]
  149. Egli D, Birkhoff G, Eggan K. 149.  2008. Mediators of reprogramming: transcription factors and transitions through mitosis. Nat. Rev. Mol. Cell Biol. 9:505–16 [Google Scholar]
  150. Davis RL, Weintraub H, Lassar AB. 150.  1987. Expression of a single transfected cDNA converts fibroblasts to myoblasts. Cell 51:987–1000 [Google Scholar]
  151. Takahashi K, Yamanaka S. 151.  2006. Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126:663–76 [Google Scholar]
  152. Hanna J, Saha K, Pando B, van Zon J, Lengner CJ. 152.  et al. 2009. Direct cell reprogramming is a stochastic process amenable to acceleration. Nature 462:595–601 [Google Scholar]
  153. Hirai H, Tani T, Kikyo N. 153.  2010. Structure and functions of powerful transactivators: VP16, MyoD and FoxA. Int. J. Dev. Biol. 54:1589–96 [Google Scholar]
  154. Wang Y, Chen J, Hu JL, Wei XX, Qin D. 154.  et al. 2011. Reprogramming of mouse and human somatic cells by high-performance engineered factors. EMBO Rep 12:373–78 [Google Scholar]
  155. Zhu G, Li Y, Zhu F, Wang T, Jin W. 155.  et al. 2014. Coordination of engineered factors with TET1/2 promotes early-stage epigenetic modification during somatic cell reprogramming. Stem. Cell Rep. 2:253–61 [Google Scholar]
  156. Kabadi AM, Thakore PI, Vockley CM, Ousterout DG, Gibson TM. 156.  et al. 2015. Enhanced MyoD-induced transdifferentiation to a myogenic lineage by fusion to a potent transactivation domain. ACS Synth. Biol. 4:689–99 [Google Scholar]
  157. Gao X, Yang J, Tsang JC, Ooi J, Wu D, Liu P. 157.  2013. Reprogramming to pluripotency using designer TALE transcription factors targeting enhancers. Stem. Cell Rep. 1:183–97 [Google Scholar]
  158. Chakraborty S, Ji H, Kabadi AM, Gersbach CA, Christoforou N, Leong KW. 158.  2014. A CRISPR/Cas9-based system for reprogramming cell lineage specification. Stem. Cell Rep. 3:940–47 [Google Scholar]
  159. Chavez A, Scheiman J, Vora S, Pruitt BW, Tuttle M. 159.  et al. 2015. Highly efficient Cas9-mediated transcriptional programming. Nat. Methods 12:326–28 [Google Scholar]
  160. Balboa D, Weltner J, Eurola S, Trokovic R, Wartiovaara K, Otonkoski T. 160.  2015. Conditionally stabilized dCas9 activator for controlling gene expression in human cell reprogramming and differentiation. Stem. Cell Rep. 5:448–59 [Google Scholar]
  161. Wei S, Zou Q, Lai S, Zhang Q, Li L. 161.  et al. 2016. Conversion of embryonic stem cells into extraembryonic lineages by CRISPR-mediated activators. Sci. Rep. 6:19648 [Google Scholar]
  162. Black JB, Adler AF, Wang H-G, D'Ippolito AM, Hutchinson HA. 162.  et al. 2016. Targeted epigenetic remodeling of endogenous loci by CRISPR/Cas9-based transcriptional activators directly converts fibroblasts to neuronal cells. Cell Stem Cell 19:406–14 [Google Scholar]
  163. Eguchi A, Wleklinski MJ, Spurgat MC, Heiderscheit EA, Kropornicka AS. 163.  et al. 2016. Reprogramming cell fate with a genome-scale library of artificial transcription factors. PNAS 113:E8257–66 [Google Scholar]
  164. Wapinski OL, Vierbuchen T, Qu K, Lee QY, Chanda S. 164.  et al. 2013. Hierarchical mechanisms for direct reprogramming of fibroblasts to neurons. Cell 155:621–35 [Google Scholar]
  165. Burrill DR, Inniss MC, Boyle PM, Silver PA. 165.  2012. Synthetic memory circuits for tracking human cell fate. Genes Dev 26:1486–97 [Google Scholar]
  166. Saxena P, Heng BC, Bai P, Folcher M, Zulewski H, Fussenegger M. 166.  2016. A programmable synthetic lineage-control network that differentiates human IPSCs into glucose-sensitive insulin-secreting β-like cells. Nat. Commun. 7:11247 [Google Scholar]
  167. Deans TL, Singh A, Gibson M, Elisseeff JH. 167.  2012. Regulating synthetic gene networks in 3D materials. PNAS 109:15217–22 [Google Scholar]
  168. Stranger BE, Stahl EA, Raj T. 168.  2011. Progress and promise of genome-wide association studies for human complex trait genetics. Genetics 187:367–83 [Google Scholar]
  169. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E. 169.  et al. 2012. Systematic localization of common disease-associated variation in regulatory DNA. Science 337:1190–95 [Google Scholar]
  170. Kelly TK, De Carvalho DD, Jones PA. 170.  2010. Epigenetic modifications as therapeutic targets. Nat. Biotechnol. 28:1069–78 [Google Scholar]
  171. Spisak S, Lawrenson K, Fu Y, Csabai I, Cottman RT. 171.  et al. 2015. CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants. Nat. Med. 21:1357–63 [Google Scholar]
  172. Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR. 172.  2016. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–24 [Google Scholar]
  173. Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M. 173.  et al. 2016. Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems. Science 353:aaf8729 [Google Scholar]
  174. Robison AJ, Nestler EJ. 174.  2011. Transcriptional and epigenetic mechanisms of addiction. Nat. Rev. Neurosci. 12:623–37 [Google Scholar]
  175. Heller EA, Cates HM, Pena CJ, Sun H, Shao N. 175.  et al. 2014. Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors. Nat. Neurosci. 17:1720–27 [Google Scholar]
  176. Heller EA, Hamilton PJ, Burek DD, Lombroso SI, Pena CJ. 176.  et al. 2016. Targeted epigenetic remodeling of the Cdk5 gene in nucleus accumbens regulates cocaine- and stress-evoked behavior. J. Neurosci. 36:4690–97 [Google Scholar]
  177. Wallace J, Hu R, Mosbruger TL, Dahlem TJ, Stephens WZ. 177.  et al. 2016. Genome-wide CRISPR–Cas9 screen identifies microRNAs that regulate myeloid leukemia cell growth. PLOS ONE 11:e0153689 [Google Scholar]
  178. Gersbach CA, Perez-Pinera P. 178.  2014. Activating human genes with zinc finger proteins, transcription activator–like effectors and CRISPR/Cas9 for gene therapy and regenerative medicine. Expert Opin. Ther. Targets 18:835–39 [Google Scholar]
  179. Rebar EJ, Huang Y, Hickey R, Nath AK, Meoli D. 179.  et al. 2002. Induction of angiogenesis in a mouse model using engineered transcription factors. Nat. Med. 8:1427–32 [Google Scholar]
  180. Garriga-Canut M, Agustín-Pavón C, Hermann F, Sánchez A, Dierssen M. 180.  et al. 2012. Synthetic zinc finger repressors reduce mutant huntingtin expression in the brain of R6.2 mice. PNAS 109:E3136–45 [Google Scholar]
  181. Yin H, Song CQ, Dorkin JR, Zhu LJ, Li Y. 181.  et al. 2016. Therapeutic genome editing by combined viral and non-viral delivery of CRISPR system components in vivo. Nat. Biotechnol. 34:328–33 [Google Scholar]
  182. Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA. 182.  et al. 2016. In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. Science 351:403–7 [Google Scholar]
  183. Tabebordbar M, Zhu K, Cheng JK, Chew WL, Widrick JJ. 183.  et al. 2016. In vivo gene editing in dystrophic mouse muscle and muscle stem cells. Science 351:407–11 [Google Scholar]
  184. Long C, Amoasii L, Mireault AA, McAnally JR, Li H. 184.  et al. 2016. Postnatal genome editing partially restores dystrophin expression in a mouse model of muscular dystrophy. Science 351:400–3 [Google Scholar]
  185. Liu Y, Zeng Y, Liu L, Zhuang C, Fu X. 185.  et al. 2014. Synthesizing AND gate genetic circuits based on CRISPR–Cas9 for identification of bladder cancer cells. Nat. Commun. 5:5393 [Google Scholar]
  186. Slomovic S, Collins JJ. 186.  2015. DNA sense-and-respond protein modules for mammalian cells. Nat. Methods 12:1085–90 [Google Scholar]
  187. Perli SD, Cui CH, Lu TK. 187.  2016. Continuous genetic recording with self-targeting CRISPR–Cas in human cells. Science 353:aag0511 [Google Scholar]
  188. Ferraris R, Colombatti G, Fiorentini MT, Carosso R, Arossa W, de La Pierre M. 188.  1983. Diagnostic value of serum bile acids and routine liver function tests in hepatobiliary diseases. Dig. Dis. Sci. 28:129–36 [Google Scholar]
  189. Bai P, Haifeng Y, Mingqi X, Saxena P, Zulewski H. 189.  et al. 2016. A synthetic biology–based device prevents liver injury in mice. J. Hepatol. 65:84–94 [Google Scholar]
  190. Auslander D, Auslander S, Charpin–El Hamri G, Sedlmayer F, Muller M. 190.  et al. 2014. A synthetic multifunctional mammalian pH sensor and CO2 transgene-control device. Mol. Cell 55:397–408 [Google Scholar]
  191. Rossger K, Charpin–El Hamri G, Fussenegger M. 191.  2013. Reward-based hypertension control by a synthetic brain–dopamine interface. PNAS 110:18150–55 [Google Scholar]
  192. Kang J, Hu J, Karra R, Dickson AL, Tornini VA. 192.  et al. 2016. Modulation of tissue repair by regeneration enhancer elements. Nature 532:201–6 [Google Scholar]
  193. Kemmer C, Gitzinger M, Daoud-El-Baba M, Djonov V, Stelling J, Fussenegger M. 193.  2010. Self-sufficient control of urate homeostasis in mice by a synthetic circuit. Nat. Biotechnol. 28:355–60 [Google Scholar]
  194. Ye H, Baba MD, Peng RW, Fussenegger M. 194.  2011. A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice. Science 332:1565–68 [Google Scholar]
  195. Ye H, Hamri GC, Zwicky K, Christen M, Folcher M, Fussenegger M. 195.  2013. Pharmaceutically controlled designer circuit for the treatment of the metabolic syndrome. PNAS 110:141–46 [Google Scholar]
  196. Barrett DM, Singh N, Porter DL, Grupp SA, June CH. 196.  2014. Chimeric antigen receptor therapy for cancer. Annu. Rev. Med. 65:333–47 [Google Scholar]
  197. Lienert F, Lohmueller JJ, Garg A, Silver PA. 197.  2014. Synthetic biology in mammalian cells: next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15:95–107 [Google Scholar]
  198. Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA. 198.  et al. 2016. Precision tumor recognition by T cells with combinatorial antigen-sensing circuits. Cell 164:770–79 [Google Scholar]
  199. Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA. 199.  2015. Remote control of therapeutic T cells through a small molecule–gated chimeric receptor. Science 350:aab4077 [Google Scholar]
  200. Nissim L, Bar-Ziv RH. 200.  2010. A tunable dual-promoter integrator for targeting of cancer cells. Mol. Syst. Biol. 6:444 [Google Scholar]
  201. Xie Z, Wroblewska L, Prochazka L, Weiss R, Benenson Y. 201.  2011. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333:1307–11 [Google Scholar]
  202. Culler SJ, Hoff KG, Smolke CD. 202.  2010. Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins. Science 330:1251–55 [Google Scholar]
  203. DeKelver RC, Choi VM, Moehle EA, Paschon DE, Hockemeyer D. 203.  et al. 2010. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease–driven transgenesis into a safe harbor locus in the human genome. Genome Res 20:1133–42 [Google Scholar]
  204. Nelson CE, Gersbach CA. 204.  2016. Engineering delivery vehicles for genome editing. Annu. Rev. Chem. Biomol. Eng. 7:637–62 [Google Scholar]
  205. Ye H, Fussenegger M. 205.  2014. Synthetic therapeutic gene circuits in mammalian cells. FEBS Lett 588:2537–44 [Google Scholar]
  206. Gaj T, Epstein BE, Schaffer DV. 206.  2016. Genome engineering using adeno-associated virus: basic and clinical research applications. Mol. Ther. 24:458–64 [Google Scholar]

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