iBet uBet web content aggregator. Adding the entire web to your favor.
iBet uBet web content aggregator. Adding the entire web to your favor.



Link to original content: https://doi.org/10.1038/s41586-018-0382-x
Creating a functional single-chromosome yeast | Nature
Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Article
  • Published:

Creating a functional single-chromosome yeast

Nature volume 560, pages 331–335 (2018)Cite this article

Subjects

Abstract

Eukaryotic genomes are generally organized in multiple chromosomes. Here we have created a functional single-chromosome yeast from a Saccharomyces cerevisiae haploid cell containing sixteen linear chromosomes, by successive end-to-end chromosome fusions and centromere deletions. The fusion of sixteen native linear chromosomes into a single chromosome results in marked changes to the global three-dimensional structure of the chromosome due to the loss of all centromere-associated inter-chromosomal interactions, most telomere-associated inter-chromosomal interactions and 67.4% of intra-chromosomal interactions. However, the single-chromosome and wild-type yeast cells have nearly identical transcriptome and similar phenome profiles. The giant single chromosome can support cell life, although this strain shows reduced growth across environments, competitiveness, gamete production and viability. This synthetic biology study demonstrates an approach to exploration of eukaryote evolution with respect to chromosome structure and function.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Fig. 1: Creation of a single-chromosome yeast.
Fig. 2: Confirmation of chromosome fusion(s) in yeast strains.
Fig. 3: Chromosomal interactions and 3D structures of genomes in BY4742, SY6, SY13 and SY14 strains.
Fig. 4: Transcriptome and phenome analyses.
Fig. 5: Sporulation and competition fitness.

Similar content being viewed by others

References

  1. Crosland, M. W. & Crozier, R. H. Myrmecia pilosula, an ant with only one pair of chromosomes. Science 231, 1278 (1986).

    Article  ADS  CAS  Google Scholar 

  2. Green, E. D., Watson, J. D. & Collins, F. S. Human Genome Project: Twenty-five years of big biology. Nature 526, 29–31 (2015).

    Article  ADS  CAS  Google Scholar 

  3. Lee, J. Y. et al. Simple purification of human chromosomes to homogeneity using muntjac hybrid cells. Nat. Genet. 7, 29–33 (1994).

    Article  CAS  Google Scholar 

  4. Goffeau, A. et al. Life with 6000 genes. Science 274, 546–567 (1996).

    Article  ADS  CAS  Google Scholar 

  5. Wood, V. et al. The genome sequence of Schizosaccharomyces pombe. Nature 415, 871–880 (2002).

    Article  ADS  CAS  Google Scholar 

  6. McClintock, B. The stability of broken ends of chromosomes in Zea mays. Genetics 26, 234–282 (1941).

    CAS  PubMed  PubMed Central  Google Scholar 

  7. DiCarlo, J. E. et al. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 41, 4336–4343 (2013).

    Article  CAS  Google Scholar 

  8. Moretti, P., Freeman, K., Coodly, L. & Shore, D. Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1. Genes Dev. 8, 2257–2269 (1994).

    Article  CAS  Google Scholar 

  9. Gotta, M. et al. The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae. J. Cell Biol. 134, 1349–1363 (1996).

    Article  CAS  Google Scholar 

  10. Zhou, J., Zhou, B. O., Lenzmeier, B. A. & Zhou, J. Q. Histone deacetylase Rpd3 antagonizes Sir2-dependent silent chromatin propagation. Nucleic Acids Res. 37, 3699–3713 (2009).

    Article  CAS  Google Scholar 

  11. Zhang, W. et al. Engineering the ribosomal DNA in a megabase synthetic chromosome. Science 355, eaaf3981 (2017).

    Article  Google Scholar 

  12. Duan, Z. et al. A three-dimensional model of the yeast genome. Nature 465, 363–367 (2010).

    Article  ADS  CAS  Google Scholar 

  13. Mercy, G. et al. 3D organization of synthetic and scrambled chromosomes. Science 355, eaaf4597 (2017).

    Article  Google Scholar 

  14. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).

    Article  ADS  CAS  Google Scholar 

  15. van Berkum, N. L. et al. Hi-C: a method to study the three-dimensional architecture of genomes. J. Vis. Exp. 39, 1869 (2010).

    Google Scholar 

  16. Le, T. B., Imakaev, M. V., Mirny, L. A. & Laub, M. T. High-resolution mapping of the spatial organization of a bacterial chromosome. Science 342, 731–734 (2013).

    Article  ADS  CAS  Google Scholar 

  17. Engel, S. R. et al. The reference genome sequence of Saccharomyces cerevisiae: then and now. G3 (Bethesda) 4, 389–398 (2014).

    Article  Google Scholar 

  18. Wellinger, R. J. & Zakian, V. A. Everything you ever wanted to know about Saccharomyces cerevisiae telomeres: beginning to end. Genetics 191, 1073–1105 (2012).

    Article  CAS  Google Scholar 

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

    Article  ADS  CAS  Google Scholar 

  20. Xie, Z. X. et al. Rapid and efficient CRISPR/Cas9-based mating-type switching of Saccharomyces cerevisiae. G3 (Bethesda) 8, 173–183 (2018).

    Article  CAS  Google Scholar 

  21. Richardson, S. M. et al. Design of a synthetic yeast genome. Science 355, 1040–1044 (2017).

    Article  ADS  CAS  Google Scholar 

  22. Spilianakis, C. G., Lalioti, M. D., Town, T., Lee, G. R. & Flavell, R. A. Interchromosomal associations between alternatively expressed loci. Nature 435, 637–645 (2005).

    Article  ADS  CAS  Google Scholar 

  23. Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010).

    Article  Google Scholar 

  24. Verdaasdonk, J. S. & Bloom, K. Centromeres: unique chromatin structures that drive chromosome segregation. Nat. Rev. Mol. Cell Biol. 12, 320–332 (2011).

    Article  CAS  Google Scholar 

  25. Kegel, A. et al. Chromosome length influences replication-induced topological stress. Nature 471, 392–396 (2011).

    Article  ADS  CAS  Google Scholar 

  26. Yue, J. X. et al. Contrasting evolutionary genome dynamics between domesticated and wild yeasts. Nat. Genet. 49, 913–924 (2017).

    Article  CAS  Google Scholar 

  27. Luo, J., Sun, X., Cormack, B. P. & Boeke, J. D. Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast. Nature https://doi.org/10.1038/s41586-018-0374-x (2018).

    Article  ADS  CAS  Google Scholar 

  28. Zhou, J., Wu, R., Xue, X. & Qin, Z. CasHRA (Cas9-facilitated Homologous Recombination Assembly) method of constructing megabase-sized DNA. Nucleic Acids Res. 44, e124 (2016).

    Article  Google Scholar 

  29. Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

    Article  CAS  Google Scholar 

  30. Gietz, R. D. & Schiestl, R. H. High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method. Nat. Protocols 2, 31–34 (2007).

    Article  CAS  Google Scholar 

  31. Wu, Z. et al. Rad6-Bre1-mediated H2B ubiquitination regulates telomere replication by promoting telomere-end resection. Nucleic Acids Res. 45, 3308–3322 (2017).

    Article  CAS  Google Scholar 

  32. Koren, S. et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res. 27, 722–736 (2017).

    Article  CAS  Google Scholar 

  33. Li, H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 32, 2103–2110 (2016).

    Article  CAS  Google Scholar 

  34. Frith, M. C. & Kawaguchi, R. Split-alignment of genomes finds orthologies more accurately. Genome Biol. 16, 106 (2015).

    Article  Google Scholar 

  35. Krzywinski, M. et al. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639–1645 (2009).

    Article  CAS  Google Scholar 

  36. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    Article  ADS  CAS  Google Scholar 

  37. Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012).

    Article  CAS  Google Scholar 

  38. Crane, E. et al. Condensin-driven remodelling of X chromosome topology during dosage compensation. Nature 523, 240–244 (2015).

    Article  ADS  CAS  Google Scholar 

  39. Varoquaux, N., Ay, F., Noble, W. S. & Vert, J. P. A statistical approach for inferring the 3D structure of the genome. Bioinformatics 30, i26–i33 (2014).

    Article  CAS  Google Scholar 

  40. Sauria, M. E., Phillips-Cremins, J. E., Corces, V. G. & Taylor, J. HiFive: a tool suite for easy and efficient HiC and 5C data analysis. Genome Biol. 16, 237 (2015).

    Article  Google Scholar 

  41. Yardimci, G. et al. Measuring the reproducibility and quality of Hi-C data. Preprint at https://www.biorxiv.org/content/early/2018/02/05/188755 (2017).

  42. Ay, F., Bailey, T. L. & Noble, W. S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999–1011 (2014).

    Article  CAS  Google Scholar 

  43. Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995).

    MathSciNet  MATH  Google Scholar 

  44. Xie, T., Yang, Q.-Y., Wang, X.-T., McLysaght, A. & Zhang, H.-Y. Spatial colocalization of human ohnolog pairs acts to maintain dosage-balance. Mol. Biol. Evol. 33, 2368–2375 (2016).

    Article  CAS  Google Scholar 

  45. Gayral, P. et al. Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals. Mol. Ecol. Resour. 11, 650–661 (2011).

    Article  CAS  Google Scholar 

  46. Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article  CAS  Google Scholar 

  47. Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323 (2011).

    Article  CAS  Google Scholar 

  48. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article  Google Scholar 

  49. Bennis, S., Chami, F., Chami, N., Bouchikhi, T. & Remmal, A. Surface alteration of Saccharomyces cerevisiae induced by thymol and eugenol. Lett. Appl. Microbiol. 38, 454–458 (2004).

    Article  CAS  Google Scholar 

  50. Manukyan, A., Abraham, L., Dungrawala, H. & Schneider, B. L. Synchronization of yeast. Methods Mol. Biol. 761, 173–200 (2011).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank X. Gao, W. Zhao, and J. Li for technical help. This research was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB19000000), the National Natural Science Foundation of China (31421061, 31770099, 31370120, 31230040), the National Key Basic Research Program of China (973 Program) (2011CBA00801, 2012CB721102), and the National Key Research and Development Program of China (2016YFA0500701).

Reviewer information

Nature thanks G. Liti, K. Wolfe and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Authors and Affiliations

  1. Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China

    Yangyang Shao, Ning Lu, Chen Yang, Guoping Zhao, Xiaoli Xue & Zhongjun Qin

  2. University of Chinese Academy of Sciences, Beijing, China

    Yangyang Shao, Ning Lu, Chen Cai & Ling-Li Zhang

  3. The State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China

    Zhenfang Wu, Chen Cai, Shanshan Wang, Ling-Li Zhang & Jin-Qiu Zhou

  4. Frasergen Bioinformatics Co., Ltd, Wuhan, China

    Fan Zhou, Shijun Xiao, Lin Liu & Xiaofei Zeng

  5. Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China

    Huajun Zheng & Guoping Zhao

  6. Beijing Institute of Biotechnology, Beijing, China

    Zhihu Zhao

  7. Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China

    Guoping Zhao

  8. State Key Laboratory of Genetic Engineering, Department of Microbiology, School of Life Sciences and Institute of Biomedical Sciences, Fudan University, Shanghai, China

    Guoping Zhao

Authors
  1. Yangyang Shao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ning Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zhenfang Wu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Chen Cai
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Shanshan Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ling-Li Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Fan Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Shijun Xiao
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Lin Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Xiaofei Zeng
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Huajun Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Chen Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Zhihu Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Guoping Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Jin-Qiu Zhou
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Xiaoli Xue
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Zhongjun Qin
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Z.Q. and X.X. designed and analysed all experiments. J.-Q.Z. and G.Z. contributed to the experiment designs and data evaluation. Y.S. constructed the single-chromosome yeast and conducted the scanning electron microscopy characterization. N.L. conducted the PFGE confirmation, growth characterization and cell cycle experiments. C.C. and L.-L.Z. conducted meiosis and genotoxin sensitivity experiments. Z.W. and S.W. conducted telomere characterization. S.X., X.Z. and H.Z. performed genome analysis. Z.Z. designed the Hi-C and part of the RNA-seq experiments and data interpretation. F.Z., L.L. and Z.Z. performed chromosome Hi-C data analysis. F.Z. analysed the RNA-seq data. X.X. and C.Y. analysed the phenotype microarray data. X.X. wrote the primary manuscript with contributions from J.-Q.Z., Z.Q., G.Z., Z.Z., C.Y., S.X. and Z.W.

Corresponding authors

Correspondence to Guoping Zhao, Jin-Qiu Zhou, Xiaoli Xue or Zhongjun Qin.

Ethics declarations

Competing interests

The authors declare no competing interests.

Additional information

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data figures and tables

Extended Data Fig. 1 Theoretical XhoI digestion pattern of chromosome ends.

The X, STR, and Y′ elements in each subtelomeric regions are marked with black, grey and white boxes, respectively. The TG1–3 telomeric sequences are marked with arrow tips. The XhoI digestion sites in telomere regions are indicated, and the numbers in kb in parenthesis indicate the sizes of DNA fragments recognized by the TG1–3 probe in the Southern blot analysis.

Extended Data Fig. 2 De novo sequence comparison of BY4742 (light grey) and SY14 (dark grey) genomes.

The chromosomes are labelled with Roman numerals of the yeast reference genome. The telomeres (blue), centromeres (red) and telomere-associated repeats (green) that were cut by experimental design are shown in BY4742 chromosomes. Sequence deletions and insertions identified by genomic comparison between BY4742 and SY14 are highlighted in purple and black, respectively, in SY14 chromosomes.

Extended Data Fig. 3 Comparison of the chromosomal interactions of SY6, SY13 and SY14 cells with those of BY4742 cells.

a, Z-score difference heatmaps. Bin length, 10 kb; red and blue show increased and decreased chromatin interactions, respectively. Green box highlights the interactions of the chromosome XV centromere with other chromosomes. b, Venn diagram of the number of significant (P < 0.01, q < 0.01) ‘inter’- and intra-chromosomal interactions (referring to their locations in the BY4742 genome). c, Strong chromosomal interactions of chromosome XV centromere regions in the BY4742, SY6, SY13 and SY14 genomes. The red bars indicate the centromeres and their flanking regions of 50 MboI restriction sites. Each arc throughout the chromosome XV centromere area represents one strong interaction. In SY6, SY13 and SY14, the reserved interactions are marked with black arcs and new interactions are marked with orange arcs. The green arrowheads mark the ten residual interactions near the centromere regions found in all four strains. d, 3D structures of chromosomes XV and II in SY6, SY13 and SY14 cells compared to those in BY4742 cells. The locations of the 10 residual interactions on Chr. XV and II are marked green.

Extended Data Fig. 4 3D structures of single chromosomes.

Chromosome structures in SY6, SY13 and SY14 cells are compared to those in BY4742 cells.

Extended Data Fig. 5 Directional preference plots of SY6, SY13, and SY14 cells compared to BY4742 cells.

Red, BY4742; moss green, SY6; purple, SY13; bright green, SY14. The y-axis denotes the t-test value between the upstream and downstream interactions of each bin. A positive t-value indicates that a bin has more downstream interactions, as described previously16.

Extended Data Fig. 6 Growth competition between SY14/SY14a and BY4742/BY4742a diploid cells.

a, Blue circles represent BY4742/BY4742a (with HIS3 marker) cells that could grow only on SC-His plates; pink triangles represent SY14/SY14a (with URA3 marker) cells that could grow only on SC-Ura plates; green diamonds represent ‘fusion’ cells of BY4742/BY4742a and SY14/SY14a that could grow on both SC-His and SC-Ura plates. Data from three biological replicates are presented. b, FACS analysis of DNA content of BY4742/BY4742a and SY14/SY14a diploid cells before and after co-culture. Data are representative of two independent experiments. c, PCR verification of genomes from BY4742/BY4742a and SY14/SY14a diploid cells. H1–H3: colonies grown only on SC-His plates; HU1–3: colonies grown on both SC-His and SC-Ura plates. The BY4742/BY4742a and SY14/SY14a diploid cells before co-cultivation were used as control. Two pairs of primers, specific for genomes of BY4742/BY4742a and SY14/SY14a, were used. Data shown are representative images of two independent experiments.

Extended Data Table 1 Details of the creation of a single chromosome yeast
Full size table
Extended Data Table 2 Information regarding long repeat sequences near chromosome ends
Full size table
Extended Data Table 3 SNPs and indels confirmed by re-sequencing
Full size table
Extended Data Table 4 Differentially expressed genes in SY14 compared to BY4742 cells
Full size table

Supplementary information

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Shao, Y., Lu, N., Wu, Z. et al. Creating a functional single-chromosome yeast. Nature 560, 331–335 (2018). https://doi.org/10.1038/s41586-018-0382-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/s41586-018-0382-x

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing