Translating dosage compensation to trisomy 21

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’.

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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.

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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).

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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.

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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.

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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

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