"Perfect" designer chromosome v and behavior of a ring derivative

Ze Xiong Xie; Bing Zhi Li; Leslie A. Mitchell; Yi Wu; Xin Qi; Zhu Jin; Bin Jia; Xia Wang; Bo Xuan Zeng; Hui Min Liu; Xiao Le Wu; Qi Feng; Wen Zheng Zhang; Wei Liu; Ming Zhu Ding; Xia Li; Guang Rong Zhao; Jian Jun Qiao; Jing Sheng Cheng; Meng Zhao; Zheng Kuang; Xuya Wang; J. Andrew Martin; Giovanni Stracquadanio; Kun Yang; Xue Bai; Juan Zhao; Meng Long Hu; Qiu Hui Lin; Wen Qian Zhang; Ming Hua Shen; Si Chen; Wan Su; En Xu Wang; Rui Guo; Fang Zhai; Xue Jiao Guo; Hao Xing Du; Jia Qing Zhu; Tian Qing Song; Jun Jun Dai; Fei Fei Li; Guo Zhen Jiang; Shi Lei Han; Shi Yang Liu; Zhi Chao Yu; Xiao Na Yang; Ken Chen; Cheng Hu; Da Shuai Li; Nan Jia; Yue Liu; Lin Ting Wang; Su Wang; Xiao Tong Wei; Mei Qing Fu; Lan Meng Qu; Si Yu Xin; Ting Liu; Kai Ren Tian; Xue Nan Li; Jin Hua Zhang; Li Xiang Song; Jin Gui Liu; Jia Fei Lv; Hang Xu; Ran Tao; Yan Wang; Ting Ting Zhang; Ye Xuan Deng; Yi Ran Wang; Ting Li; Guang Xin Ye; Xiao Ran Xu; Zheng Bao Xia; Wei Zhang; Shi Lan Yang; Yi Lin Liu; Wen Qi Ding; Zhen Ning Liu; Jun Qi Zhu; Ning Zhi Liu; Roy Walker; Yisha Luo; Yun Wang; Yue Shen; Huanming Yang; Yizhi Cai; Ping Sheng Ma; Chun Ting Zhang; Joel S. Bader; Jef D. Boeke; Ying Jin Yuan

doi:10.1126/science.aaf4704

"Perfect" designer chromosome v and behavior of a ring derivative

Ze Xiong Xie, Bing Zhi Li, Leslie A. Mitchell, Yi Wu, Xin Qi, Zhu Jin, Bin Jia, Xia Wang, Bo Xuan Zeng, Hui Min Liu, Xiao Le Wu, Qi Feng, Wen Zheng Zhang, Wei Liu, Ming Zhu Ding, Xia Li, Guang Rong Zhao, Jian Jun Qiao, Jing Sheng Cheng, Meng ZhaoZheng Kuang, Xuya Wang, J. Andrew Martin, Giovanni Stracquadanio, Kun Yang, Xue Bai, Juan Zhao, Meng Long Hu, Qiu Hui Lin, Wen Qian Zhang, Ming Hua Shen, Si Chen, Wan Su, En Xu Wang, Rui Guo, Fang Zhai, Xue Jiao Guo, Hao Xing Du, Jia Qing Zhu, Tian Qing Song, Jun Jun Dai, Fei Fei Li, Guo Zhen Jiang, Shi Lei Han, Shi Yang Liu, Zhi Chao Yu, Xiao Na Yang, Ken Chen, Cheng Hu, Da Shuai Li, Nan Jia, Yue Liu, Lin Ting Wang, Su Wang, Xiao Tong Wei, Mei Qing Fu, Lan Meng Qu, Si Yu Xin, Ting Liu, Kai Ren Tian, Xue Nan Li, Jin Hua Zhang, Li Xiang Song, Jin Gui Liu, Jia Fei Lv, Hang Xu, Ran Tao, Yan Wang, Ting Ting Zhang, Ye Xuan Deng, Yi Ran Wang, Ting Li, Guang Xin Ye, Xiao Ran Xu, Zheng Bao Xia, Wei Zhang, Shi Lan Yang, Yi Lin Liu, Wen Qi Ding, Zhen Ning Liu, Jun Qi Zhu, Ning Zhi Liu, Roy Walker, Yisha Luo, Yun Wang, Yue Shen, Huanming Yang, Yizhi Cai, Ping Sheng Ma, Chun Ting Zhang, Joel S. Bader, Jef D. Boeke, Ying Jin Yuan

Immunology

Research output: Contribution to journal › Article › peer-review

195 Scopus citations

Abstract

Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis.We designed and de novo synthesized 536, 024-base pair chromosome synV in the "Build-A-Genome China" course.We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.

Original language	English (US)
Article number	eaaf4704
Journal	Science
Volume	355
Issue number	6329
DOIs	https://doi.org/10.1126/science.aaf4704
State	Published - Mar 10 2017

ASJC Scopus subject areas

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10.1126/science.aaf4704

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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., Wu, X. L., Feng, Q., Zhang, W. Z., Liu, W., Ding, M. Z., Li, X., Zhao, G. R., Qiao, J. J., Cheng, J. S., ... Yuan, Y. J. (2017). "Perfect" designer chromosome v and behavior of a ring derivative. Science, 355(6329), Article eaaf4704. https://doi.org/10.1126/science.aaf4704

Xie, ZX, Li, BZ, Mitchell, LA, Wu, Y, Qi, X, Jin, Z, Jia, B, Wang, X, Zeng, BX, Liu, HM, Wu, XL, Feng, Q, Zhang, WZ, Liu, W, Ding, MZ, Li, X, Zhao, GR, Qiao, JJ, Cheng, JS, Zhao, M, Kuang, Z, Wang, X, Martin, JA, Stracquadanio, G, Yang, K, Bai, X, Zhao, J, Hu, ML, Lin, QH, Zhang, WQ, Shen, MH, Chen, S, Su, W, Wang, EX, Guo, R, Zhai, F, Guo, XJ, Du, HX, Zhu, JQ, Song, TQ, Dai, JJ, Li, FF, Jiang, GZ, Han, SL, Liu, SY, Yu, ZC, Yang, XN, Chen, K, Hu, C, Li, DS, Jia, N, Liu, Y, Wang, LT, Wang, S, Wei, XT, Fu, MQ, Qu, LM, Xin, SY, Liu, T, Tian, KR, Li, XN, Zhang, JH, Song, LX, Liu, JG, Lv, JF, Xu, H, Tao, R, Wang, Y, Zhang, TT, Deng, YX, Wang, YR, Li, T, Ye, GX, Xu, XR, Xia, ZB, Zhang, W, Yang, SL, Liu, YL, Ding, WQ, Liu, ZN, Zhu, JQ, Liu, NZ, Walker, R, Luo, Y, Wang, Y, Shen, Y, Yang, H, Cai, Y, Ma, PS, Zhang, CT, Bader, JS, Boeke, JD & Yuan, YJ 2017, '"Perfect" designer chromosome v and behavior of a ring derivative', Science, vol. 355, no. 6329, eaaf4704. https://doi.org/10.1126/science.aaf4704

@article{393fc6b3f6e64d7da568a873fb4904bb,

title = "{"}Perfect{"} designer chromosome v and behavior of a ring derivative",

abstract = "Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis.We designed and de novo synthesized 536, 024-base pair chromosome synV in the {"}Build-A-Genome China{"} course.We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.",

author = "Xie, {Ze Xiong} and Li, {Bing Zhi} and Mitchell, {Leslie A.} and Yi Wu and Xin Qi and Zhu Jin and Bin Jia and Xia Wang and Zeng, {Bo Xuan} and Liu, {Hui Min} and Wu, {Xiao Le} and Qi Feng and Zhang, {Wen Zheng} and Wei Liu and Ding, {Ming Zhu} and Xia Li and Zhao, {Guang Rong} and Qiao, {Jian Jun} and Cheng, {Jing Sheng} and Meng Zhao and Zheng Kuang and Xuya Wang and Martin, {J. Andrew} and Giovanni Stracquadanio and Kun Yang and Xue Bai and Juan Zhao and Hu, {Meng Long} and Lin, {Qiu Hui} and Zhang, {Wen Qian} and Shen, {Ming Hua} and Si Chen and Wan Su and Wang, {En Xu} and Rui Guo and Fang Zhai and Guo, {Xue Jiao} and Du, {Hao Xing} and Zhu, {Jia Qing} and Song, {Tian Qing} and Dai, {Jun Jun} and Li, {Fei Fei} and Jiang, {Guo Zhen} and Han, {Shi Lei} and Liu, {Shi Yang} and Yu, {Zhi Chao} and Yang, {Xiao Na} and Ken Chen and Cheng Hu and Li, {Da Shuai} and Nan Jia and Yue Liu and Wang, {Lin Ting} and Su Wang and Wei, {Xiao Tong} and Fu, {Mei Qing} and Qu, {Lan Meng} and Xin, {Si Yu} and Ting Liu and Tian, {Kai Ren} and Li, {Xue Nan} and Zhang, {Jin Hua} and Song, {Li Xiang} and Liu, {Jin Gui} and Lv, {Jia Fei} and Hang Xu and Ran Tao and Yan Wang and Zhang, {Ting Ting} and Deng, {Ye Xuan} and Wang, {Yi Ran} and Ting Li and Ye, {Guang Xin} and Xu, {Xiao Ran} and Xia, {Zheng Bao} and Wei Zhang and Yang, {Shi Lan} and Liu, {Yi Lin} and Ding, {Wen Qi} and Liu, {Zhen Ning} and Zhu, {Jun Qi} and Liu, {Ning Zhi} and Roy Walker and Yisha Luo and Yun Wang and Yue Shen and Huanming Yang and Yizhi Cai and Ma, {Ping Sheng} and Zhang, {Chun Ting} and Bader, {Joel S.} and Boeke, {Jef D.} and Yuan, {Ying Jin}",

note = "Funding Information: This work in TJU was funded by the {"}863{"} program, 2012AA02A708; the International Cooperative Project, 2015DFA00960; the {"}973{"} program, 2014CB745100; and the National Natural Science Foundation of China program, 21390203 and 21621004. Work in the United States was funded by U.S. NSF grants MCB-1026068 and MCB-1158201 to J.D.B. and U.S. NSF grant MCB-1445545 to J.S.B. J.D.B. and J.S.B. are founders and directors of Neochromosome. J.D.B. serves as a scientific advisor to Recombinetics and Sample6. These arrangements are reviewed and managed by the Committees on Conflict of Interest at New York University (NYU) Langone Medical Center (J.D.B.) and Johns Hopkins University (J.S.B.). We thank A. Heguy and her staff at NYU's Genome Technology Center for outstanding deep sequencing services. We thank P. Hare for the help with editing and N. Agmon for assistance with use of CRISPR/Cas9. Additional information [synV design diagram, PCRTag sequences, Feature summary table (wild-type V, designed synV, physical strains; yeast-chr05-9-01 to yeast-chr05-9-22), variants in physical strains (yeast-chr05-9-01 to yeast-chr05-9-22), PCR primers, and a summary of BBs and minichunks] related to synV can be accessed on the Sc2.0 website (www.syntheticyeast.org). All genomic data for this paper are available under the Sc2.0 umbrella BioProject accession no. PRJNA351844.",

year = "2017",

month = mar,

day = "10",

doi = "10.1126/science.aaf4704",

language = "English (US)",

volume = "355",

journal = "Science",

issn = "0036-8075",

publisher = "American Association for the Advancement of Science",

number = "6329",

}

TY - JOUR

T1 - "Perfect" designer chromosome v and behavior of a ring derivative

AU - Xie, Ze Xiong

AU - Li, Bing Zhi

AU - Mitchell, Leslie A.

AU - Wu, Yi

AU - Qi, Xin

AU - Jin, Zhu

AU - Jia, Bin

AU - Wang, Xia

AU - Zeng, Bo Xuan

AU - Liu, Hui Min

AU - Wu, Xiao Le

AU - Feng, Qi

AU - Zhang, Wen Zheng

AU - Liu, Wei

AU - Ding, Ming Zhu

AU - Li, Xia

AU - Zhao, Guang Rong

AU - Qiao, Jian Jun

AU - Cheng, Jing Sheng

AU - Zhao, Meng

AU - Kuang, Zheng

AU - Wang, Xuya

AU - Martin, J. Andrew

AU - Stracquadanio, Giovanni

AU - Yang, Kun

AU - Bai, Xue

AU - Zhao, Juan

AU - Hu, Meng Long

AU - Lin, Qiu Hui

AU - Zhang, Wen Qian

AU - Shen, Ming Hua

AU - Chen, Si

AU - Su, Wan

AU - Wang, En Xu

AU - Guo, Rui

AU - Zhai, Fang

AU - Guo, Xue Jiao

AU - Du, Hao Xing

AU - Zhu, Jia Qing

AU - Song, Tian Qing

AU - Dai, Jun Jun

AU - Li, Fei Fei

AU - Jiang, Guo Zhen

AU - Han, Shi Lei

AU - Liu, Shi Yang

AU - Yu, Zhi Chao

AU - Yang, Xiao Na

AU - Chen, Ken

AU - Hu, Cheng

AU - Li, Da Shuai

AU - Jia, Nan

AU - Liu, Yue

AU - Wang, Lin Ting

AU - Wang, Su

AU - Wei, Xiao Tong

AU - Fu, Mei Qing

AU - Qu, Lan Meng

AU - Xin, Si Yu

AU - Liu, Ting

AU - Tian, Kai Ren

AU - Li, Xue Nan

AU - Zhang, Jin Hua

AU - Song, Li Xiang

AU - Liu, Jin Gui

AU - Lv, Jia Fei

AU - Xu, Hang

AU - Tao, Ran

AU - Wang, Yan

AU - Zhang, Ting Ting

AU - Deng, Ye Xuan

AU - Wang, Yi Ran

AU - Li, Ting

AU - Ye, Guang Xin

AU - Xu, Xiao Ran

AU - Xia, Zheng Bao

AU - Zhang, Wei

AU - Yang, Shi Lan

AU - Liu, Yi Lin

AU - Ding, Wen Qi

AU - Liu, Zhen Ning

AU - Zhu, Jun Qi

AU - Liu, Ning Zhi

AU - Walker, Roy

AU - Luo, Yisha

AU - Wang, Yun

AU - Shen, Yue

AU - Yang, Huanming

AU - Cai, Yizhi

AU - Ma, Ping Sheng

AU - Zhang, Chun Ting

AU - Bader, Joel S.

AU - Boeke, Jef D.

AU - Yuan, Ying Jin

N1 - Funding Information: This work in TJU was funded by the "863" program, 2012AA02A708; the International Cooperative Project, 2015DFA00960; the "973" program, 2014CB745100; and the National Natural Science Foundation of China program, 21390203 and 21621004. Work in the United States was funded by U.S. NSF grants MCB-1026068 and MCB-1158201 to J.D.B. and U.S. NSF grant MCB-1445545 to J.S.B. J.D.B. and J.S.B. are founders and directors of Neochromosome. J.D.B. serves as a scientific advisor to Recombinetics and Sample6. These arrangements are reviewed and managed by the Committees on Conflict of Interest at New York University (NYU) Langone Medical Center (J.D.B.) and Johns Hopkins University (J.S.B.). We thank A. Heguy and her staff at NYU's Genome Technology Center for outstanding deep sequencing services. We thank P. Hare for the help with editing and N. Agmon for assistance with use of CRISPR/Cas9. Additional information [synV design diagram, PCRTag sequences, Feature summary table (wild-type V, designed synV, physical strains; yeast-chr05-9-01 to yeast-chr05-9-22), variants in physical strains (yeast-chr05-9-01 to yeast-chr05-9-22), PCR primers, and a summary of BBs and minichunks] related to synV can be accessed on the Sc2.0 website (www.syntheticyeast.org). All genomic data for this paper are available under the Sc2.0 umbrella BioProject accession no. PRJNA351844.

PY - 2017/3/10

Y1 - 2017/3/10

N2 - Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis.We designed and de novo synthesized 536, 024-base pair chromosome synV in the "Build-A-Genome China" course.We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.

AB - Perfect matching of an assembled physical sequence to a specified designed sequence is crucial to verify design principles in genome synthesis.We designed and de novo synthesized 536, 024-base pair chromosome synV in the "Build-A-Genome China" course.We corrected an initial isolate of synV to perfectly match the designed sequence using integrative cotransformation and clustered regularly interspaced short palindromic repeats (CRISPR)/ CRISPR-associated protein 9 (Cas9)-mediated editing in 22 steps; synV strains exhibit high fitness under a variety of culture conditions, compared with that of wild-type V strains. A ring synV derivative was constructed, which is fully functional in Saccharomyces cerevisiae under all conditions tested and exhibits lower spore viability during meiosis. Ring synV chromosome can extends Sc2.0 design principles and provides a model with which to study genomic rearrangement, ring chromosome evolution, and human ring chromosome disorders.

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UR - http://www.scopus.com/inward/citedby.url?scp=85014846316&partnerID=8YFLogxK

U2 - 10.1126/science.aaf4704

DO - 10.1126/science.aaf4704

M3 - Article

C2 - 28280151

AN - SCOPUS:85014846316

SN - 0036-8075

VL - 355

JO - Science

JF - Science

IS - 6329

M1 - eaaf4704

ER -

"Perfect" designer chromosome v and behavior of a ring derivative

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