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. 1997 Jun;60(6):1354–1362. doi: 10.1086/515456

Characterization of FMR1 promoter elements by in vivo-footprinting analysis.

S Schwemmle 1, E de Graaff 1, H Deissler 1, D Gläser 1, D Wöhrle 1, I Kennerknecht 1, W Just 1, B A Oostra 1, W Döerfler 1, W Vogel 1, P Steinbach 1, W Dörfler 1
PMCID: PMC1716109  PMID: 9199556

Abstract

Fragile X syndrome is associated with silencing of the FMR1 gene. We studied the transcriptional regulation, by analysis of the FMR1 promoter region for the presence of in vivo protein/DNA interactions and for cytosine methylation at the single-nucleotide level. Four protein-binding sites were present in the unmethylated promoter of the active FMR1 gene. In the methylated promoter of inactive genes no footprints were detected, and no evidence of active repression was found in the region investigated. We propose that the silencing of FMR1 gene transcription results from a lack of transcription-factor binding.

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Selected References

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

  1. Ariga H., Imamura Y., Iguchi-Ariga S. M. DNA replication origin and transcriptional enhancer in c-myc gene share the c-myc protein binding sequences. EMBO J. 1989 Dec 20;8(13):4273–4279. doi: 10.1002/j.1460-2075.1989.tb08613.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bell M. V., Hirst M. C., Nakahori Y., MacKinnon R. N., Roche A., Flint T. J., Jacobs P. A., Tommerup N., Tranebjaerg L., Froster-Iskenius U. Physical mapping across the fragile X: hypermethylation and clinical expression of the fragile X syndrome. Cell. 1991 Feb 22;64(4):861–866. doi: 10.1016/0092-8674(91)90514-y. [DOI] [PubMed] [Google Scholar]
  3. Blackwell T. K., Kretzner L., Blackwood E. M., Eisenman R. N., Weintraub H. Sequence-specific DNA binding by the c-Myc protein. Science. 1990 Nov 23;250(4984):1149–1151. doi: 10.1126/science.2251503. [DOI] [PubMed] [Google Scholar]
  4. Blackwood E. M., Eisenman R. N. Max: a helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with Myc. Science. 1991 Mar 8;251(4998):1211–1217. doi: 10.1126/science.2006410. [DOI] [PubMed] [Google Scholar]
  5. Chan J. Y., Han X. L., Kan Y. W. Cloning of Nrf1, an NF-E2-related transcription factor, by genetic selection in yeast. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11371–11375. doi: 10.1073/pnas.90.23.11371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Dang C. V., Barrett J., Villa-Garcia M., Resar L. M., Kato G. J., Fearon E. R. Intracellular leucine zipper interactions suggest c-Myc hetero-oligomerization. Mol Cell Biol. 1991 Feb;11(2):954–962. doi: 10.1128/mcb.11.2.954. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Feinberg A. P., Vogelstein B. A technique for radiolabeling DNA restriction endonuclease fragments to high specific activity. Anal Biochem. 1983 Jul 1;132(1):6–13. doi: 10.1016/0003-2697(83)90418-9. [DOI] [PubMed] [Google Scholar]
  8. Fu Y. H., Kuhl D. P., Pizzuti A., Pieretti M., Sutcliffe J. S., Richards S., Verkerk A. J., Holden J. J., Fenwick R. G., Jr, Warren S. T. Variation of the CGG repeat at the fragile X site results in genetic instability: resolution of the Sherman paradox. Cell. 1991 Dec 20;67(6):1047–1058. doi: 10.1016/0092-8674(91)90283-5. [DOI] [PubMed] [Google Scholar]
  9. Hansen R. S., Gartler S. M., Scott C. R., Chen S. H., Laird C. D. Methylation analysis of CGG sites in the CpG island of the human FMR1 gene. Hum Mol Genet. 1992 Nov;1(8):571–578. doi: 10.1093/hmg/1.8.571. [DOI] [PubMed] [Google Scholar]
  10. Harrington M. A., Jones P. A., Imagawa M., Karin M. Cytosine methylation does not affect binding of transcription factor Sp1. Proc Natl Acad Sci U S A. 1988 Apr;85(7):2066–2070. doi: 10.1073/pnas.85.7.2066. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Hergersberg M., Matsuo K., Gassmann M., Schaffner W., Lüscher B., Rülicke T., Aguzzi A. Tissue-specific expression of a FMR1/beta-galactosidase fusion gene in transgenic mice. Hum Mol Genet. 1995 Mar;4(3):359–366. doi: 10.1093/hmg/4.3.359. [DOI] [PubMed] [Google Scholar]
  12. Hornstra I. K., Nelson D. L., Warren S. T., Yang T. P. High resolution methylation analysis of the FMR1 gene trinucleotide repeat region in fragile X syndrome. Hum Mol Genet. 1993 Oct;2(10):1659–1665. doi: 10.1093/hmg/2.10.1659. [DOI] [PubMed] [Google Scholar]
  13. Hwu W. L., Lee Y. M., Lee S. C., Wang T. R. In vitro DNA methylation inhibits FMR-1 promoter. Biochem Biophys Res Commun. 1993 May 28;193(1):324–329. doi: 10.1006/bbrc.1993.1627. [DOI] [PubMed] [Google Scholar]
  14. Höller M., Westin G., Jiricny J., Schaffner W. Sp1 transcription factor binds DNA and activates transcription even when the binding site is CpG methylated. Genes Dev. 1988 Sep;2(9):1127–1135. doi: 10.1101/gad.2.9.1127. [DOI] [PubMed] [Google Scholar]
  15. Jacob W. F., Silverman T. A., Cohen R. B., Safer B. Identification and characterization of a novel transcription factor participating in the expression of eukaryotic initiation factor 2 alpha. J Biol Chem. 1989 Dec 5;264(34):20372–20384. [PubMed] [Google Scholar]
  16. Nakahori Y., Knight S. J., Holland J., Schwartz C., Roche A., Tarleton J., Wong S., Flint T. J., Froster-Iskenius U., Bentley D. Molecular heterogeneity of the fragile X syndrome. Nucleic Acids Res. 1991 Aug 25;19(16):4355–4359. doi: 10.1093/nar/19.16.4355. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Pfeifer G. P., Riggs A. D. Genomic sequencing. Methods Mol Biol. 1993;23:169–181. doi: 10.1385/0-89603-248-5:169. [DOI] [PubMed] [Google Scholar]
  18. Pfeifer G. P., Steigerwald S. D., Mueller P. R., Wold B., Riggs A. D. Genomic sequencing and methylation analysis by ligation mediated PCR. Science. 1989 Nov 10;246(4931):810–813. doi: 10.1126/science.2814502. [DOI] [PubMed] [Google Scholar]
  19. Pieretti M., Zhang F. P., Fu Y. H., Warren S. T., Oostra B. A., Caskey C. T., Nelson D. L. Absence of expression of the FMR-1 gene in fragile X syndrome. Cell. 1991 Aug 23;66(4):817–822. doi: 10.1016/0092-8674(91)90125-i. [DOI] [PubMed] [Google Scholar]
  20. Richards R. I., Holman K., Yu S., Sutherland G. R. Fragile X syndrome unstable element, p(CCG)n, and other simple tandem repeat sequences are binding sites for specific nuclear proteins. Hum Mol Genet. 1993 Sep;2(9):1429–1435. doi: 10.1093/hmg/2.9.1429. [DOI] [PubMed] [Google Scholar]
  21. Smeets H. J., Smits A. P., Verheij C. E., Theelen J. P., Willemsen R., van de Burgt I., Hoogeveen A. T., Oosterwijk J. C., Oostra B. A. Normal phenotype in two brothers with a full FMR1 mutation. Hum Mol Genet. 1995 Nov;4(11):2103–2108. doi: 10.1093/hmg/4.11.2103. [DOI] [PubMed] [Google Scholar]
  22. Steinbach P., Wöhrle D., Tariverdian G., Kennerknecht I., Barbi G., Edlinger H., Enders H., Götz-Sothmann M., Heilbronner H., Hosenfeld D. Molecular analysis of mutations in the gene FMR-1 segregating in fragile X families. Hum Genet. 1993 Nov;92(5):491–498. doi: 10.1007/BF00216457. [DOI] [PubMed] [Google Scholar]
  23. Sutcliffe J. S., Nelson D. L., Zhang F., Pieretti M., Caskey C. T., Saxe D., Warren S. T. DNA methylation represses FMR-1 transcription in fragile X syndrome. Hum Mol Genet. 1992 Sep;1(6):397–400. doi: 10.1093/hmg/1.6.397. [DOI] [PubMed] [Google Scholar]
  24. Verheij C., Bakker C. E., de Graaff E., Keulemans J., Willemsen R., Verkerk A. J., Galjaard H., Reuser A. J., Hoogeveen A. T., Oostra B. A. Characterization and localization of the FMR-1 gene product associated with fragile X syndrome. Nature. 1993 Jun 24;363(6431):722–724. doi: 10.1038/363722a0. [DOI] [PubMed] [Google Scholar]
  25. Verkerk A. J., Pieretti M., Sutcliffe J. S., Fu Y. H., Kuhl D. P., Pizzuti A., Reiner O., Richards S., Victoria M. F., Zhang F. P. Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome. Cell. 1991 May 31;65(5):905–914. doi: 10.1016/0092-8674(91)90397-h. [DOI] [PubMed] [Google Scholar]
  26. Vincent A., Heitz D., Petit C., Kretz C., Oberlé I., Mandel J. L. Abnormal pattern detected in fragile-X patients by pulsed-field gel electrophoresis. Nature. 1991 Feb 14;349(6310):624–626. doi: 10.1038/349624a0. [DOI] [PubMed] [Google Scholar]
  27. Wasylyk B. Enhancers and transcription factors in the control of gene expression. Biochim Biophys Acta. 1988 Nov 10;951(1):17–35. doi: 10.1016/0167-4781(88)90021-8. [DOI] [PubMed] [Google Scholar]
  28. de Graaff E., Willemsen R., Zhong N., de Die-Smulders C. E., Brown W. T., Freling G., Oostra B. Instability of the CGG repeat and expression of the FMR1 protein in a male fragile X patient with a lung tumor. Am J Hum Genet. 1995 Sep;57(3):609–618. [PMC free article] [PubMed] [Google Scholar]

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