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. 1994 Apr 11;22(7):1138–1146. doi: 10.1093/nar/22.7.1138

A nuclear factor that binds purine-rich, single-stranded oligonucleotides derived from S1-sensitive elements upstream of the CFTR gene and the MUC1 gene.

M A Hollingsworth 1, C Closken 1, A Harris 1, C D McDonald 1, G S Pahwa 1, L J Maher 3rd 1
PMCID: PMC523634  PMID: 7513081

Abstract

We have identified two regions of non-random purine/pyrimidine strand asymmetry that were nearly identical in sequence in the 5' flanking (promoter) regions of the human cystic fibrosis transmembrane conductance regulator (CFTR) gene and the human MUC1 gene. These regions contain perfect mirror repeat elements, a sequence motif previously found to be associated with the formation of H-DNA conformations. In this report we demonstrate that a single-stranded non-B DNA conformation exists at low pH in supercoiled plasmids containing the similar mirror repeat elements, and that S1 nuclease digestion maps the single-stranded region to the position of the mirror repeats. In addition, we identify a nuclear protein of approximately 27 kD that binds to single-stranded oligonucleotides corresponding to the purine-rich strand of this region, but not to the pyrimidine-rich strands or to double-stranded oligonucleotides with corresponding purine/pyrimidine strand asymmetry.

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Selected References

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

  1. Abe M., Kufe D. Characterization of cis-acting elements regulating transcription of the human DF3 breast carcinoma-associated antigen (MUC1) gene. Proc Natl Acad Sci U S A. 1993 Jan 1;90(1):282–286. doi: 10.1073/pnas.90.1.282. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bergemann A. D., Johnson E. M. The HeLa Pur factor binds single-stranded DNA at a specific element conserved in gene flanking regions and origins of DNA replication. Mol Cell Biol. 1992 Mar;12(3):1257–1265. doi: 10.1128/mcb.12.3.1257. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Brunel F., Alzari P. M., Ferrara P., Zakin M. M. Cloning and sequencing of PYBP, a pyrimidine-rich specific single strand DNA-binding protein. Nucleic Acids Res. 1991 Oct 11;19(19):5237–5245. doi: 10.1093/nar/19.19.5237. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chambers J. A., Harris A. Expression of the cystic fibrosis gene and the major pancreatic mucin gene, MUC1, in human ductal epithelial cells. J Cell Sci. 1993 Jun;105(Pt 2):417–422. doi: 10.1242/jcs.105.2.417. [DOI] [PubMed] [Google Scholar]
  5. Chou J. L., Rozmahel R., Tsui L. C. Characterization of the promoter region of the cystic fibrosis transmembrane conductance regulator gene. J Biol Chem. 1991 Dec 25;266(36):24471–24476. [PubMed] [Google Scholar]
  6. Christophe D., Cabrer B., Bacolla A., Targovnik H., Pohl V., Vassart G. An unusually long poly(purine)-poly(pyrimidine) sequence is located upstream from the human thyroglobulin gene. Nucleic Acids Res. 1985 Jul 25;13(14):5127–5144. doi: 10.1093/nar/13.14.5127. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Collier D. A., Wells R. D. Effect of length, supercoiling, and pH on intramolecular triplex formation. Multiple conformers at pur.pyr mirror repeats. J Biol Chem. 1990 Jun 25;265(18):10652–10658. [PubMed] [Google Scholar]
  8. Davis T. L., Firulli A. B., Kinniburgh A. J. Ribonucleoprotein and protein factors bind to an H-DNA-forming c-myc DNA element: possible regulators of the c-myc gene. Proc Natl Acad Sci U S A. 1989 Dec;86(24):9682–9686. doi: 10.1073/pnas.86.24.9682. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Hanvey J. C., Klysik J., Wells R. D. Influence of DNA sequence on the formation of non-B right-handed helices in oligopurine.oligopyrimidine inserts in plasmids. J Biol Chem. 1988 May 25;263(15):7386–7396. [PubMed] [Google Scholar]
  10. Htun H., Dahlberg J. E. Single strands, triple strands, and kinks in H-DNA. Science. 1988 Sep 30;241(4874):1791–1796. doi: 10.1126/science.3175620. [DOI] [PubMed] [Google Scholar]
  11. Koh J., Sferra T. J., Collins F. S. Characterization of the cystic fibrosis transmembrane conductance regulator promoter region. Chromatin context and tissue-specificity. J Biol Chem. 1993 Jul 25;268(21):15912–15921. [PubMed] [Google Scholar]
  12. Kolluri R., Torrey T. A., Kinniburgh A. J. A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif. Nucleic Acids Res. 1992 Jan 11;20(1):111–116. doi: 10.1093/nar/20.1.111. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Kovarik A., Peat N., Wilson D., Gendler S. J., Taylor-Papadimitriou J. Analysis of the tissue-specific promoter of the MUC1 gene. J Biol Chem. 1993 May 5;268(13):9917–9926. [PubMed] [Google Scholar]
  14. Larsen A., Weintraub H. An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell. 1982 Jun;29(2):609–622. doi: 10.1016/0092-8674(82)90177-5. [DOI] [PubMed] [Google Scholar]
  15. Lilley D. M. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6468–6472. doi: 10.1073/pnas.77.11.6468. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Lyamichev V. I., Mirkin S. M., Frank-Kamenetskii M. D. A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. J Biomol Struct Dyn. 1985 Oct;3(2):327–338. doi: 10.1080/07391102.1985.10508420. [DOI] [PubMed] [Google Scholar]
  17. Panayotatos N., Wells R. D. Cruciform structures in supercoiled DNA. Nature. 1981 Feb 5;289(5797):466–470. doi: 10.1038/289466a0. [DOI] [PubMed] [Google Scholar]
  18. Schmidt A. M., Herterich S. U., Krauss G. A single-stranded DNA binding protein from S. cerevisiae specifically recognizes the T-rich strand of the core sequence of ARS elements and discriminates against mutant sequences. EMBO J. 1991 Apr;10(4):981–985. doi: 10.1002/j.1460-2075.1991.tb08032.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Tomizawa J. Control of ColE1 plasmid replication: the process of binding of RNA I to the primer transcript. Cell. 1984 Oct;38(3):861–870. doi: 10.1016/0092-8674(84)90281-2. [DOI] [PubMed] [Google Scholar]
  20. Trezise A. E., Chambers J. A., Wardle C. J., Gould S., Harris A. Expression of the cystic fibrosis gene in human foetal tissues. Hum Mol Genet. 1993 Mar;2(3):213–218. doi: 10.1093/hmg/2.3.213. [DOI] [PubMed] [Google Scholar]
  21. Wang Z. Y., Lin X. H., Nobuyoshi M., Deuel T. F. Identification of a single-stranded DNA-binding protein that interacts with an S1 nuclease-sensitive region in the platelet-derived growth factor A-chain gene promoter. J Biol Chem. 1993 May 15;268(14):10681–10685. [PubMed] [Google Scholar]
  22. Wells R. D., Collier D. A., Hanvey J. C., Shimizu M., Wohlrab F. The chemistry and biology of unusual DNA structures adopted by oligopurine.oligopyrimidine sequences. FASEB J. 1988 Nov;2(14):2939–2949. [PubMed] [Google Scholar]
  23. Yee H. A., Wong A. K., van de Sande J. H., Rattner J. B. Identification of novel single-stranded d(TC)n binding proteins in several mammalian species. Nucleic Acids Res. 1991 Feb 25;19(4):949–953. doi: 10.1093/nar/19.4.949. [DOI] [PMC free article] [PubMed] [Google Scholar]

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