IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-44112-2.html
   My bibliography  Save this article

Building synthetic chromosomes from natural DNA

Author

Listed:
  • Alessandro L. V. Coradini

    (University of Southern California)

  • Christopher Ne Ville

    (University of Southern California)

  • Zachary A. Krieger

    (University of Southern California)

  • Joshua Roemer

    (University of Southern California)

  • Cara Hull

    (University of Southern California)

  • Shawn Yang

    (University of Southern California)

  • Daniel T. Lusk

    (University of Southern California)

  • Ian M. Ehrenreich

    (University of Southern California)

Abstract

De novo chromosome synthesis is costly and time-consuming, limiting its use in research and biotechnology. Building synthetic chromosomes from natural components is an unexplored alternative with many potential applications. In this paper, we report CReATiNG (Cloning, Reprogramming, and Assembling Tiled Natural Genomic DNA), a method for constructing synthetic chromosomes from natural components in yeast. CReATiNG entails cloning segments of natural chromosomes and then programmably assembling them into synthetic chromosomes that can replace the native chromosomes in cells. We use CReATiNG to synthetically recombine chromosomes between strains and species, to modify chromosome structure, and to delete many linked, non-adjacent regions totaling 39% of a chromosome. The multiplex deletion experiment reveals that CReATiNG also enables recovery from flaws in synthetic chromosome design via recombination between a synthetic chromosome and its native counterpart. CReATiNG facilitates the application of chromosome synthesis to diverse biological problems.

Suggested Citation

  • Alessandro L. V. Coradini & Christopher Ne Ville & Zachary A. Krieger & Joshua Roemer & Cara Hull & Shawn Yang & Daniel T. Lusk & Ian M. Ehrenreich, 2023. "Building synthetic chromosomes from natural DNA," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-44112-2
    DOI: 10.1038/s41467-023-44112-2
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-44112-2
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-44112-2?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Wenjun Jiang & Xuejin Zhao & Tslil Gabrieli & Chunbo Lou & Yuval Ebenstein & Ting F. Zhu, 2015. "Cas9-Assisted Targeting of CHromosome segments CATCH enables one-step targeted cloning of large gene clusters," Nature Communications, Nature, vol. 6(1), pages 1-8, November.
    2. Dariusz R. Kutyna & Cristobal A. Onetto & Thomas C. Williams & Hugh D. Goold & Ian T. Paulsen & Isak S. Pretorius & Daniel L. Johnson & Anthony R. Borneman, 2022. "Construction of a synthetic Saccharomyces cerevisiae pan-genome neo-chromosome," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Julius Fredens & Kaihang Wang & Daniel Torre & Louise F. H. Funke & Wesley E. Robertson & Yonka Christova & Tiongsun Chia & Wolfgang H. Schmied & Daniel L. Dunkelmann & Václav Beránek & Chayasith Utta, 2019. "Total synthesis of Escherichia coli with a recoded genome," Nature, Nature, vol. 569(7757), pages 514-518, May.
    4. Alessandro L. V. Coradini & Cara B. Hull & Ian M. Ehrenreich, 2020. "Building genomes to understand biology," Nature Communications, Nature, vol. 11(1), pages 1-11, December.
    5. Jessica S. Dymond & Sarah M. Richardson & Candice E. Coombes & Timothy Babatz & Héloïse Muller & Narayana Annaluru & William J. Blake & Joy W. Schwerzmann & Junbiao Dai & Derek L. Lindstrom & Annabel , 2011. "Synthetic chromosome arms function in yeast and generate phenotypic diversity by design," Nature, Nature, vol. 477(7365), pages 471-476, September.
    6. Behnam Enghiad & Chunshuai Huang & Fang Guo & Guangde Jiang & Bin Wang & S. Kasra Tabatabaei & Teresa A. Martin & Huimin Zhao, 2021. "Cas12a-assisted precise targeted cloning using in vivo Cre-lox recombination," Nature Communications, Nature, vol. 12(1), pages 1-11, December.
    7. Manolis Kellis & Nick Patterson & Matthew Endrizzi & Bruce Birren & Eric S. Lander, 2003. "Sequencing and comparison of yeast species to identify genes and regulatory elements," Nature, Nature, vol. 423(6937), pages 241-254, May.
    8. Jingchuan Luo & Xiaoji Sun & Brendan P. Cormack & Jef D. Boeke, 2018. "Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast," Nature, Nature, vol. 560(7718), pages 392-396, August.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Shuangying Jiang & Zhouqing Luo & Jie Wu & Kang Yu & Shijun Zhao & Zelin Cai & Wenfei Yu & Hui Wang & Li Cheng & Zhenzhen Liang & Hui Gao & Marco Monti & Daniel Schindler & Linsen Huang & Cheng Zeng &, 2023. "Building a eukaryotic chromosome arm by de novo design and synthesis," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    2. Hideto Mori & Nozomu Yachie, 2022. "A framework to efficiently describe and share reproducible DNA materials and construction protocols," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    3. Yuting Chen & Eriona Hysolli & Anlu Chen & Stephen Casper & Songlei Liu & Kevin Yang & Chenli Liu & George Church, 2022. "Multiplex base editing to convert TAG into TAA codons in the human genome," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    4. Huiming Zhang & Xian Fu & Xuemei Gong & Yun Wang & Haolin Zhang & Yu Zhao & Yue Shen, 2022. "Systematic dissection of key factors governing recombination outcomes by GCE-SCRaMbLE," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    5. Sinha, Shreya & Narain, Nivedita & Bhanjdeo, Arundhita, 2022. "Building back better? Resilience as wellbeing for rural migrant households in Bihar, India," World Development, Elsevier, vol. 159(C).
    6. Li, Yufan & Teng, Weichen & Tsai, Limin & Lin, Tom M.Y., 2022. "Does English proficiency support the economic development of non-English-speaking countries? The case of Asia," International Journal of Educational Development, Elsevier, vol. 92(C).
    7. Hengqian Ren & Shravan R. Dommaraju & Chunshuai Huang & Haiyang Cui & Yuwei Pan & Marko Nesic & Lingyang Zhu & David Sarlah & Douglas A. Mitchell & Huimin Zhao, 2023. "Genome mining unveils a class of ribosomal peptides with two amino termini," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    8. Valerie Storms & Marleen Claeys & Aminael Sanchez & Bart De Moor & Annemieke Verstuyf & Kathleen Marchal, 2010. "The Effect of Orthology and Coregulation on Detecting Regulatory Motifs," PLOS ONE, Public Library of Science, vol. 5(2), pages 1-11, February.
    9. Robert K Bradley & Adam Roberts & Michael Smoot & Sudeep Juvekar & Jaeyoung Do & Colin Dewey & Ian Holmes & Lior Pachter, 2009. "Fast Statistical Alignment," PLOS Computational Biology, Public Library of Science, vol. 5(5), pages 1-15, May.
    10. J Roman Arguello & Carolina Sellanes & Yann Ru Lou & Robert A Raguso, 2013. "Can Yeast (S. cerevisiae) Metabolic Volatiles Provide Polymorphic Signaling?," PLOS ONE, Public Library of Science, vol. 8(8), pages 1-12, August.
    11. Fabio Pardi & Nick Goldman, 2005. "Species Choice for Comparative Genomics: Being Greedy Works," PLOS Genetics, Public Library of Science, vol. 1(6), pages 1-1, December.
    12. Krishna B. S. Swamy & Hsin-Yi Lee & Carmina Ladra & Chien-Fu Jeff Liu & Jung-Chi Chao & Yi-Yun Chen & Jun-Yi Leu, 2022. "Proteotoxicity caused by perturbed protein complexes underlies hybrid incompatibility in yeast," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    13. Yin Liu & Xinyi Liu & Dongyi Wei & Lu Dang & Xiaoran Xu & Shisheng Huang & Liwen Li & Sanyun Wu & Jinxian Wu & Xiaoyan Liu & Wenjun Sun & Wanyu Tao & Yongchang Wei & Xingxu Huang & Kui Li & Xinjie Wan, 2024. "CoHIT: a one-pot ultrasensitive ERA-CRISPR system for detecting multiple same-site indels," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    14. Abel Brodeur & David Gray & Anik Islam & Suraiya Bhuiyan, 2021. "A literature review of the economics of COVID‐19," Journal of Economic Surveys, Wiley Blackwell, vol. 35(4), pages 1007-1044, September.
    15. Tiantian Chang & Weichao Ding & Shirui Yan & Yun Wang & Haoling Zhang & Yu Zhang & Zhi Ping & Huiming Zhang & Yijian Huang & Jiahui Zhang & Dan Wang & Wenwei Zhang & Xun Xu & Yue Shen & Xian Fu, 2023. "A robust yeast biocontainment system with two-layered regulation switch dependent on unnatural amino acid," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    16. Eilon Sharon & Shai Lubliner & Eran Segal, 2008. "A Feature-Based Approach to Modeling Protein–DNA Interactions," PLOS Computational Biology, Public Library of Science, vol. 4(8), pages 1-17, August.
    17. Donghui Choe & Connor A. Olson & Richard Szubin & Hannah Yang & Jaemin Sung & Adam M. Feist & Bernhard O. Palsson, 2024. "Advancing the scale of synthetic biology via cross-species transfer of cellular functions enabled by iModulon engraftment," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    18. Vincent Libis & Logan W. MacIntyre & Rabia Mehmood & Liliana Guerrero & Melinda A. Ternei & Niv Antonovsky & Ján Burian & Zongqiang Wang & Sean F. Brady, 2022. "Multiplexed mobilization and expression of biosynthetic gene clusters," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    19. Prakash, Navendu & Srivastava, Bhavya & Singh, Shveta & Sharma, Seema & Jain, Sonali, 2022. "Effectiveness of social distancing interventions in containing COVID-19 incidence: International evidence using Kalman filter," Economics & Human Biology, Elsevier, vol. 44(C).
    20. Taotao Li & Duo Du & Dandan Zhang & Yicheng Lin & Jiakang Ma & Mengyu Zhou & Weida Meng & Zelin Jin & Ziqiang Chen & Haozhe Yuan & Jue Wang & Shulong Dong & Shaoyang Sun & Wenjing Ye & Bosen Li & Houb, 2023. "CRISPR-based targeted haplotype-resolved assembly of a megabase region," Nature Communications, Nature, vol. 14(1), pages 1-15, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-44112-2. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.