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High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology

Nature Methods volume 6, pages 837–842 (2009)Cite this article

Abstract

Balanced chromosomal rearrangements can cause disease, but techniques for their rapid and accurate identification are missing. Here we demonstrate that chromatin conformation capture on chip (4C) technology can be used to screen large genomic regions for balanced and complex inversions and translocations at high resolution. The 4C technique can be used to detect breakpoints also in repetitive DNA sequences as it uniquely relies on capturing genomic fragments across the breakpoint. Using 4C, we uncovered LMO3 as a potentially leukemogenic translocation partner of TRB@. We developed multiplex 4C to simultaneously screen for translocation partners of multiple selected loci. We identified unsuspected translocations and complex rearrangements. Furthermore, using 4C we detected translocations even in small subpopulations of cells. This strategy opens avenues for the rapid fine-mapping of cytogenetically identified translocations and inversions, and the efficient screening for balanced rearrangements near candidate loci, even when rearrangements exist only in subpopulations of cells.

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Figure 1: 4C accurately detects a balanced translocation.
Figure 2: 4C accurately detects a balanced inversion and an unbalanced translocation.
Figure 3: 4C detects translocations in small subpopulations of cells.
Figure 4: 4C identifies novel translocation partners.
Figure 5: 4C can be used to analyze multiple sites frequently involved in rearrangements in T-ALL cells on one microarray.

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References

  1. Iafrate, A.J. et al. Detection of large-scale variation in the human genome. Nat. Genet. 36, 949–951 (2004).

    Article  CAS  Google Scholar 

  2. Mehan, M.R., Freimer, N.B. & Ophoff, R.A. A genome-wide survey of segmental duplications that mediate common human genetic variation of chromosomal architecture. Hum. Genomics 1, 335–344 (2004).

    Article  CAS  Google Scholar 

  3. Sharp, A.J., Cheng, Z. & Eichler, E.E. Structural variation of the human genome. Annu. Rev. Genomics Hum. Genet. 7, 407–442 (2006).

    Article  CAS  Google Scholar 

  4. Easton, D.F. et al. Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447, 1087–1093 (2007).

    Article  CAS  Google Scholar 

  5. Eichler, E.E. et al. Completing the map of human genetic variation. Nature 447, 161–165 (2007).

    Article  CAS  Google Scholar 

  6. Feuk, L., Carson, A.R. & Scherer, S.W. Structural variation in the human genome. Nat. Rev. Genet. 7, 85–97 (2006).

    Article  CAS  Google Scholar 

  7. Campbell, P.J. et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat. Genet. 40, 722–729 (2008).

    Article  CAS  Google Scholar 

  8. Korbel, J.O. et al. Paired-end mapping reveals extensive structural variation in the human genome. Science 318, 420–426 (2007).

    Article  CAS  Google Scholar 

  9. Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348–1354 (2006).

    Article  CAS  Google Scholar 

  10. Simonis, M., Kooren, J. & de Laat, W. An evaluation of 3C-based methods to capture DNA interactions. Nat. Methods 4, 895–901 (2007).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  12. Burnett, R.C., Thirman, M.J., Rowley, J.D. & Diaz, M.O. Molecular analysis of the T-cell acute lymphoblastic leukemia-associated t(1;7)(p34;q34) that fuses LCK and TCRB. Blood 84, 1232–1236 (1994).

    CAS  PubMed  Google Scholar 

  13. Soulier, J. et al. HOXA genes are included in genetic and biologic networks defining human acute T-cell leukemia (T-ALL). Blood 106, 274–286 (2005).

    Article  CAS  Google Scholar 

  14. Speleman, F. et al. A new recurrent inversion, inv(7)(p15q34), leads to transcriptional activation of HOXA10 and HOXA11 in a subset of T-cell acute lymphoblastic leukemias. Leukemia 19, 358–366 (2005).

    Article  CAS  Google Scholar 

  15. Galjaard, R.J. et al. Isolated postaxial polydactyly type B with mosaicism of a submicroscopic unbalanced translocation leading to an extended phenotype in offspring. Am. J. Med. Genet. A. 121, 168–173 (2003).

    Article  Google Scholar 

  16. Aoyama, M. et al. LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Cancer Res. 65, 4587–4597 (2005).

    Article  CAS  Google Scholar 

  17. Armstrong, S.A. & Look, A.T. Molecular genetics of acute lymphoblastic leukemia. J. Clin. Oncol. 23, 6306–6315 (2005).

    Article  CAS  Google Scholar 

  18. Graux, C., Cools, J., Michaux, L., Vandenberghe, P. & Hagemeijer, A. Cytogenetics and molecular genetics of T-cell acute lymphoblastic leukemia: from thymocyte to lymphoblast. Leukemia 20, 1496–1510 (2006).

    Article  CAS  Google Scholar 

  19. Hatano, M., Roberts, C.W. & Minden, M. Crist. W.M. and Korsmeyer, S.J. Deregulation of a homeobox gene, HOX11, by the t(10;14) in T cell leukemia. Science 253, 79–82 (1991).

    Article  CAS  Google Scholar 

  20. Kennedy, M.A. et al. HOX11, a homeobox-containing T-cell oncogene on human chromosome 10q24. Proc. Natl. Acad. Sci. USA 88, 8900–8904 (1991).

    Article  CAS  Google Scholar 

  21. Boehm, T. Foroni, L., Kaneko, Y., Perutz, M.F. & Rabbitts, T.H. The rhombotin family of cysteine-rich LIM-domain oncogenes: distinct members are involved in T-cell translocations to human chromosomes 11p15 and 11p13. Proc. Natl. Acad. Sci. USA 88, 4367–4371 (1991).

    Article  CAS  Google Scholar 

  22. Van Vlierberghe, P. et al. The cryptic chromosomal deletion del(11)(p12p13) as a new activation mechanism of LMO2 in pediatric T-cell acute lymphoblastic leukemia. Blood 108, 3520–3529 (2006).

    Article  CAS  Google Scholar 

  23. Ling, J.Q. et al. CTCF mediates interchromosomal colocalization between Igf2/H19 and Wsb1/Nf1. Science 312, 269–272 (2006).

    Article  CAS  Google Scholar 

  24. Lomvardas, S. et al. Interchromosomal interactions and olfactory receptor choice. Cell 126, 403–413 (2006).

    Article  CAS  Google Scholar 

  25. Wurtele, H. & Chartrand, P. Genome-wide scanning of HoxB1-associated loci in mouse ES cells using an open-ended Chromosome Conformation Capture methodology. Chromosome Res. 14, 477–495 (2006).

    Article  Google Scholar 

  26. Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).

    Article  CAS  Google Scholar 

  27. Tomlins, S.A. et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644–648 (2005).

    Article  CAS  Google Scholar 

  28. Chen, W. et al. Mapping translocation breakpoints by next-generation sequencing. Genome Res. 18, 1143–1149 (2008).

    Article  CAS  Google Scholar 

  29. Fiegler, H. et al. Array painting: a method for the rapid analysis of aberrant chromosomes using DNA microarrays. J. Med. Genet. 40, 664–670 (2003).

    Article  CAS  Google Scholar 

  30. van Vlierberghe, P. et al. A new recurrent 9q34 duplication in pediatric T-cell acute lymphoblastic leukemia. Leukemia 20, 1245–1253 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank A. de Klein, W. van Ijcken, J. Gladdines, J. Veltman, A. Hoischen and E. Splinter for assistance. This work was supported by grants from the Dutch Cancer Society (KWF-EMCR 2006-3500) to J.P.P.M., grants from the European Union and the Cancer Genomics Centre to F.G., grants from the Dutch Scientific Organization (NWO) (912-04-082), Netherlands Genomics Initiative (050-71-324) and the Erasmus MC to W.d.L.

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Authors and Affiliations

  1. Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, The Netherlands

    Marieke Simonis, Petra Klous & Wouter de Laat

  2. Department of Pediatric Oncology, Erasmus Medical Center, Rotterdam, The Netherlands

    Irene Homminga & Jules P P Meijerink

  3. Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands

    Robert-Jan Galjaard

  4. Department of Biochemistry, Erasmus Medical Center, Rotterdam, The Netherlands

    Erik-Jan Rijkers

  5. Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands

    Marieke Simonis, Petra Klous, Frank Grosveld & Wouter de Laat

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Contributions

M.S. designed, performed and analyzed experiments and wrote the manuscript; P.K. performed and analyzed experiments; I.H. helped perform experiments; R.-J.G.: provided PAP cell line and helped design the PAP experiment; E.-J.R. designed the microarray. F.G. helped design experiments; J.P.P.M. provided leukemia samples, helped design T-ALL experiments and helped write the manuscript; and W.d.L. designed experiments, supervised the project and wrote the manuscript.

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Correspondence to Wouter de Laat.

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Competing interests

W.d.L. and F.G hold patent applications PCT/IB2006/002268 and PCT/IB2008/000625 on 4C technology (published by World Intellectual Property Organization).

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Supplementary Figures 1–10, Supplementary Table 1 (PDF 6740 kb)

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Simonis, M., Klous, P., Homminga, I. et al. High-resolution identification of balanced and complex chromosomal rearrangements by 4C technology. Nat Methods 6, 837–842 (2009). https://doi.org/10.1038/nmeth.1391

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