Whole genome synthesis: from poliovirus to synthetic yeast

References

[1] DeLisi, C. (2008) Meetings that changed the world: Santa Fe 1986: Human genome baby-steps. Nature, 455, 876–877

[2] Battelle Technology Partnership Practice, (2011) Economic impact of the Human Genome Project

[3] Mali, P., Yang, L., Esvelt, K. M., Aach, J., Guell, M., DiCarlo, J. E., Norville, J. E. and Church, G. M. (2013) RNA-guided human genome engineering via Cas9. Science, 339, 823–826

[4] Cong, L., Ran, F. A., Cox, D., Lin, S., Barretto, R., Habib, N., Hsu, P. D., Wu, X., Jiang, W., Marraffini, L. A., (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339, 819–823

[5] Hsu, P. D., Lander, E. S. and Zhang, F. (2014) Development and applications of CRISPR-Cas9 for genome engineering. Cell, 157, 1262–1278

[6] Sander, J. D. and Joung, J. K. (2014) CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol., 32, 347–355

[7] Sliva, A., Yang, H., Boeke, J. D. and Mathews, D. J. (2015) Freedom and responsibility in synthetic genomics: the synthetic yeast project. Genetics, 200, 1021–1028

[8] Service, R. F. (2013) The life force. Science, 342, 1032–1034

[9] Wang, H. H., Kim, H., Cong, L., Jeong, J., Bang, D. and Church, G. M. (2012) Genome-scale promoter engineering by coselection MAGE. Nat. Methods, 9, 591–593

[10] Isaacs, F. J., Carr, P. A., Wang, H. H., Lajoie, M. J., Sterling, B., Kraal, L., Tolonen, A. C., Gianoulis, T. A., Goodman, D. B., Reppas, N. B., (2011) Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science, 333, 348–353

[11] Lajoie, M. J., Rovner, A. J., Goodman, D. B., Aerni, H.-R., Haimovich, A. D., Kuznetsov, G., Mercer, J. A., Wang, H. H., Carr, P. A., Mosberg, J. A., (2013) Genomically recoded organisms expand biological functions. Science, 342, 357–360

[12] Mandell, D. J., Lajoie, M. J., Mee, M. T., Takeuchi, R., Kuznetsov, G., Norville, J. E., Gregg, C. J., Stoddard, B. L. and Church, G. M. (2015) Biocontainment of genetically modified organisms by synthetic protein design. Nature, 518, 55–60

[13] Rovner, A. J., Haimovich, A. D., Katz, S. R., Li, Z., Grome, M. W., Gassaway, B. M., Amiram, M., Patel, J. R., Gallagher, R. R., Rinehart, J., (2015) Recoded organisms engineered to depend on synthetic amino acids. Nature, 518, 89–93

[14] Ostrov, N., Landon, M., Guell, M., Kuznetsov, G., Teramoto, J., Cervantes, N., Zhou, M., Singh, K., Napolitano, M. G., Moosburner, M., (2016) Design, synthesis, and testing toward a 57-codon genome. Science, 353, 819–822

[15] Cello, J., Paul, A. V. and Wimmer, E. (2002) Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science, 297, 1016–1018

[16] Smith, H. O., Hutchison, C. A. 3rd, Pfannkoch, C. and Venter, J. C. (2003) Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc. Natl. Acad. Sci. USA, 100, 15440–15445

[17] Sanger, F., Coulson, A. R., Friedmann, T., Air, G. M., Barrell, B. G., Brown, N. L., Fiddes, J. C., Hutchison, C. A. III, Slocombe, P. M. and Smith, M. (1978) The nucleotide sequence of bacteriophage phiX174. J. Mol. Biol., 125, 225–246

[18] 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., (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science, 319, 1215–1220

[19] Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R.-Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52–56

[20] Lartigue, C., Vashee, S., Algire, M. A., Chuang, R. -Y., Benders, G. A., Ma, L., Noskov, V. N., Denisova, E. A., Gibson, D. G., Assad-Garcia, N., (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science, 325, 1693–1696

[21] Hutchison, C. A. Ⅲ, Chuang, R. -Y., Noskov, V. N., Assad-Garcia, N., Deerinck, T. J., Ellisman, M. H., Gill, J., Kannan, K., Karas, B. J., Ma, L., (2016) Design and synthesis of a minimal bacterial genome. Science, 351, aad6253

[22] Schatz, M. C. and Phillippy, A. M. (2012) The rise of a digital immune system. Gigascience, 1, 4

[23] Kosuri, S., Eroshenko, N., LeProust, E. M., Super, M., Way, J., Li, J. B. and Church, G. M. (2010) Scalable gene synthesis by selective amplification of DNA pools from high-fidelity microchips. Nat. Biotechnol., 28, 1295–1299

[24] Matzas, M., Stähler, P. F., Kefer, N., Siebelt, N., Boisguérin, V., Leonard, J. T., Keller, A., Stähler, C. F., Häberle, P., Gharizadeh, B., (2010) High-fidelity gene synthesis by retrieval of sequence-verified DNA identified using high-throughput pyrosequencing. Nat. Biotechnol., 28, 1291–1294

[25] Kim, H., Kim, J., Kim, E.-G., Heinz, A. J., Kwon, S. and Chun, H. (2010) Optofluidic in situ maskless lithography of charge selective nanoporous hydrogel for DNA preconcentration. Biomicrofluidics, 4, 043014

[26] Lin, Q., Jia, B., Mitchell, L. A., Luo, J., Yang, K., Zeller, K. I., Zhang, W., Xu, Z., Stracquadanio, G., Bader , J., (2014) RADOM, an efficient in vivo method for assembling designed DNA fragments up to 10 kb long in Saccharomyces cerevisiae. ACS Synth. Biol. 4, 213–220

[27] Gibson, D. G., Smith, H. O., Hutchison, C. A. Ⅲ, Venter, J. C. and Merryman, C. (2010) Chemical synthesis of the mouse mitochondrial genome. Nat. Methods, 7, 901–903

[28] Engler, C., Kandzia, R. and Marillonnet, S. (2008) A one pot, one step, precision cloning method with high throughput capability. PLoS One, 3, e3647

[29] Engler, C., Gruetzner, R., Kandzia, R. and Marillonnet, S. (2009) Golden gate shuffling: a one-pot DNA shuffling method based on type IIs restriction enzymes. PLoS One, 4, e5553

[30] Shao, Z., Zhao, H. and Zhao, H. (2009) DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways. Nucleic Acids Res., 37, e16

[31] Guo, Y., Dong, J., Zhou, T., Auxillos, J., Li, T., Zhang, W., Wang, L., Shen, Y., Luo, Y., Zheng, Y., (2015) YeastFab: the design and construction of standard biological parts for metabolic engineering in Saccharomyces cerevisiae. Nucleic Acids Res., 43, e88

[32] Dymond, J. S., Richardson, S. M., Coombes, C. E., Babatz, T., Muller, H., Annaluru, N., Blake, W. J., Schwerzmann, J. W., Dai, J., Lindstrom, D. L., (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature, 477, 471–476

[33] Shen, Y., Stracquadanio, G., Wang, Y., Yang, K., Mitchell, L. A., Xue, Y., Cai, Y., Chen, T., Dymond, J. S., Kang, K., (2016) SCRaMbLE generates designed combinatorial stochastic diversity in synthetic chromosomes. Genome Res., 26, 36–49

[34] 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., (2014) Total synthesis of a functional designer eukaryotic chromosome. Science, 344, 55–58

[35] Mercy, G., Mozziconacci, J., Scolari, V. F., Yang, K., Zhao, G., Thierry, A., Luo, Y., Mitchell, L. A., Shen, M., Shen, Y., (2017) 3D organization of synthetic and scrambled chromosomes. Science, 355, eaaf4597

[36] Mitchell, L. A., Wang, A., Stracquadanio, G., Kuang, Z., Wang, X., Yang, K., Richardson, S., Martin, J. A., Zhao, Y., Walker, R., (2017) Synthesis, debugging and consolidation of synthetic chromosomes in yeast: synVI and beyond. Science, 355, eaaf4831

[37] Richardson, S. M., Mitchell, L. A., Stracquadanio,G., Yang, K., Dymond, J. S., DiCarlo, J. E., Lee, D., Huang,C. L. V., Chandrasegaran, S., Cai, Y., (2017) Design of a synthetic yeast genome. Science, 355, eaaf4557

[38] Shen, Y., Wang, Y., Chen, T., Gao, F., Gong, J., Abramczyk, D., Walker, R., Zhao, H., Chen, S., Liu, W., (2017) Deep functional analysis of synII, a 770–kilobase synthetic yeast chromosome. Science, 355, eaaf4791

[39] Wu, Y., Li, B. Z., Zhao, M., Mitchell, L.A., Xie, Z.X., Lin, Q. H., Wang, X., Xiao, W. H., Wang, Y., Zhou, X., (2017) Bug mapping and fitness testing of chemically synthesized chromosome X. Science, 355, eaaf4706

[40] Xie, Z. X., Li,B. Z. , Mitchell, L. A., Wu, Y., Qi, X., Jin, Z., Jia, B., Wang, X., Zeng, B. X.,, Liu, H. M., (2017) “Perfect” designer chromosome V and behavior of a ring derivative. Science, 355, eaaf4704

[41] Zhang, W., Zhao, G., Luo, Z., Lin, Y., Wang, L., Guo, Y., Wang, A., Jiang, S., Jiang, Q., Gong, J., (2017) Engineering the ribosomal DNA in a megabase synthetic chromosome. Science, 355, eaaf3981

[42] Dymond, J. S., Scheifele, L. Z., Richardson, S., Lee, P., Chandrasegaran, S., Bader, J. S. and Boeke, J. D. (2009) Teaching synthetic biology, bioinformatics and engineering to undergraduates: the interdisciplinary build-a-genome course. Genetics, 181, 13–21

[43] Mitchell, L. A., Cai, Y., Taylor, M., Noronha, A. M., Chuang, J., Dai, L. and Boeke, J. D. (2013) Multichange isothermal mutagenesis: a new strategy for multiple site-directed mutations in plasmid DNA. ACS Synth. Biol., 2, 473–477

[44] Mitchell, L. A. and Boeke, J. D. (2014) Circular permutation of a synthetic eukaryotic chromosome with the telomerator. Proc. Natl. Acad. Sci. USA, 111, 17003–17010

[45] Cai, Y., Agmon, N., Choi, W. J., Ubide, A., Stracquadanio, G., Caravelli, K., Hao, H., Bader, J. S. and Boeke, J. D. (2015) Intrinsic biocontainment: multiplex genome safeguards combine transcriptional and recombinational control of essential yeast genes. Proc. Natl. Acad. Sci. USA, 112, 1803–1808

[46] DiCarlo, J. E., Chavez, A., Dietz, S. L., Esvelt, K. M. and Church, G. M. (2015) Safeguarding CRISPR-Cas9 gene drives in yeast. Nat. Biotechnol., 33, 1250–1255

[47] Gallagher, R. R., Patel, J. R., Interiano, A. L., Rovner, A. J. and Isaacs, F. J. (2015) Multilayered genetic safeguards limit growth of microorganisms to defined environments. Nucleic Acids Res., 43, 1945–1954

[48] Boeke, J. D., Church, G., Hessel, A., Kelley, N. J., Arkin, A., Cai, Y., Carlson, R., Chakravarti, A., Cornish, V. W., Holt, L., (2016) The Genome Project-Write. Science, 353, 126–127

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