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.

Translating dosage compensation to trisomy 21

Nature volume 500, pages 296–300 (2013)Cite this article

Subjects

Abstract

Down’s syndrome is a common disorder with enormous medical and social costs, caused by trisomy for chromosome 21. We tested the concept that gene imbalance across an extra chromosome can be de facto corrected by manipulating a single gene, XIST (the X-inactivation gene). Using genome editing with zinc finger nucleases, we inserted a large, inducible XIST transgene into the DYRK1A locus on chromosome 21, in Down’s syndrome pluripotent stem cells. The XIST non-coding RNA coats chromosome 21 and triggers stable heterochromatin modifications, chromosome-wide transcriptional silencing and DNA methylation to form a ‘chromosome 21 Barr body’. This provides a model to study human chromosome inactivation and creates a system to investigate genomic expression changes and cellular pathologies of trisomy 21, free from genetic and epigenetic noise. Notably, deficits in proliferation and neural rosette formation are rapidly reversed upon silencing one chromosome 21. Successful trisomy silencing in vitro also surmounts the major first step towards potential development of ‘chromosome therapy’.

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Figure 1: Genome editing integrates XIST into chromosome 21 in trisomic iPS cells.
Figure 2: XIST induces heterochromatin modifications and condensed chromosome 21 Barr body.
Figure 3: XIST induces long-range silencing in targeted iPS cells.
Figure 4: Genomic expression and methylation reveal widespread silencing of chromosome 21.
Figure 5: ‘Trisomy correction’ affects cell proliferation and neurogenesis.

Accession codes

Accessions

Gene Expression Omnibus

Data deposits

Microarray data for 27 samples is deposited in GEO under accession number GSE47014.

References

  1. Mégarbané, A. et al. The 50th anniversary of the discovery of trisomy 21: the past, present, and future of research and treatment of Down syndrome. Genet. Med. 11, 611–616 (2009)

    Article  PubMed  Google Scholar 

  2. Gardiner, K. J. Molecular basis of pharmacotherapies for cognition in Down syndrome. Trends Pharmacol. Sci. 31, 66–73 (2010)

    Article  CAS  PubMed  Google Scholar 

  3. Prandini, P. et al. Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. Am. J. Hum. Genet. 81, 252–263 (2007)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Haydar, T. F. & Reeves, R. H. Trisomy 21 and early brain development. Trends Neurosci. 35, 81–91 (2012)

    Article  CAS  PubMed  Google Scholar 

  5. O’Doherty, A. et al. An aneuploid mouse strain carrying human chromosome 21 with Down syndrome phenotypes. Science 309, 2033–2037 (2005)

    Article  ADS  PubMed  PubMed Central  Google Scholar 

  6. Lee, B. & Davidson, B. L. Gene therapy grows into young adulthood: special review issue. Hum. Mol. Genet. 20, R1 (2011)

    Article  CAS  PubMed  Google Scholar 

  7. Hall, L. L. et al. X-inactivation reveals epigenetic anomalies in most hESC but identifies sublines that initiate as expected. J. Cell. Physiol. 216, 445–452 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Nazor, K. L. et al. Recurrent variations in DNA methylation in human pluripotent stem cells and their differentiated derivatives. Cell Stem Cell 10, 620–634 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Brown, C. J. et al. The human XIST gene: analysis of a 17 kb inactive X-specific RNA that contains conserved repeats and is highly localized within the nucleus. Cell 71, 527–542 (1992)

    Article  CAS  PubMed  Google Scholar 

  10. Clemson, C. M., McNeil, J. A., Willard, H. F. & Lawrence, J. B. XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure. J. Cell Biol. 132, 259–275 (1996)

    Article  CAS  PubMed  Google Scholar 

  11. Heard, E. Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr. Opin. Genet. Dev. 15, 482–489 (2005)

    Article  CAS  PubMed  Google Scholar 

  12. Hall, L. L. & Lawrence, J. B. XIST RNA and architecture of the inactive X chromosome: implications for the repeat genome. Cold Spring Harb. Symp. Quant. Biol. 75, 345–356 (2010)

    Article  CAS  PubMed  Google Scholar 

  13. Carrel, L. & Willard, H. F. X-inactivation profile reveals extensive variability in X-linked gene expression in females. Nature 434, 400–404 (2005)

    Article  CAS  ADS  PubMed  Google Scholar 

  14. Lee, J. T., Strauss, W. M., Dausman, J. A. & Jaenisch, R. A 450 kb transgene displays properties of the mammalian X-inactivation center. Cell 86, 83–94 (1996)

    Article  CAS  PubMed  Google Scholar 

  15. Hall, L. L., Clemson, C. M., Byron, M., Wydner, K. & Lawrence, J. B. Unbalanced X;autosome translocations provide evidence for sequence specificity in the association of XIST RNA with chromatin. Hum. Mol. Genet. 11, 3157–3165 (2002)

    Article  CAS  PubMed  Google Scholar 

  16. Hall, L. L. et al. An ectopic human XIST gene can induce chromosome inactivation in postdifferentiation human HT-1080 cells. Proc. Natl Acad. Sci. USA 99, 8677–8682 (2002)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  17. Moehle, E. A. et al. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc. Natl Acad. Sci. USA 104, 3055–3060 (2007)

    Article  CAS  ADS  PubMed  PubMed Central  Google Scholar 

  18. Urnov, F. D., Rebar, E. J., Holmes, M. C., Zhang, H. S. & Gregory, P. D. Genome editing with engineered zinc finger nucleases. Nature Rev. Genet. 11, 636–646 (2010)

    Article  CAS  PubMed  Google Scholar 

  19. DeKelver, R. C. et al. Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome. Genome Res. 20, 1133–1142 (2010)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Park, I. H. et al. Disease-specific induced pluripotent stem cells. Cell 134, 877–886 (2008)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Aït Yahya-Graison, E. et al. Classification of human chromosome 21 gene-expression variations in Down syndrome: impact on disease phenotypes. Am. J. Hum. Genet. 81, 475–491 (2007)

    Article  PubMed  PubMed Central  Google Scholar 

  22. Biancotti, J. C. et al. Human embryonic stem cells as models for aneuploid chromosomal syndromes. Stem Cells 28, 1530–1540 (2010)

    Article  CAS  PubMed  Google Scholar 

  23. Csankovszki, G., Nagy, A. & Jaenisch, R. Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J. Cell Biol. 153, 773–784 (2001)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Cotton, A. M. et al. Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation. Hum. Genet. 130, 187–201 (2011)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Guidi, S., Ciani, E., Bonasoni, P., Santini, D. & Bartesaghi, R. Widespread proliferation impairment and hypocellularity in the cerebellum of fetuses with down syndrome. Brain Pathol. 21, 361–373 (2011)

    Article  PubMed  Google Scholar 

  26. Shi, Y. et al. A human stem cell model of early Alzheimer’s disease pathology in Down syndrome. Sci. Transl. Med. 4, 124ra29 (2012)

    PubMed  PubMed Central  Google Scholar 

  27. Lavon, N. et al. Derivation of euploid human embryonic stem cells from aneuploid embryos. Stem Cells 26, 1874–1882 (2008)

    Article  CAS  PubMed  Google Scholar 

  28. Li, L. B. et al. Trisomy correction in down syndrome induced pluripotent stem cells. Cell Stem Cell 11, 615–619 (2012)

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Doyon, J. B. et al. Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells. Nature Cell Biol. 13, 331–337 (2011)

    Article  CAS  PubMed  Google Scholar 

  30. Miller, J. C. et al. An improved zinc-finger nuclease architecture for highly specific genome editing. Nature Biotechnol. 25, 778–785 (2007)

    Article  CAS  Google Scholar 

  31. Guschin, D. Y. et al. A rapid and general assay for monitoring endogenous gene modification. Methods Mol. Biol. 649, 247–256 (2010)

    Article  CAS  PubMed  Google Scholar 

  32. Urnov, F. D. et al. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435, 646–651 (2005)

    Article  CAS  ADS  PubMed  Google Scholar 

  33. Byron, M., Hall, L. L. & Lawrence, J. B. A multifaceted FISH approach to study endogenous RNAs and DNAs in native nuclear and cell structures. Curr. Protoc. Hum. Gen. Chapter 4, Unit 4 15. (2013)

  34. Irizarry, R. A. et al. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 31, e15 (2003)

    Article  PubMed  PubMed Central  Google Scholar 

  35. Weber, M. et al. Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature Genet. 39, 457–466 (2007)

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We appreciate recent initiatives by administrators of NIGMS and NIH to support more high-risk, high-impact research. Research began with support from GM053234 to J.B.L. for basic X chromosome research, and was made fully possible by GM085548 and GM096400 RC4 to J.B.L. C.J.B. and A.M.C. were supported by CIHR (MOP-13680) to C.J.B. We thank T. Flotte for encouragement and advice regarding genome editing strategies, and similarly appreciate the support of S. Jones and P. Newburger. We thank T. Collingwood for initial discussions regarding this project, and the George Daley laboratory (Harvard) for the Down’s syndrome iPS cell line. L. Lizotte, Z. Matijasevic, K. Smith and E. Swanson provided various assistance. M. S. Kobor and L. Lam (Kobor laboratory) assisted with methylation analysis. D.M.C. is supported by an NIH fellowship 1F32CA154086 and B.R.C. (O. Rando laboratory) is supported by NIH training grant 2T32HD007439 (G. Witman, PI).

Author information

Authors and Affiliations

  1. Department of Cell and Developmental Biology, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, Massachusetts 01655, USA,

    Jun Jiang, Yuanchun Jing, Jen-Chieh Chiang, Heather J. Kolpa, Dawn M. Carone, Benjamin R. Carone, Meg Byron, Lisa L. Hall & Jeanne B. Lawrence

  2. Sangamo BioSciences, 501 Canal Boulevard, Richmond, 94804, California, USA

    Gregory J. Cost, David A. Shivak, Dmitry Y. Guschin, Jocelynn R. Pearl, Edward J. Rebar, Philip D. Gregory & Fyodor D. Urnov

  3. Department of Medical Genetics, University of British Columbia, 2350 Health Sciences Mall, Vancouver, British Columbia V6T 1Z3, Canada,

    Allison M. Cotton & Carolyn J. Brown

Authors
  1. Jun Jiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yuanchun Jing
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Gregory J. Cost
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jen-Chieh Chiang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Heather J. Kolpa
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Allison M. Cotton
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Dawn M. Carone
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Benjamin R. Carone
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. David A. Shivak
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Dmitry Y. Guschin
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Jocelynn R. Pearl
    View author publications

    You can also search for this author in PubMed Google Scholar

  12. Edward J. Rebar
    View author publications

    You can also search for this author in PubMed Google Scholar

  13. Meg Byron
    View author publications

    You can also search for this author in PubMed Google Scholar

  14. Philip D. Gregory
    View author publications

    You can also search for this author in PubMed Google Scholar

  15. Carolyn J. Brown
    View author publications

    You can also search for this author in PubMed Google Scholar

  16. Fyodor D. Urnov
    View author publications

    You can also search for this author in PubMed Google Scholar

  17. Lisa L. Hall
    View author publications

    You can also search for this author in PubMed Google Scholar

  18. Jeanne B. Lawrence
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

J.J., with the assistance of Y.J., designed and produced all constructs, edited all cell lines, and designed and performed most experiments. J.B.L., J.J. and L.L.H. were the main contributors to designing experiments and interpreting results. J.B.L., J.J., L.L.H. and F.D.U. wrote the manuscript. F.D.U., P.D.G. and G.J.C. engineered and validated ZFNs. J.R.P. performed Cel1 and Southern analysis. J.-C.C. performed SNP analysis, characterized three sub-clones, and helped with proliferation experiments. J.J. and Y.J., with help from J.-C.C., M.B., H.J.K. and L.L.H., carried out initial screening of targeted iPS cell sub-clones. H.J.K. edited and characterized primary Down’s syndrome fibroblast line. A.M.C. and C.J.B. carried out DNA methylation analysis and provided XIST cDNA. J.J. and F.D.U. prepared the microarray library. D.M.C. and B.R.C. analysed microarray data with help from D.A.S., D.Y.G. and E.J.R.

Corresponding authors

Correspondence to Fyodor D. Urnov or Jeanne B. Lawrence.

Ethics declarations

Competing interests

J.B.L. and L.L.H. are the inventors on an issued patent describing the concept of epigenetic chromosome therapy by targeted addition of non-coding RNA. G.J.C., D.A.S., D.Y.G., J.R.P., E.J.R., P.D.G. and F.D.U. are full-time employees of Sangamo BioSciences.

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-9 and Supplementary Tables 1-4. (PDF 5079 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Jiang, J., Jing, Y., Cost, G. et al. Translating dosage compensation to trisomy 21. Nature 500, 296–300 (2013). https://doi.org/10.1038/nature12394

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature12394

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing: Translational Research

Sign up for the Nature Briefing: Translational Research newsletter — top stories in biotechnology, drug discovery and pharma.

Get what matters in translational research, free to your inbox weekly. Sign up for Nature Briefing: Translational Research