Skip to main content
PMC home page
American Journal of Human Genetics logoLink to American Journal of Human Genetics
. 1999 Jul;65(1):111–124. doi: 10.1086/302455

Campomelic dysplasia translocation breakpoints are scattered over 1 Mb proximal to SOX9: evidence for an extended control region.

D Pfeifer 1, R Kist 1, K Dewar 1, K Devon 1, E S Lander 1, B Birren 1, L Korniszewski 1, E Back 1, G Scherer 1
PMCID: PMC1378081  PMID: 10364523

Abstract

Campomelic dysplasia (CD), a skeletal malformation syndrome with or without XY sex reversal, is usually caused by mutations within the SOX9 gene on distal 17q. Several CD translocation and inversion cases have been described with breakpoints outside the coding region, mapping to locations >130 kb proximal to SOX9. Such cases are generally less severely affected than cases with SOX9 coding-region mutations, as is borne out by three new translocation cases that we present. We have cloned the region extending 1.2 Mb upstream of the SOX9 gene in overlapping bacterial-artificial-chromosome and P1-artificial-chromosome clones and have established a restriction map with rare-cutter enzymes. With sequence-tagged-site-content mapping in somatic-cell hybrids, as well as with FISH, we have precisely mapped the breakpoints of the three new and of three previously described CD cases. The six CD breakpoints map to an interval that is 140-950 kb proximal to the SOX9 gene. With exon trapping, we could isolate five potential exons from the YAC 946E12 that spans the region, four of which could be placed in the contig in the vicinity of the breakpoints. They show the same transcriptional orientation, but only two have an open reading frame (ORF). We failed to detect expression of these fragments in several human and mouse cDNA libraries, as well as on northern blots. Genomic sequence totaling 1,063 kb from the SOX9 5'-flanking region was determined and was analyzed by the gene-prediction program GENSCAN and by a search of dbEST and other databases. No genes or transcripts could be identified. Together, these data suggest that the chromosomal rearrangements most likely remove one or more cis-regulatory elements from an extended SOX9 control region.

Full Text

The Full Text of this article is available as a PDF (515.4 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Bedell M. A., Brannan C. I., Evans E. P., Copeland N. G., Jenkins N. A., Donovan P. J. DNA rearrangements located over 100 kb 5' of the Steel (Sl)-coding region in Steel-panda and Steel-contrasted mice deregulate Sl expression and cause female sterility by disrupting ovarian follicle development. Genes Dev. 1995 Feb 15;9(4):455–470. doi: 10.1101/gad.9.4.455. [DOI] [PubMed] [Google Scholar]
  3. Bedell M. A., Jenkins N. A., Copeland N. G. Good genes in bad neighbourhoods. Nat Genet. 1996 Mar;12(3):229–232. doi: 10.1038/ng0396-229. [DOI] [PubMed] [Google Scholar]
  4. Bell D. M., Leung K. K., Wheatley S. C., Ng L. J., Zhou S., Ling K. W., Sham M. H., Koopman P., Tam P. P., Cheah K. S. SOX9 directly regulates the type-II collagen gene. Nat Genet. 1997 Jun;16(2):174–178. doi: 10.1038/ng0697-174. [DOI] [PubMed] [Google Scholar]
  5. Bernardi G. The human genome: organization and evolutionary history. Annu Rev Genet. 1995;29:445–476. doi: 10.1146/annurev.ge.29.120195.002305. [DOI] [PubMed] [Google Scholar]
  6. Brown C. J., Hendrich B. D., Rupert J. L., Lafrenière R. G., Xing Y., Lawrence J., Willard H. F. 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. 1992 Oct 30;71(3):527–542. doi: 10.1016/0092-8674(92)90520-m. [DOI] [PubMed] [Google Scholar]
  7. Burge C., Karlin S. Prediction of complete gene structures in human genomic DNA. J Mol Biol. 1997 Apr 25;268(1):78–94. doi: 10.1006/jmbi.1997.0951. [DOI] [PubMed] [Google Scholar]
  8. Cameron F. J., Hageman R. M., Cooke-Yarborough C., Kwok C., Goodwin L. L., Sillence D. O., Sinclair A. H. A novel germ line mutation in SOX9 causes familial campomelic dysplasia and sex reversal. Hum Mol Genet. 1996 Oct;5(10):1625–1630. doi: 10.1093/hmg/5.10.1625. [DOI] [PubMed] [Google Scholar]
  9. De Santa Barbara P., Bonneaud N., Boizet B., Desclozeaux M., Moniot B., Sudbeck P., Scherer G., Poulat F., Berta P. Direct interaction of SRY-related protein SOX9 and steroidogenic factor 1 regulates transcription of the human anti-Müllerian hormone gene. Mol Cell Biol. 1998 Nov;18(11):6653–6665. doi: 10.1128/mcb.18.11.6653. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Fantes J., Redeker B., Breen M., Boyle S., Brown J., Fletcher J., Jones S., Bickmore W., Fukushima Y., Mannens M. Aniridia-associated cytogenetic rearrangements suggest that a position effect may cause the mutant phenotype. Hum Mol Genet. 1995 Mar;4(3):415–422. doi: 10.1093/hmg/4.3.415. [DOI] [PubMed] [Google Scholar]
  11. Foster J. W., Dominguez-Steglich M. A., Guioli S., Kwok C., Weller P. A., Stevanović M., Weissenbach J., Mansour S., Young I. D., Goodfellow P. N. Campomelic dysplasia and autosomal sex reversal caused by mutations in an SRY-related gene. Nature. 1994 Dec 8;372(6506):525–530. doi: 10.1038/372525a0. [DOI] [PubMed] [Google Scholar]
  12. Goji K., Nishijima E., Tsugawa C., Nishio H., Pokharel R. K., Matsuo M. Novel missense mutation in the HMG box of SOX9 gene in a Japanese XY male resulted in campomelic dysplasia and severe defect in masculinization. Hum Mutat. 1998;Suppl 1:S114–S116. doi: 10.1002/humu.1380110138. [DOI] [PubMed] [Google Scholar]
  13. Grosschedl R., Giese K., Pagel J. HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet. 1994 Mar;10(3):94–100. doi: 10.1016/0168-9525(94)90232-1. [DOI] [PubMed] [Google Scholar]
  14. Hageman R. M., Cameron F. J., Sinclair A. H. Mutation analysis of the SOX9 gene in a patient with campomelic dysplasia. Hum Mutat. 1998;Suppl 1:S112–S113. doi: 10.1002/humu.1380110137. [DOI] [PubMed] [Google Scholar]
  15. Houston C. S., Opitz J. M., Spranger J. W., Macpherson R. I., Reed M. H., Gilbert E. F., Herrmann J., Schinzel A. The campomelic syndrome: review, report of 17 cases, and follow-up on the currently 17-year-old boy first reported by Maroteaux et al in 1971. Am J Med Genet. 1983 May;15(1):3–28. doi: 10.1002/ajmg.1320150103. [DOI] [PubMed] [Google Scholar]
  16. Kent J., Wheatley S. C., Andrews J. E., Sinclair A. H., Koopman P. A male-specific role for SOX9 in vertebrate sex determination. Development. 1996 Sep;122(9):2813–2822. doi: 10.1242/dev.122.9.2813. [DOI] [PubMed] [Google Scholar]
  17. Kwok C., Weller P. A., Guioli S., Foster J. W., Mansour S., Zuffardi O., Punnett H. H., Dominguez-Steglich M. A., Brook J. D., Young I. D. Mutations in SOX9, the gene responsible for Campomelic dysplasia and autosomal sex reversal. Am J Hum Genet. 1995 Nov;57(5):1028–1036. [PMC free article] [PubMed] [Google Scholar]
  18. Lefebvre V., Huang W., Harley V. R., Goodfellow P. N., de Crombrugghe B. SOX9 is a potent activator of the chondrocyte-specific enhancer of the pro alpha1(II) collagen gene. Mol Cell Biol. 1997 Apr;17(4):2336–2346. doi: 10.1128/mcb.17.4.2336. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Lengauer C., Green E. D., Cremer T. Fluorescence in situ hybridization of YAC clones after Alu-PCR amplification. Genomics. 1992 Jul;13(3):826–828. doi: 10.1016/0888-7543(92)90160-t. [DOI] [PubMed] [Google Scholar]
  20. Lenz S., Lohse P., Seidel U., Arnold H. H. The alkali light chains of human smooth and nonmuscle myosins are encoded by a single gene. Tissue-specific expression by alternative splicing pathways. J Biol Chem. 1989 May 25;264(15):9009–9015. [PubMed] [Google Scholar]
  21. Mansour S., Hall C. M., Pembrey M. E., Young I. D. A clinical and genetic study of campomelic dysplasia. J Med Genet. 1995 Jun;32(6):415–420. doi: 10.1136/jmg.32.6.415. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Maraia R., Saal H. M., Wangsa D. A chromosome 17q de novo paracentric inversion in a patient with campomelic dysplasia; case report and etiologic hypothesis. Clin Genet. 1991 Jun;39(6):401–408. doi: 10.1111/j.1399-0004.1991.tb03050.x. [DOI] [PubMed] [Google Scholar]
  23. Marra M. A., Kucaba T. A., Dietrich N. L., Green E. D., Brownstein B., Wilson R. K., McDonald K. M., Hillier L. W., McPherson J. D., Waterston R. H. High throughput fingerprint analysis of large-insert clones. Genome Res. 1997 Nov;7(11):1072–1084. doi: 10.1101/gr.7.11.1072. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Meyer J., Südbeck P., Held M., Wagner T., Schmitz M. L., Bricarelli F. D., Eggermont E., Friedrich U., Haas O. A., Kobelt A. Mutational analysis of the SOX9 gene in campomelic dysplasia and autosomal sex reversal: lack of genotype/phenotype correlations. Hum Mol Genet. 1997 Jan;6(1):91–98. doi: 10.1093/hmg/6.1.91. [DOI] [PubMed] [Google Scholar]
  25. Morais da Silva S., Hacker A., Harley V., Goodfellow P., Swain A., Lovell-Badge R. Sox9 expression during gonadal development implies a conserved role for the gene in testis differentiation in mammals and birds. Nat Genet. 1996 Sep;14(1):62–68. doi: 10.1038/ng0996-62. [DOI] [PubMed] [Google Scholar]
  26. Nehls M., Lüno K., Schorpp M., Pfeifer D., Krause S., Matysiak-Scholze U., Dierbach H., Boehm T. YAC/P1 contigs defining the location of 56 microsatellite markers and several genes across a 3.4-cM interval on mouse chromosome 11. Mamm Genome. 1995 May;6(5):321–331. doi: 10.1007/BF00364794. [DOI] [PubMed] [Google Scholar]
  27. Nehls M., Pfeifer D., Boehm T. Exon amplification from complete libraries of genomic DNA using a novel phage vector with automatic plasmid excision facility: application to the mouse neurofibromatosis-1 locus. Oncogene. 1994 Aug;9(8):2169–2175. [PubMed] [Google Scholar]
  28. Ng L. J., Wheatley S., Muscat G. E., Conway-Campbell J., Bowles J., Wright E., Bell D. M., Tam P. P., Cheah K. S., Koopman P. SOX9 binds DNA, activates transcription, and coexpresses with type II collagen during chondrogenesis in the mouse. Dev Biol. 1997 Mar 1;183(1):108–121. doi: 10.1006/dbio.1996.8487. [DOI] [PubMed] [Google Scholar]
  29. Ninomiya S., Isomura M., Narahara K., Seino Y., Nakamura Y. Isolation of a testis-specific cDNA on chromosome 17q from a region adjacent to the breakpoint of t(12;17) observed in a patient with acampomelic campomelic dysplasia and sex reversal. Hum Mol Genet. 1996 Jan;5(1):69–72. doi: 10.1093/hmg/5.1.69. [DOI] [PubMed] [Google Scholar]
  30. Ninomiya S., Narahara K., Tsuji K., Yokoyama Y., Ito S., Seino Y. Acampomelic campomelic syndrome and sex reversal associated with de novo t(12;17) translocation. Am J Med Genet. 1995 Mar 13;56(1):31–34. doi: 10.1002/ajmg.1320560109. [DOI] [PubMed] [Google Scholar]
  31. Pevny L. H., Lovell-Badge R. Sox genes find their feet. Curr Opin Genet Dev. 1997 Jun;7(3):338–344. doi: 10.1016/s0959-437x(97)80147-5. [DOI] [PubMed] [Google Scholar]
  32. Savarirayan R., Bankier A. Acampomelic campomelic dysplasia with de novo 5q;17q reciprocal translocation and severe phenotype. J Med Genet. 1998 Jul;35(7):597–599. doi: 10.1136/jmg.35.7.597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Sinclair A. H., Berta P., Palmer M. S., Hawkins J. R., Griffiths B. L., Smith M. J., Foster J. W., Frischauf A. M., Lovell-Badge R., Goodfellow P. N. A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif. Nature. 1990 Jul 19;346(6281):240–244. doi: 10.1038/346240a0. [DOI] [PubMed] [Google Scholar]
  34. Sutherland H. F., Wadey R., McKie J. M., Taylor C., Atif U., Johnstone K. A., Halford S., Kim U. J., Goodship J., Baldini A. Identification of a novel transcript disrupted by a balanced translocation associated with DiGeorge syndrome. Am J Hum Genet. 1996 Jul;59(1):23–31. [PMC free article] [PubMed] [Google Scholar]
  35. Südbeck P., Schmitz M. L., Baeuerle P. A., Scherer G. Sex reversal by loss of the C-terminal transactivation domain of human SOX9. Nat Genet. 1996 Jun;13(2):230–232. doi: 10.1038/ng0696-230. [DOI] [PubMed] [Google Scholar]
  36. Toder R., Rappold G. A., Schiebel K., Schempp W. ANT3 and STS are autosomal in prosimian lemurs: implications for the evolution of the pseudoautosomal region. Hum Genet. 1995 Jan;95(1):22–28. doi: 10.1007/BF00225068. [DOI] [PubMed] [Google Scholar]
  37. Tommerup N., Schempp W., Meinecke P., Pedersen S., Bolund L., Brandt C., Goodpasture C., Guldberg P., Held K. R., Reinwein H. Assignment of an autosomal sex reversal locus (SRA1) and campomelic dysplasia (CMPD1) to 17q24.3-q25.1. Nat Genet. 1993 Jun;4(2):170–174. doi: 10.1038/ng0693-170. [DOI] [PubMed] [Google Scholar]
  38. Wagner T., Tommerup N., Wirth J., Leffers H., Zimmer J., Back E., Weissenbach J., Scherer G. A somatic cell hybrid panel for distal 17q: GDIA1 maps to 17q25.3. Cytogenet Cell Genet. 1997;76(3-4):172–175. doi: 10.1159/000134538. [DOI] [PubMed] [Google Scholar]
  39. Wagner T., Wirth J., Meyer J., Zabel B., Held M., Zimmer J., Pasantes J., Bricarelli F. D., Keutel J., Hustert E. Autosomal sex reversal and campomelic dysplasia are caused by mutations in and around the SRY-related gene SOX9. Cell. 1994 Dec 16;79(6):1111–1120. doi: 10.1016/0092-8674(94)90041-8. [DOI] [PubMed] [Google Scholar]
  40. Wirth J., Wagner T., Meyer J., Pfeiffer R. A., Tietze H. U., Schempp W., Scherer G. Translocation breakpoints in three patients with campomelic dysplasia and autosomal sex reversal map more than 130 kb from SOX9. Hum Genet. 1996 Feb;97(2):186–193. doi: 10.1007/BF02265263. [DOI] [PubMed] [Google Scholar]
  41. Wright E., Hargrave M. R., Christiansen J., Cooper L., Kun J., Evans T., Gangadharan U., Greenfield A., Koopman P. The Sry-related gene Sox9 is expressed during chondrogenesis in mouse embryos. Nat Genet. 1995 Jan;9(1):15–20. doi: 10.1038/ng0195-15. [DOI] [PubMed] [Google Scholar]
  42. Wunderle V. M., Critcher R., Hastie N., Goodfellow P. N., Schedl A. Deletion of long-range regulatory elements upstream of SOX9 causes campomelic dysplasia. Proc Natl Acad Sci U S A. 1998 Sep 1;95(18):10649–10654. doi: 10.1073/pnas.95.18.10649. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Young I. D., Zuccollo J. M., Maltby E. L., Broderick N. J. Campomelic dysplasia associated with a de novo 2q;17q reciprocal translocation. J Med Genet. 1992 Apr;29(4):251–252. doi: 10.1136/jmg.29.4.251. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. de Kok Y. J., Vossenaar E. R., Cremers C. W., Dahl N., Laporte J., Hu L. J., Lacombe D., Fischel-Ghodsian N., Friedman R. A., Parnes L. S. Identification of a hot spot for microdeletions in patients with X-linked deafness type 3 (DFN3) 900 kb proximal to the DFN3 gene POU3F4. Hum Mol Genet. 1996 Sep;5(9):1229–1235. doi: 10.1093/hmg/5.9.1229. [DOI] [PubMed] [Google Scholar]

Articles from American Journal of Human Genetics are provided here courtesy of American Society of Human Genetics

RESOURCES