Mammalian Synthetic Biology: Time for Big MACs

ACS Synthetic Biology

Volumn 5, Issue 10, 2016, Pages 1040-1049

  Martella, Andrea ^a   Pollard, Steven M ^b   Dai, Junbiao ^c   Cai, Yizhi ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c TSINGHUA UNIVERSITY   (China)

Author keywords

artificial chromosome; chromosome engineering; mammalian synthetic biology

Indexed keywords

DNA; SYNTHETIC DNA;

BOTTOM UP APPROACH; CELL DIVISION; CHROMOSOME DUPLICATION; DAUGHTER CELL; DNA SYNTHESIS; EPISOME; EXPRESSION VECTOR; GENE EXPRESSION; GENE LOADING; HUMAN; HUMAN ARTIFICIAL CHROMOSOME; MAMMALIAN ARTIFICIAL CHROMOSOME; NONHUMAN; ORTHOGONAL VECTOR; PRIORITY JOURNAL; REVIEW; SYNTHETIC BIOLOGY; TOP DOWN APPROACH; ANIMAL; CELL LINE; GENETIC ENGINEERING; GENETICS; MAMMAL; TRANSGENE; TRANSGENIC ORGANISM;

ANIMALS; CELL LINE; CHROMOSOMES, ARTIFICIAL, MAMMALIAN; GENE EXPRESSION; GENES, SYNTHETIC; GENETIC ENGINEERING; HUMANS; MAMMALS; ORGANISMS, GENETICALLY MODIFIED; SYNTHETIC BIOLOGY; TRANSGENES;

EID: 84994052324     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/acssynbio.6b00074     Document Type: Review

References (115)

1. Auslander, S., Auslander, D., Muller, M., Wieland, M., and Fussenegger, M. (2012) Programmable single-cell mammalian biocomputers Nature 487, 123-127 10.1038/nature11149
2. Khalil, A. S. and Collins, J. J. (2010) Synthetic biology: applications come of age Nat. Rev. Genet. 11, 367-379 10.1038/nrg2775
3. Lienert, F., Lohmueller, J. J., Garg, A., and Silver, P. A. (2014) Synthetic biology in mammalian cells: next generation research tools and therapeutics Nat. Rev. Mol. Cell Biol. 15, 95-107 10.1038/nrm3738
4. Kramer, B. P., Viretta, A. U., Daoud-El-Baba, M., Aubel, D., Weber, W., and Fussenegger, M. (2004) An engineered epigenetic transgene switch in mammalian cells Nat. Biotechnol. 22, 867-870 10.1038/nbt980
5. Kramer, B. P., Fischer, C., and Fussenegger, M. (2004) BioLogic gates enable logical transcription control in mammalian cells Biotechnol. Bioeng. 87, 478-484 10.1002/bit.20142
6. Kramer, B. P. and Fussenegger, M. (2005) Hysteresis in a synthetic mammalian gene network Proc. Natl. Acad. Sci. U. S. A. 102, 9517-9522 10.1073/pnas.0500345102
7. Tigges, M., Marquez-Lago, T. T., Stelling, J., and Fussenegger, M. (2009) A tunable synthetic mammalian oscillator Nature 457, 309-312 10.1038/nature07616
8. Muller, K. and Weber, W. (2013) Optogenetic tools for mammalian systems Mol. BioSyst. 9, 596-608 10.1039/c3mb25590e
9. Cameron, D. E., Bashor, C. J., and Collins, J. J. (2014) A brief history of synthetic biology Nat. Rev. Microbiol. 12, 381-390 10.1038/nrmicro3239
10. Casini, A., Storch, M., Baldwin, G. S., and Ellis, T. (2015) Bricks and blueprints: methods and standards for DNA assembly Nat. Rev. Mol. Cell Biol. 16, 568-576 10.1038/nrm4014
11. Kosuri, S. and Church, G. M. (2014) Large-scale de novo DNA synthesis: technologies and applications Nat. Methods 11, 499-507 10.1038/nmeth.2918
12. Merrihew, R. V., Marburger, K., Pennington, S. L., Roth, D. B., and Wilson, J. H. (1996) High-frequency illegitimate integration of transfected DNA at preintegrated target sites in a mammalian genome Mol. Cell. Biol. 16, 10-18 10.1128/MCB.16.1.10
13. Wurtele, H., Little, K. C., and Chartrand, P. (2003) Illegitimate DNA integration in mammalian cells Gene Ther. 10, 1791-1799 10.1038/sj.gt.3302074
14. Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., Stockwell, T. B., Brownley, A., Thomas, D. W., Algire, M. A., Merryman, C., Young, L., Noskov, V. N., Glass, J. I., Venter, J. C., Hutchison, C. A., 3rd, and Smith, H. O. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome Science 319, 1215-1220 10.1126/science.1151721
15. Hutchison, C. A., 3rd, Chuang, R. Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., Gill, J., Kannan, K., Karas, B. J., Ma, L., Pelletier, J. F., Qi, Z. Q., Richter, R. A., Strychalski, E. A., Sun, L., Suzuki, Y., Tsvetanova, B., Wise, K. S., Smith, H. O., Glass, J. I., Merryman, C., Gibson, D. G., and Venter, J. C. (2016) Design and synthesis of a minimal bacterial genome Science 351, aad6253 10.1126/science.aad6253
16. Annaluru, N., Muller, H., Mitchell, L. A., Ramalingam, S., Stracquadanio, G., Richardson, S. M., Dymond, J. S., Kuang, Z., Scheifele, L. Z., Cooper, E. M., Cai, Y., Zeller, K., Agmon, N., Han, J. S., Hadjithomas, M., Tullman, J., Caravelli, K., Cirelli, K., Guo, Z., London, V., Yeluru, A., Murugan, S., Kandavelou, K., Agier, N., Fischer, G., Yang, K., Martin, J. A., Bilgel, M., Bohutski, P., Boulier, K. M., Capaldo, B. J., Chang, J., Charoen, K., Choi, W. J., Deng, P., DiCarlo, J. E., Doong, J., Dunn, J., Feinberg, J. I., Fernandez, C., Floria, C. E., Gladowski, D., Hadidi, P., Ishizuka, I., Jabbari, J., Lau, C. Y., Lee, P. A., Li, S., Lin, D., Linder, M. E., Ling, J., Liu, J., London, M., Ma, H., Mao, J., McDade, J. E., McMillan, A., Moore, A. M., Oh, W. C., Ouyang, Y., Patel, R., Paul, M., Paulsen, L. C., Qiu, J., Rhee, A., Rubashkin, M. G., Soh, I. Y., Sotuyo, N. E., Srinivas, V., Suarez, A., Wong, A., Wong, R., Xie, W. R., Xu, Y., Yu, A. T., Koszul, R., Bader, J. S., Boeke, J. D., and Chandrasegaran, S. (2014) Total synthesis of a functional designer eukaryotic chromosome Science 344, 55-58 10.1126/science.1249252
17. Jovicevic, D., Blount, B. A., and Ellis, T. (2014) Total synthesis of a eukaryotic chromosome: Redesigning and SCRaMbLE-ing yeast BioEssays 36, 855-860 10.1002/bies.201400086
18. Clarke, L. and Carbon, J. (1980) Isolation of a yeast centromere and construction of functional small circular chromosomes Nature 287, 504-509 10.1038/287504a0
19. Ohzeki, J., Larionov, V., Earnshaw, W. C., and Masumoto, H. (2015) Genetic and epigenetic regulation of centromeres: a look at HAC formation Chromosome Res. 23, 87-103 10.1007/s10577-015-9470-z
20. Bergmann, J. H., Martins, N. M., Larionov, V., Masumoto, H., and Earnshaw, W. C. (2012) HACking the centromere chromatin code: insights from human artificial chromosomes Chromosome Res. 20, 505-519 10.1007/s10577-012-9293-0
21. Kopniczky, M. B., Moore, S. J., and Freemont, P. S. (2015) Multilevel Regulation and Translational Switches in Synthetic Biology IEEE Trans Biomed Circuits Syst 9, 485-496 10.1109/TBCAS.2015.2451707
22. McGinness, K. E., Baker, T. A., and Sauer, R. T. (2006) Engineering controllable protein degradation Mol. Cell 22, 701-707 10.1016/j.molcel.2006.04.027
23. Bacchus, W. and Fussenegger, M. (2013) Engineering of synthetic intercellular communication systems Metab. Eng. 16, 33-41 10.1016/j.ymben.2012.12.001
24. Deans, T. L., Cantor, C. R., and Collins, J. J. (2007) A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells Cell 130, 363-372 10.1016/j.cell.2007.05.045
25. Stanton, B. C., Siciliano, V., Ghodasara, A., Wroblewska, L., Clancy, K., Trefzer, A. C., Chesnut, J. D., Weiss, R., and Voigt, C. A. (2014) Systematic transfer of prokaryotic sensors and circuits to mammalian cells ACS Synth. Biol. 3, 880-891 10.1021/sb5002856
26. Khalil, A. S., Lu, T. K., Bashor, C. J., Ramirez, C. L., Pyenson, N. C., Joung, J. K., and Collins, J. J. (2012) A synthetic biology framework for programming eukaryotic transcription functions Cell 150, 647-658 10.1016/j.cell.2012.05.045
27. Kabadi, A. M. and Gersbach, C. A. (2014) Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression Methods 69, 188-197 10.1016/j.ymeth.2014.06.014
28. Lim, W. A. (2010) Designing customized cell signalling circuits Nat. Rev. Mol. Cell Biol. 11, 393-403 10.1038/nrm2904
29. Des Soye, B. J., Patel, J. R., Isaacs, F. J., and Jewett, M. C. (2015) Repurposing the translation apparatus for synthetic biology Curr. Opin. Chem. Biol. 28, 83-90 10.1016/j.cbpa.2015.06.008
30. Guo, Y., Dong, J., Zhou, T., Auxillos, J., Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., Lin, J., Chen, G. Q., Wu, Q., Cai, Y., and Dai, J. (2015) YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae Nucleic Acids Res. 43, e88 10.1093/nar/gkv464
31. Stanton, B. C., Nielsen, A. A., Tamsir, A., Clancy, K., Peterson, T., and Voigt, C. A. (2014) Genomic mining of prokaryotic repressors for orthogonal logic gates Nat. Chem. Biol. 10, 99-105 10.1038/nchembio.1411
32. Temme, K., Hill, R., Segall-Shapiro, T. H., Moser, F., and Voigt, C. A. (2012) Modular control of multiple pathways using engineered orthogonal T7 polymerases Nucleic Acids Res. 40, 8773-8781 10.1093/nar/gks597
33. Lanctot, C., Cheutin, T., Cremer, M., Cavalli, G., and Cremer, T. (2007) Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions Nat. Rev. Genet. 8, 104-115 10.1038/nrg2041
34. Batenchuk, C., St-Pierre, S., Tepliakova, L., Adiga, S., Szuto, A., Kabbani, N., Bell, J. C., Baetz, K., and Kaern, M. (2011) Chromosomal position effects are linked to sir2-mediated variation in transcriptional burst size Biophys. J. 100, L56-58 10.1016/j.bpj.2011.04.021
35. Gaj, T., Gersbach, C. A., and Barbas, C. F., 3rd (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering Trends Biotechnol. 31, 397-405 10.1016/j.tibtech.2013.04.004
36. Duportet, X., Wroblewska, L., Guye, P., Li, Y., Eyquem, J., Rieders, J., Rimchala, T., Batt, G., and Weiss, R. (2014) A platform for rapid prototyping of synthetic gene networks in mammalian cells Nucleic Acids Res. 42, 13440-13451 10.1093/nar/gku1082
37. Papapetrou, E. P., Lee, G., Malani, N., Setty, M., Riviere, I., Tirunagari, L. M., Kadota, K., Roth, S. L., Giardina, P., Viale, A., Leslie, C., Bushman, F. D., Studer, L., and Sadelain, M. (2011) Genomic safe harbors permit high beta-globin transgene expression in thalassemia induced pluripotent stem cells Nat. Biotechnol. 29, 73-78 10.1038/nbt.1717
38. Sadelain, M., Papapetrou, E. P., and Bushman, F. D. (2012) Safe harbours for the integration of new DNA in the human genome Nat. Rev. Cancer 12, 51-58 10.1038/nrc3179
39. Gingeras, T. R. (2007) Origin of phenotypes: genes and transcripts Genome Res. 17, 682-690 10.1101/gr.6525007
40. Lupianez, D. G., Spielmann, M., and Mundlos, S. (2016) Breaking TADs: How Alterations of Chromatin Domains Result in Disease Trends Genet. 32, 225-237 10.1016/j.tig.2016.01.003
41. Nunez, E., Fu, X. D., and Rosenfeld, M. G. (2009) Nuclear organization in the 3D space of the nucleus-cause or consequence? Curr. Opin. Genet. Dev. 19, 424-436 10.1016/j.gde.2009.07.005
42. de Laat, W. and Duboule, D. (2013) Topology of mammalian developmental enhancers and their regulatory landscapes Nature 502, 499-506 10.1038/nature12753
43. Fraser, P. (2006) Transcriptional control thrown for a loop Curr. Opin. Genet. Dev. 16, 490-495 10.1016/j.gde.2006.08.002
44. Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., Fox, E. A., Silver, P. A., and Brown, M. (2005) Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1 Cell 122, 33-43 10.1016/j.cell.2005.05.008
45. Ribeiro de Almeida, C., Stadhouders, R., Thongjuea, S., Soler, E., and Hendriks, R. W. (2012) DNA-binding factor CTCF and long-range gene interactions in V(D)J recombination and oncogene activation Blood 119, 6209-6218 10.1182/blood-2012-03-402586
46. Cheeseman, I. M. and Desai, A. (2008) Molecular architecture of the kinetochore-microtubule interface Nat. Rev. Mol. Cell Biol. 9, 33-46 10.1038/nrm2310
47. Kazuki, Y., Hoshiya, H., Takiguchi, M., Abe, S., Iida, Y., Osaki, M., Katoh, M., Hiratsuka, M., Shirayoshi, Y., Hiramatsu, K., Ueno, E., Kajitani, N., Yoshino, T., Kazuki, K., Ishihara, C., Takehara, S., Tsuji, S., Ejima, F., Toyoda, A., Sakaki, Y., Larionov, V., Kouprina, N., and Oshimura, M. (2011) Refined human artificial chromosome vectors for gene therapy and animal transgenesis Gene Ther. 18, 384-393 10.1038/gt.2010.147
48. Kouprina, N., Tomilin, A. N., Masumoto, H., Earnshaw, W. C., and Larionov, V. (2014) Human artificial chromosome-based gene delivery vectors for biomedicine and biotechnology Expert Opin. Drug Delivery 11, 517-535 10.1517/17425247.2014.882314
49. Kouprina, N., Earnshaw, W. C., Masumoto, H., and Larionov, V. (2013) A new generation of human artificial chromosomes for functional genomics and gene therapy Cell. Mol. Life Sci. 70, 1135-1148 10.1007/s00018-012-1113-3
50. Hoshiya, H., Kazuki, Y., Abe, S., Takiguchi, M., Kajitani, N., Watanabe, Y., Yoshino, T., Shirayoshi, Y., Higaki, K., Messina, G., Cossu, G., and Oshimura, M. (2009) A highly stable and nonintegrated human artificial chromosome (HAC) containing the 2.4 Mb entire human dystrophin gene Mol. Ther. 17, 309-317 10.1038/mt.2008.253
51. Farr, C. J., Stevanovic, M., Thomson, E. J., Goodfellow, P. N., and Cooke, H. J. (1992) Telomere-associated chromosome fragmentation: applications in genome manipulation and analysis Nat. Genet. 2, 275-282 10.1038/ng1292-275
52. Suzuki, N., Nishii, K., Okazaki, T., and Ikeno, M. (2006) Human artificial chromosomes constructed using the bottom-up strategy are stably maintained in mitosis and efficiently transmissible to progeny mice J. Biol. Chem. 281, 26615-26623 10.1074/jbc.M603053200
53. Hasegawa, Y., Ishikura, T., Hasegawa, T., Watanabe, T., Suzuki, J., Nakayama, M., Okamura, Y., Okazaki, T., Koseki, H., Ohara, O., Ikeno, M., and Masumoto, H. (2015) Generating a transgenic mouse line stably expressing human MHC surface antigen from a HAC carrying multiple genomic BACs Chromosoma 124, 107-118 10.1007/s00412-014-0488-3
54. Liskovykh, M., Ponomartsev, S., Popova, E., Bader, M., Kouprina, N., Larionov, V., Alenina, N., and Tomilin, A. (2015) Stable maintenance of de novo assembled human artificial chromosomes in embryonic stem cells and their differentiated progeny in mice Cell Cycle 14, 1268-1273 10.1080/15384101.2015.1014151
55. Takiguchi, M., Kazuki, Y., Hiramatsu, K., Abe, S., Iida, Y., Takehara, S., Nishida, T., Ohbayashi, T., Wakayama, T., and Oshimura, M. (2014) A novel and stable mouse artificial chromosome vector ACS Synth. Biol. 3, 903-914 10.1021/sb3000723
56. Argyros, O., Wong, S. P., and Harbottle, R. P. (2011) Non-viral episomal modification of cells using S/MAR elements Expert Opin. Biol. Ther. 11, 1177-1191 10.1517/14712598.2011.582035
57. Lufino, M. M., Edser, P. A., and Wade-Martins, R. (2008) Advances in high-capacity extrachromosomal vector technology: episomal maintenance, vector delivery, and transgene expression Mol. Ther. 16, 1525-1538 10.1038/mt.2008.156
58. Black, J. and Vos, J. M. (2002) Establishment of an oriP/EBNA1-based episomal vector transcribing human genomic beta-globin in cultured murine fibroblasts Gene Ther. 9, 1447-1454 10.1038/sj.gt.3301808
59. Haase, R., Argyros, O., Wong, S. P., Harbottle, R. P., Lipps, H. J., Ogris, M., Magnusson, T., Vizoso Pinto, M. G., Haas, J., and Baiker, A. (2010) pEPito: a significantly improved non-viral episomal expression vector for mammalian cells BMC Biotechnol. 10, 20 10.1186/1472-6750-10-20
60. Baiker, A., Maercker, C., Piechaczek, C., Schmidt, S. B., Bode, J., Benham, C., and Lipps, H. J. (2000) Mitotic stability of an episomal vector containing a human scaffold/matrix-attached region is provided by association with nuclear matrix Nat. Cell Biol. 2, 182-184 10.1038/35004061
61. Stehle, I. M., Postberg, J., Rupprecht, S., Cremer, T., Jackson, D. A., and Lipps, H. J. (2007) Establishment and mitotic stability of an extra-chromosomal mammalian replicon BMC Cell Biol. 8, 33 10.1186/1471-2121-8-33
62. Kuroiwa, Y., Tomizuka, K., Shinohara, T., Kazuki, Y., Yoshida, H., Ohguma, A., Yamamoto, T., Tanaka, S., Oshimura, M., and Ishida, I. (2000) Manipulation of human minichromosomes to carry greater than megabase-sized chromosome inserts Nat. Biotechnol. 18, 1086-1090 10.1038/80287
63. Kazuki, Y., Hiratsuka, M., Takiguchi, M., Osaki, M., Kajitani, N., Hoshiya, H., Hiramatsu, K., Yoshino, T., Kazuki, K., Ishihara, C., Takehara, S., Higaki, K., Nakagawa, M., Takahashi, K., Yamanaka, S., and Oshimura, M. (2010) Complete genetic correction of ips cells from Duchenne muscular dystrophy Mol. Ther. 18, 386-393 10.1038/mt.2009.274
64. Co, D. O., Borowski, A. H., Leung, J. D., van der Kaa, J., Hengst, S., Platenburg, G. J., Pieper, F. R., Perez, C. F., Jirik, F. R., and Drayer, J. I. (2000) Generation of transgenic mice and germline transmission of a mammalian artificial chromosome introduced into embryos by pronuclear microinjection Chromosome Res. 8, 183-191 10.1023/A:1009206926548
65. Kuroiwa, Y., Kasinathan, P., Sathiyaseelan, T., Jiao, J. A., Matsushita, H., Sathiyaseelan, J., Wu, H., Mellquist, J., Hammitt, M., Koster, J., Kamoda, S., Tachibana, K., Ishida, I., and Robl, J. M. (2009) Antigen-specific human polyclonal antibodies from hyperimmunized cattle Nat. Biotechnol. 27, 173-181 10.1038/nbt.1521
66. Matsushita, H., Sano, A., Wu, H., Wang, Z., Jiao, J. A., Kasinathan, P., Sullivan, E. J., and Kuroiwa, Y. (2015) Species-Specific Chromosome Engineering Greatly Improves Fully Human Polyclonal Antibody Production Profile in Cattle PLoS One 10, e0130699 10.1371/journal.pone.0130699
67. Shinohara, T., Tomizuka, K., Takehara, S., Yamauchi, K., Katoh, M., Ohguma, A., Ishida, I., and Oshimura, M. (2000) Stability of transferred human chromosome fragments in cultured cells and in mice Chromosome Res. 8, 713-725 10.1023/A:1026741321193
68. Kazuki, Y. and Oshimura, M. (2011) Human artificial chromosomes for gene delivery and the development of animal models Mol. Ther. 19, 1591-1601 10.1038/mt.2011.136
69. Katoh, M., Ayabe, F., Norikane, S., Okada, T., Masumoto, H., Horike, S., Shirayoshi, Y., and Oshimura, M. (2004) Construction of a novel human artificial chromosome vector for gene delivery Biochem. Biophys. Res. Commun. 321, 280-290 10.1016/j.bbrc.2004.06.145
70. Oshimura, M., Uno, N., Kazuki, Y., Katoh, M., and Inoue, T. (2015) A pathway from chromosome transfer to engineering resulting in human and mouse artificial chromosomes for a variety of applications to bio-medical challenges Chromosome Res. 23, 111-133 10.1007/s10577-014-9459-z
71. Heller, R., Brown, K. E., Burgtorf, C., and Brown, W. R. (1996) Mini-chromosomes derived from the human Y chromosome by telomere directed chromosome breakage Proc. Natl. Acad. Sci. U. S. A. 93, 7125-7130 10.1073/pnas.93.14.7125
72. Kakeda, M., Nagata, K., Osawa, K., Matsuno, H., Hiratsuka, M., Sano, A., Okazaki, A., Shitara, S., Nishikawa, S., Masuya, A., Hata, T., Wako, S., Osaki, M., Kazuki, Y., Oshimura, M., and Tomizuka, K. (2011) A new chromosome 14-based human artificial chromosome (HAC) vector system for efficient transgene expression in human primary cells Biochem. Biophys. Res. Commun. 415, 439-444 10.1016/j.bbrc.2011.10.088
73. Mills, W., Critcher, R., Lee, C., and Farr, C. J. (1999) Generation of an approximately 2.4 Mb human X centromere-based minichromosome by targeted telomere-associated chromosome fragmentation in DT40 Hum. Mol. Genet. 8, 751-761 10.1093/hmg/8.5.751
74. Shen, M. H., Mee, P. J., Nichols, J., Yang, J., Brook, F., Gardner, R. L., Smith, A. G., and Brown, W. R. (2000) A structurally defined mini-chromosome vector for the mouse germ line Curr. Biol. 10, 31-34 10.1016/S0960-9822(99)00261-4
75. Yang, J. W., Pendon, C., Yang, J., Haywood, N., Chand, A., and Brown, W. R. (2000) Human mini-chromosomes with minimal centromeres Hum. Mol. Genet. 9, 1891-1902 10.1093/hmg/9.12.1891
76. Choo, K. H., Vissel, B., Nagy, A., Earle, E., and Kalitsis, P. (1991) A survey of the genomic distribution of alpha satellite DNA on all the human chromosomes, and derivation of a new consensus sequence Nucleic Acids Res. 19, 1179-1182 10.1093/nar/19.6.1179
77. Okada, T., Ohzeki, J., Nakano, M., Yoda, K., Brinkley, W. R., Larionov, V., and Masumoto, H. (2007) CENP-B controls centromere formation depending on the chromatin context Cell 131, 1287-1300 10.1016/j.cell.2007.10.045
78. Erliandri, I., Fu, H., Nakano, M., Kim, J. H., Miga, K. H., Liskovykh, M., Earnshaw, W. C., Masumoto, H., Kouprina, N., Aladjem, M. I., and Larionov, V. (2014) Replication of alpha-satellite DNA arrays in endogenous human centromeric regions and in human artificial chromosome Nucleic Acids Res. 42, 11502-11516 10.1093/nar/gku835
79. Ikeno, M., Grimes, B., Okazaki, T., Nakano, M., Saitoh, K., Hoshino, H., McGill, N. I., Cooke, H., and Masumoto, H. (1998) Construction of YAC-based mammalian artificial chromosomes Nat. Biotechnol. 16, 431-439 10.1038/nbt0598-431
80. Ebersole, T. A., Ross, A., Clark, E., McGill, N., Schindelhauer, D., Cooke, H., and Grimes, B. (2000) Mammalian artificial chromosome formation from circular alphoid input DNA does not require telomere repeats Hum. Mol. Genet. 9, 1623-1631 10.1093/hmg/9.11.1623
81. Basu, J., Stromberg, G., Compitello, G., Willard, H. F., and Van Bokkelen, G. (2005) Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays Nucleic Acids Res. 33, 587-596 10.1093/nar/gki207
82. Kotzamanis, G., Cheung, W., Abdulrazzak, H., Perez-Luz, S., Howe, S., Cooke, H., and Huxley, C. (2005) Construction of human artificial chromosome vectors by recombineering Gene 351, 29-38 10.1016/j.gene.2005.01.017
83. Moralli, D. and Monaco, Z. L. (2015) Developing de novo human artificial chromosomes in embryonic stem cells using HSV-1 amplicon technology Chromosome Res. 23, 105-110 10.1007/s10577-014-9456-2
84. Harrington, J. J., Van Bokkelen, G., Mays, R. W., Gustashaw, K., and Willard, H. F. (1997) Formation of de novo centromeres and construction of first-generation human artificial microchromosomes Nat. Genet. 15, 345-355 10.1038/ng0497-345
85. Ohzeki, J., Bergmann, J. H., Kouprina, N., Noskov, V. N., Nakano, M., Kimura, H., Earnshaw, W. C., Larionov, V., and Masumoto, H. (2012) Breaking the HAC Barrier: histone H3K9 acetyl/methyl balance regulates CENP-A assembly EMBO J. 31, 2391-2402 10.1038/emboj.2012.82
86. Mandegar, M. A., Moralli, D., Khoja, S., Cowley, S., Chan, D. Y., Yusuf, M., Mukherjee, S., Blundell, M. P., Volpi, E. V., Thrasher, A. J., James, W., and Monaco, Z. L. (2011) Functional human artificial chromosomes are generated and stably maintained in human embryonic stem cells Hum. Mol. Genet. 20, 2905-2913 10.1093/hmg/ddr144
87. Iida, Y., Kim, J. H., Kazuki, Y., Hoshiya, H., Takiguchi, M., Hayashi, M., Erliandri, I., Lee, H. S., Samoshkin, A., Masumoto, H., Earnshaw, W. C., Kouprina, N., Larionov, V., and Oshimura, M. (2010) Human artificial chromosome with a conditional centromere for gene delivery and gene expression DNA Res. 17, 293-301 10.1093/dnares/dsq020
88. Kononenko, A. V., Lee, N. C., Liskovykh, M., Masumoto, H., Earnshaw, W. C., Larionov, V., and Kouprina, N. (2015) Generation of a conditionally self-eliminating HAC gene delivery vector through incorporation of a tTAVP64 expression cassette Nucleic Acids Res. 43, e57 10.1093/nar/gkv124
89. Kouprina, N., Samoshkin, A., Erliandri, I., Nakano, M., Lee, H. S., Fu, H., Iida, Y., Aladjem, M., Oshimura, M., Masumoto, H., Earnshaw, W. C., and Larionov, V. (2012) Organization of synthetic alphoid DNA array in human artificial chromosome (HAC) with a conditional centromere ACS Synth. Biol. 1, 590-601 10.1021/sb3000436
90. Yamaguchi, S., Kazuki, Y., Nakayama, Y., Nanba, E., Oshimura, M., and Ohbayashi, T. (2011) A method for producing transgenic cells using a multi-integrase system on a human artificial chromosome vector PLoS One 6, e17267 10.1371/journal.pone.0017267
91. Suzuki, T., Kazuki, Y., Oshimura, M., and Hara, T. (2014) A novel system for simultaneous or sequential integration of multiple gene-loading vectors into a defined site of a human artificial chromosome PLoS One 9, e110404 10.1371/journal.pone.0110404
92. Qu, H. and Fang, X. (2013) A brief review on the Human Encyclopedia of DNA Elements (ENCODE) project Genomics, Proteomics Bioinf. 11, 135-141 10.1016/j.gpb.2013.05.001
93. Siggens, L. and Ekwall, K. (2014) Epigenetics, chromatin and genome organization: recent advances from the ENCODE project J. Intern. Med. 276, 201-214 10.1111/joim.12231
94. Wendt, K. S. and Grosveld, F. G. (2014) Transcription in the context of the 3D nucleus Curr. Opin. Genet. Dev. 25, 62-67 10.1016/j.gde.2013.11.020
95. Sofueva, S., Yaffe, E., Chan, W. C., Georgopoulou, D., Vietri Rudan, M., Mira-Bontenbal, H., Pollard, S. M., Schroth, G. P., Tanay, A., and Hadjur, S. (2013) Cohesin-mediated interactions organize chromosomal domain architecture EMBO J. 32, 3119-3129 10.1038/emboj.2013.237
96. Merkenschlager, M. and Odom, D. T. (2013) CTCF and cohesin: linking gene regulatory elements with their targets Cell 152, 1285-1297 10.1016/j.cell.2013.02.029
97. Ali, T., Renkawitz, R., and Bartkuhn, M. (2016) Insulators and domains of gene expression Curr. Opin. Genet. Dev. 37, 17-26 10.1016/j.gde.2015.11.009
98. Zhang, Y., Wong, C. H., Birnbaum, R. Y., Li, G., Favaro, R., Ngan, C. Y., Lim, J., Tai, E., Poh, H. M., Wong, E., Mulawadi, F. H., Sung, W. K., Nicolis, S., Ahituv, N., Ruan, Y., and Wei, C. L. (2013) Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations Nature 504, 306-310 10.1038/nature12716
99. Shchuka, V. M., Malek-Gilani, N., Singh, G., Langroudi, L., Dhaliwal, N. K., Moorthy, S. D., Davidson, S., Macpherson, N. N., and Mitchell, J. A. (2015) Chromatin Dynamics in Lineage Commitment and Cellular Reprogramming Genes 6, 641-661 10.3390/genes6030641
100. Jo, Y. I., Suresh, B., Kim, H., and Ramakrishna, S. (2015) CRISPR/Cas9 system as an innovative genetic engineering tool: Enhancements in sequence specificity and delivery methods Biochim. Biophys. Acta, Rev. Cancer 1856, 234-243 10.1016/j.bbcan.2015.09.003
101. Bell, A. C. and Felsenfeld, G. (2000) Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene Nature 405, 482-485 10.1038/35013100
102. Guo, Y., Xu, Q., Canzio, D., Shou, J., Li, J., Gorkin, D. U., Jung, I., Wu, H., Zhai, Y., Tang, Y., Lu, Y., Wu, Y., Jia, Z., Li, W., Zhang, M. Q., Ren, B., Krainer, A. R., Maniatis, T., and Wu, Q. (2015) CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function Cell 162, 900-910 10.1016/j.cell.2015.07.038
103. Keung, A. J., Bashor, C. J., Kiriakov, S., Collins, J. J., and Khalil, A. S. (2014) Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation Cell 158, 110-120 10.1016/j.cell.2014.04.047
104. Dillon, N. (2008) The impact of gene location in the nucleus on transcriptional regulation Dev. Cell 15, 182-186 10.1016/j.devcel.2008.07.013
105. Deng, W., Rupon, J. W., Krivega, I., Breda, L., Motta, I., Jahn, K. S., Reik, A., Gregory, P. D., Rivella, S., Dean, A., and Blobel, G. A. (2014) Reactivation of developmentally silenced globin genes by forced chromatin looping Cell 158, 849-860 10.1016/j.cell.2014.05.050
106. Li, L. and Blankenstein, T. (2013) Generation of transgenic mice with megabase-sized human yeast artificial chromosomes by yeast spheroplast-embryonic stem cell fusion Nat. Protoc. 8, 1567-1582 10.1038/nprot.2013.093
107. Alonso, A., Fritz, B., Hasson, D., Abrusan, G., Cheung, F., Yoda, K., Radlwimmer, B., Ladurner, A. G., and Warburton, P. E. (2007) Co-localization of CENP-C and CENP-H to discontinuous domains of CENP-A chromatin at human neocentromeres Genome Biol. 8, R148 10.1186/gb-2007-8-7-r148
108. Hiratsuka, M., Ueda, K., Uno, N., Uno, K., Fukuhara, S., Kurosaki, H., Takehara, S., Osaki, M., Kazuki, Y., Kurosawa, Y., Nakamura, T., Katoh, M., and Oshimura, M. (2015) Retargeting of microcell fusion towards recipient cell-oriented transfer of human artificial chromosome BMC Biotechnol. 15, 58 10.1186/s12896-015-0142-z
109. Dobrin, A., Saxena, P., and Fussenegger, M. (2015) Synthetic biology: applying biological circuits beyond novel therapies Integr Biol. 8, 409 10.1039/C5IB00263J
110. Ye, H. and Fussenegger, M. (2014) Synthetic therapeutic gene circuits in mammalian cells FEBS Lett. 588, 2537-2544 10.1016/j.febslet.2014.05.003
111. Xie, Z., Wroblewska, L., Prochazka, L., Weiss, R., and Benenson, Y. (2011) Multi-input RNAi-based logic circuit for identification of specific cancer cells Science 333, 1307-1311 10.1126/science.1205527
112. Culler, S. J., Hoff, K. G., and Smolke, C. D. (2010) Reprogramming cellular behavior with RNA controllers responsive to endogenous proteins Science 330, 1251-1255 10.1126/science.1192128
113. Chakravarti, D. and Wong, W. W. (2015) Synthetic biology in cell-based cancer immunotherapy Trends Biotechnol. 33, 449-461 10.1016/j.tibtech.2015.05.001
114. Stadtfeld, M. and Hochedlinger, K. (2010) Induced pluripotency: history, mechanisms, and applications Genes Dev. 24, 2239-2263 10.1101/gad.1963910
115. Trosset, J. Y. and Carbonell, P. (2015) Synthetic biology for pharmaceutical drug discovery Drug Des., Dev. Ther. 9, 6285-6302 10.2147/DDDT.S58049