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. 1992 Jun 25;20(12):2941–2945. doi: 10.1093/nar/20.12.2941

Differential binding of human nuclear proteins to Alu subfamilies.

N V Tomilin 1, V M Bozhkov 1, E M Bradbury 1, C W Schmid 1
PMCID: PMC312420  PMID: 1620588

Abstract

Several diagnostic differences that distinguish human Alu subfamilies are clustered just downstream from the B box of the RNA polymerase III promoter; we tentatively refer to this diagnostic region as the DB box. Assuming that this region might determine the relative transcriptional activity of Alu subfamilies, we examined the interaction of nuclear proteins with DB box sequences representing different Alu subfamilies. Gel mobility shift assays suggest the existence of two factors which discriminate among the DB boxes of different Alu subfamilies: 1) An abundant, ca. 50 kd, protein binds more stably to a young 'PV' Alu subfamily (PVS) than to the older major subfamily (MS). 2) Methylation of CpG dinucleotides stimulates the binding of a less abundant, ca. 70 kd, protein to the DB boxes of younger Alu subfamilies.

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Selected References

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

  1. Batzer M. A., Deininger P. L. A human-specific subfamily of Alu sequences. Genomics. 1991 Mar;9(3):481–487. doi: 10.1016/0888-7543(91)90414-a. [DOI] [PubMed] [Google Scholar]
  2. Batzer M. A., Kilroy G. E., Richard P. E., Shaikh T. H., Desselle T. D., Hoppens C. L., Deininger P. L. Structure and variability of recently inserted Alu family members. Nucleic Acids Res. 1990 Dec 11;18(23):6793–6798. doi: 10.1093/nar/18.23.6793. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Britten R. J., Baron W. F., Stout D. B., Davidson E. H. Sources and evolution of human Alu repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4770–4774. doi: 10.1073/pnas.85.13.4770. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chesnokov I., Bozhkov V., Popov B., Tomilin N. Binding specificity of human nuclear protein interacting with the Alu-family DNA repeats. Biochem Biophys Res Commun. 1991 Jul 31;178(2):613–619. doi: 10.1016/0006-291x(91)90152-w. [DOI] [PubMed] [Google Scholar]
  5. Elder J. T., Pan J., Duncan C. H., Weissman S. M. Transcriptional analysis of interspersed repetitive polymerase III transcription units in human DNA. Nucleic Acids Res. 1981 Mar 11;9(5):1171–1189. doi: 10.1093/nar/9.5.1171. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Fried M., Crothers D. M. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981 Dec 11;9(23):6505–6525. doi: 10.1093/nar/9.23.6505. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Garner M. M., Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981 Jul 10;9(13):3047–3060. doi: 10.1093/nar/9.13.3047. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Holmquist G. P. Evolution of chromosome bands: molecular ecology of noncoding DNA. J Mol Evol. 1989 Jun;28(6):469–486. doi: 10.1007/BF02602928. [DOI] [PubMed] [Google Scholar]
  9. Jurka J., Smith T. A fundamental division in the Alu family of repeated sequences. Proc Natl Acad Sci U S A. 1988 Jul;85(13):4775–4778. doi: 10.1073/pnas.85.13.4775. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Labuda D., Striker G. Sequence conservation in Alu evolution. Nucleic Acids Res. 1989 Apr 11;17(7):2477–2491. doi: 10.1093/nar/17.7.2477. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Lobo S. M., Hernandez N. A 7 bp mutation converts a human RNA polymerase II snRNA promoter into an RNA polymerase III promoter. Cell. 1989 Jul 14;58(1):55–67. doi: 10.1016/0092-8674(89)90402-9. [DOI] [PubMed] [Google Scholar]
  12. Lobo S. M., Ifill S., Hernandez N. cis-acting elements required for RNA polymerase II and III transcription in the human U2 and U6 snRNA promoters. Nucleic Acids Res. 1990 May 25;18(10):2891–2899. doi: 10.1093/nar/18.10.2891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Matera A. G., Hellmann U., Hintz M. F., Schmid C. W. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. doi: 10.1093/nar/18.20.6019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Matera A. G., Hellmann U., Schmid C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. doi: 10.1128/mcb.10.10.5424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Paulson K. E., Schmid C. W. Transcriptional inactivity of Alu repeats in HeLa cells. Nucleic Acids Res. 1986 Aug 11;14(15):6145–6158. doi: 10.1093/nar/14.15.6145. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Perez-Stable C., Ayres T. M., Shen C. K. Distinctive sequence organization and functional programming of an Alu repeat promoter. Proc Natl Acad Sci U S A. 1984 Sep;81(17):5291–5295. doi: 10.1073/pnas.81.17.5291. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Prendergast G. C., Ziff E. B. Methylation-sensitive sequence-specific DNA binding by the c-Myc basic region. Science. 1991 Jan 11;251(4990):186–189. doi: 10.1126/science.1987636. [DOI] [PubMed] [Google Scholar]
  18. Quentin Y. The Alu family developed through successive waves of fixation closely connected with primate lineage history. J Mol Evol. 1988;27(3):194–202. doi: 10.1007/BF02100074. [DOI] [PubMed] [Google Scholar]
  19. Schmid C. W. Human Alu subfamilies and their methylation revealed by blot hybridization. Nucleic Acids Res. 1991 Oct 25;19(20):5613–5617. doi: 10.1093/nar/19.20.5613. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Schreiber E., Matthias P., Müller M. M., Schaffner W. Identification of a novel lymphoid specific octamer binding protein (OTF-2B) by proteolytic clipping bandshift assay (PCBA). EMBO J. 1988 Dec 20;7(13):4221–4229. doi: 10.1002/j.1460-2075.1988.tb03319.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Singh J., Dixon G. H. High mobility group proteins 1 and 2 function as general class II transcription factors. Biochemistry. 1990 Jul 3;29(26):6295–6302. doi: 10.1021/bi00478a026. [DOI] [PubMed] [Google Scholar]
  22. Slagel V., Flemington E., Traina-Dorge V., Bradshaw H., Deininger P. Clustering and subfamily relationships of the Alu family in the human genome. Mol Biol Evol. 1987 Jan;4(1):19–29. doi: 10.1093/oxfordjournals.molbev.a040422. [DOI] [PubMed] [Google Scholar]
  23. Smith S., Stillman B. Immunological characterization of chromatin assembly factor I, a human cell factor required for chromatin assembly during DNA replication in vitro. J Biol Chem. 1991 Jun 25;266(18):12041–12047. [PubMed] [Google Scholar]
  24. Tomilin N. V., Bozhkov V. M. Human nuclear protein interacting with a conservative sequence motif of Alu-family DNA repeats. FEBS Lett. 1989 Jul 17;251(1-2):79–83. doi: 10.1016/0014-5793(89)81432-2. [DOI] [PubMed] [Google Scholar]
  25. Tomilin N. V., Iguchi-Ariga S. M., Ariga H. Transcription and replication silencer element is present within conserved region of human Alu repeats interacting with nuclear protein. FEBS Lett. 1990 Apr 9;263(1):69–72. doi: 10.1016/0014-5793(90)80707-p. [DOI] [PubMed] [Google Scholar]
  26. Tremethick D. J., Molloy P. L. High mobility group proteins 1 and 2 stimulate transcription in vitro by RNA polymerases II and III. J Biol Chem. 1986 May 25;261(15):6986–6992. [PubMed] [Google Scholar]
  27. Watt F., Molloy P. L. High mobility group proteins 1 and 2 stimulate binding of a specific transcription factor to the adenovirus major late promoter. Nucleic Acids Res. 1988 Feb 25;16(4):1471–1486. doi: 10.1093/nar/16.4.1471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Willard C., Nguyen H. T., Schmid C. W. Existence of at least three distinct Alu subfamilies. J Mol Evol. 1987;26(3):180–186. doi: 10.1007/BF02099850. [DOI] [PubMed] [Google Scholar]
  29. Zhang X. Y., Asiedu C. K., Supakar P. C., Khan R., Ehrlich K. C., Ehrlich M. Binding sites in mammalian genes and viral gene regulatory regions recognized by methylated DNA-binding protein. Nucleic Acids Res. 1990 Nov 11;18(21):6253–6260. doi: 10.1093/nar/18.21.6253. [DOI] [PMC free article] [PubMed] [Google Scholar]

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