Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1997 Jul;17(7):3649–3662. doi: 10.1128/mcb.17.7.3649

Intra- and intermolecular cooperative binding of high-mobility-group protein I(Y) to the beta-interferon promoter.

J Yie 1, S Liang 1, M Merika 1, D Thanos 1
PMCID: PMC232217  PMID: 9199299

Abstract

The mammalian high-mobility-group protein I(Y) [HMG I(Y)], while not a typical transcriptional activator, is required for the expression of many eukaryotic genes. HMG I(Y) appears to recruit and stabilize complexes of transcriptional activators through protein-DNA and protein-protein interactions. The protein binds to the minor groove of DNA via three short basic repeats, preferring tracts of adenines and thymines arranged on the same face of the DNA helix. However, the mode by which these three basic repeats function together to recognize HMG I(Y) binding sites has remained unclear. Here, using deletion mutants of HMG I(Y), DNase I footprinting, methylation interference, and in vivo transcriptional assays, we have characterized the binding of HMG I(Y) to the model beta-interferon enhancer. We show that two molecules of HMG I(Y) bind to the enhancer in a highly cooperative fashion, each molecule using a distinct pair of basic repeats to recognize the tandem AT-rich regions of the binding sites. We have also characterized the function of each basic repeat, showing that only the central repeat accounts for specific DNA binding and that the presence of a second repeat bound to an adjacent AT-rich region results in intramolecular cooperativity in binding. Surprisingly, the carboxyl-terminal acidic tail of HMG I(Y) is also important for specific binding in the context of the full-length protein. Our results present a detailed examination of HMG I(Y) binding in an important biological context, which can be extended not only to HMG I(Y) binding in other systems but also to the binding mode of many other proteins containing homologous basic repeats, which have been conserved from bacteria to humans.

Full Text

The Full Text of this article is available as a PDF (3.2 MB).

Selected References

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

  1. Abdulkadir S. A., Krishna S., Thanos D., Maniatis T., Strominger J. L., Ono S. J. Functional roles of the transcription factor Oct-2A and the high mobility group protein I/Y in HLA-DRA gene expression. J Exp Med. 1995 Aug 1;182(2):487–500. doi: 10.1084/jem.182.2.487. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Ashar H. R., Fejzo M. S., Tkachenko A., Zhou X., Fletcher J. A., Weremowicz S., Morton C. C., Chada K. Disruption of the architectural factor HMGI-C: DNA-binding AT hook motifs fused in lipomas to distinct transcriptional regulatory domains. Cell. 1995 Jul 14;82(1):57–65. doi: 10.1016/0092-8674(95)90052-7. [DOI] [PubMed] [Google Scholar]
  3. Ashley C. T., Pendleton C. G., Jennings W. W., Saxena A., Glover C. V. Isolation and sequencing of cDNA clones encoding Drosophila chromosomal protein D1. A repeating motif in proteins which recognize at DNA. J Biol Chem. 1989 May 15;264(14):8394–8401. [PubMed] [Google Scholar]
  4. Brown M. T., Goetsch L., Hartwell L. H. MIF2 is required for mitotic spindle integrity during anaphase spindle elongation in Saccharomyces cerevisiae. J Cell Biol. 1993 Oct;123(2):387–403. doi: 10.1083/jcb.123.2.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bustin M., Lehn D. A., Landsman D. Structural features of the HMG chromosomal proteins and their genes. Biochim Biophys Acta. 1990 Jul 30;1049(3):231–243. doi: 10.1016/0167-4781(90)90092-g. [DOI] [PubMed] [Google Scholar]
  6. Churchill M. E., Travers A. A. Protein motifs that recognize structural features of DNA. Trends Biochem Sci. 1991 Mar;16(3):92–97. doi: 10.1016/0968-0004(91)90040-3. [DOI] [PubMed] [Google Scholar]
  7. Claus P., Schulze E., Wiśniewski J. R. Insect proteins homologous to mammalian high mobility group proteins I/Y (HMG I/Y). Characterization and binding to linear and four-way junction DNA. J Biol Chem. 1994 Dec 30;269(52):33042–33048. [PubMed] [Google Scholar]
  8. Du W., Maniatis T. An ATF/CREB binding site is required for virus induction of the human interferon beta gene [corrected]. Proc Natl Acad Sci U S A. 1992 Mar 15;89(6):2150–2154. doi: 10.1073/pnas.89.6.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Du W., Thanos D., Maniatis T. Mechanisms of transcriptional synergism between distinct virus-inducible enhancer elements. Cell. 1993 Sep 10;74(5):887–898. doi: 10.1016/0092-8674(93)90468-6. [DOI] [PubMed] [Google Scholar]
  10. Falvo J. V., Thanos D., Maniatis T. Reversal of intrinsic DNA bends in the IFN beta gene enhancer by transcription factors and the architectural protein HMG I(Y). Cell. 1995 Dec 29;83(7):1101–1111. doi: 10.1016/0092-8674(95)90137-x. [DOI] [PubMed] [Google Scholar]
  11. Farnet C. M., Bushman F. D. HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro. Cell. 1997 Feb 21;88(4):483–492. doi: 10.1016/s0092-8674(00)81888-7. [DOI] [PubMed] [Google Scholar]
  12. French S. W., Schmidt M. C., Glorioso J. C. Involvement of a high-mobility-group protein in the transcriptional activity of herpes simplex virus latency-active promoter 2. Mol Cell Biol. 1996 Oct;16(10):5393–5399. doi: 10.1128/mcb.16.10.5393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Geierstanger B. H., Volkman B. F., Kremer W., Wemmer D. E. Short peptide fragments derived from HMG-I/Y proteins bind specifically to the minor groove of DNA. Biochemistry. 1994 May 3;33(17):5347–5355. doi: 10.1021/bi00183a043. [DOI] [PubMed] [Google Scholar]
  14. Giese K., Kingsley C., Kirshner J. R., Grosschedl R. Assembly and function of a TCR alpha enhancer complex is dependent on LEF-1-induced DNA bending and multiple protein-protein interactions. Genes Dev. 1995 Apr 15;9(8):995–1008. doi: 10.1101/gad.9.8.995. [DOI] [PubMed] [Google Scholar]
  15. Goodbourn S., Maniatis T. Overlapping positive and negative regulatory domains of the human beta-interferon gene. Proc Natl Acad Sci U S A. 1988 Mar;85(5):1447–1451. doi: 10.1073/pnas.85.5.1447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. 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]
  17. Grosschedl R. Higher-order nucleoprotein complexes in transcription: analogies with site-specific recombination. Curr Opin Cell Biol. 1995 Jun;7(3):362–370. doi: 10.1016/0955-0674(95)80091-3. [DOI] [PubMed] [Google Scholar]
  18. Himes S. R., Coles L. S., Reeves R., Shannon M. F. High mobility group protein I(Y) is required for function and for c-Rel binding to CD28 response elements within the GM-CSF and IL-2 promoters. Immunity. 1996 Nov;5(5):479–489. doi: 10.1016/s1074-7613(00)80503-8. [DOI] [PubMed] [Google Scholar]
  19. John S., Reeves R. B., Lin J. X., Child R., Leiden J. M., Thompson C. B., Leonard W. J. Regulation of cell-type-specific interleukin-2 receptor alpha-chain gene expression: potential role of physical interactions between Elf-1, HMG-I(Y), and NF-kappa B family proteins. Mol Cell Biol. 1995 Mar;15(3):1786–1796. doi: 10.1128/mcb.15.3.1786. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Johnson K. R., Lehn D. A., Elton T. S., Barr P. J., Reeves R. Complete murine cDNA sequence, genomic structure, and tissue expression of the high mobility group protein HMG-I(Y). J Biol Chem. 1988 Dec 5;263(34):18338–18342. [PubMed] [Google Scholar]
  21. Krasnow M. A., Saffman E. E., Kornfeld K., Hogness D. S. Transcriptional activation and repression by Ultrabithorax proteins in cultured Drosophila cells. Cell. 1989 Jun 16;57(6):1031–1043. doi: 10.1016/0092-8674(89)90341-3. [DOI] [PubMed] [Google Scholar]
  22. Leger H., Sock E., Renner K., Grummt F., Wegner M. Functional interaction between the POU domain protein Tst-1/Oct-6 and the high-mobility-group protein HMG-I/Y. Mol Cell Biol. 1995 Jul;15(7):3738–3747. doi: 10.1128/mcb.15.7.3738. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lewis H., Kaszubska W., DeLamarter J. F., Whelan J. Cooperativity between two NF-kappa B complexes, mediated by high-mobility-group protein I(Y), is essential for cytokine-induced expression of the E-selectin promoter. Mol Cell Biol. 1994 Sep;14(9):5701–5709. doi: 10.1128/mcb.14.9.5701. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Maher J. F., Nathans D. Multivalent DNA-binding properties of the HMG-1 proteins. Proc Natl Acad Sci U S A. 1996 Jun 25;93(13):6716–6720. doi: 10.1073/pnas.93.13.6716. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Meacock S., Pescini-Gobert R., DeLamarter J. F., Hooft van Huijsduijnen R. Transcription factor-induced, phased bending of the E-selectin promoter. J Biol Chem. 1994 Dec 16;269(50):31756–31762. [PubMed] [Google Scholar]
  26. Nicolas F. J., Cayuela M. L., Martínez-Argudo I. M., Ruiz-Vazquez R. M., Murillo F. J. High mobility group I(Y)-like DNA-binding domains on a bacterial transcription factor. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6881–6885. doi: 10.1073/pnas.93.14.6881. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Nieto-Sotelo J., Ichida A., Quail P. H. PF1: an A-T hook-containing DNA binding protein from rice that interacts with a functionally defined d(AT)-rich element in the oat phytochrome A3 gene promoter. Plant Cell. 1994 Feb;6(2):287–301. doi: 10.1105/tpc.6.2.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Nissen M. S., Reeves R. Changes in superhelicity are introduced into closed circular DNA by binding of high mobility group protein I/Y. J Biol Chem. 1995 Mar 3;270(9):4355–4360. doi: 10.1074/jbc.270.9.4355. [DOI] [PubMed] [Google Scholar]
  29. Palvimo J., Linnala-Kankkunen A. Identification of sites on chromosomal protein HMG-I phosphorylated by casein kinase II. FEBS Lett. 1989 Oct 23;257(1):101–104. doi: 10.1016/0014-5793(89)81796-x. [DOI] [PubMed] [Google Scholar]
  30. Pwee K. H., Webster C. I., Gray J. C. HMG protein binding to an A/T-rich positive regulatory region of the pea plastocyanin gene promoter. Plant Mol Biol. 1994 Dec;26(6):1907–1920. doi: 10.1007/BF00019502. [DOI] [PubMed] [Google Scholar]
  31. Reeves R., Nissen M. S. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem. 1990 May 25;265(15):8573–8582. [PubMed] [Google Scholar]
  32. Schoenmakers E. F., Wanschura S., Mols R., Bullerdiek J., Van den Berghe H., Van de Ven W. J. Recurrent rearrangements in the high mobility group protein gene, HMGI-C, in benign mesenchymal tumours. Nat Genet. 1995 Aug;10(4):436–444. doi: 10.1038/ng0895-436. [DOI] [PubMed] [Google Scholar]
  33. Solomon M. J., Strauss F., Varshavsky A. A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA. Proc Natl Acad Sci U S A. 1986 Mar;83(5):1276–1280. doi: 10.1073/pnas.83.5.1276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Strick R., Laemmli U. K. SARs are cis DNA elements of chromosome dynamics: synthesis of a SAR repressor protein. Cell. 1995 Dec 29;83(7):1137–1148. doi: 10.1016/0092-8674(95)90140-x. [DOI] [PubMed] [Google Scholar]
  35. Thanos D., Du W., Maniatis T. The high mobility group protein HMG I(Y) is an essential structural component of a virus-inducible enhancer complex. Cold Spring Harb Symp Quant Biol. 1993;58:73–81. doi: 10.1101/sqb.1993.058.01.011. [DOI] [PubMed] [Google Scholar]
  36. Thanos D., Maniatis T. In vitro assembly of enhancer complexes. Methods Enzymol. 1996;274:162–173. doi: 10.1016/s0076-6879(96)74015-6. [DOI] [PubMed] [Google Scholar]
  37. Thanos D., Maniatis T. The high mobility group protein HMG I(Y) is required for NF-kappa B-dependent virus induction of the human IFN-beta gene. Cell. 1992 Nov 27;71(5):777–789. doi: 10.1016/0092-8674(92)90554-p. [DOI] [PubMed] [Google Scholar]
  38. Thanos D., Maniatis T. Virus induction of human IFN beta gene expression requires the assembly of an enhanceosome. Cell. 1995 Dec 29;83(7):1091–1100. doi: 10.1016/0092-8674(95)90136-1. [DOI] [PubMed] [Google Scholar]
  39. Tkachuk D. C., Kohler S., Cleary M. L. Involvement of a homolog of Drosophila trithorax by 11q23 chromosomal translocations in acute leukemias. Cell. 1992 Nov 13;71(4):691–700. doi: 10.1016/0092-8674(92)90602-9. [DOI] [PubMed] [Google Scholar]
  40. Tkachuk D. C., Kohler S., Cleary M. L. Involvement of a homolog of Drosophila trithorax by 11q23 chromosomal translocations in acute leukemias. Cell. 1992 Nov 13;71(4):691–700. doi: 10.1016/0092-8674(92)90602-9. [DOI] [PubMed] [Google Scholar]
  41. Wang D. Z., Ray P., Boothby M. Interleukin 4-inducible phosphorylation of HMG-I(Y) is inhibited by rapamycin. J Biol Chem. 1995 Sep 29;270(39):22924–22932. doi: 10.1074/jbc.270.39.22924. [DOI] [PubMed] [Google Scholar]
  42. Whitley M. Z., Thanos D., Read M. A., Maniatis T., Collins T. A striking similarity in the organization of the E-selectin and beta interferon gene promoters. Mol Cell Biol. 1994 Oct;14(10):6464–6475. doi: 10.1128/mcb.14.10.6464. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Winter E., Varshavsky A. A DNA binding protein that recognizes oligo(dA).oligo(dT) tracts. EMBO J. 1989 Jun;8(6):1867–1877. doi: 10.1002/j.1460-2075.1989.tb03583.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  44. Wolffe A. P. Architectural transcription factors. Science. 1994 May 20;264(5162):1100–1101. doi: 10.1126/science.8178167. [DOI] [PubMed] [Google Scholar]
  45. Wood L. D., Farmer A. A., Richmond A. HMGI(Y) and Sp1 in addition to NF-kappa B regulate transcription of the MGSA/GRO alpha gene. Nucleic Acids Res. 1995 Oct 25;23(20):4210–4219. doi: 10.1093/nar/23.20.4210. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Zhao K., Käs E., Gonzalez E., Laemmli U. K. SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 1993 Aug;12(8):3237–3247. doi: 10.1002/j.1460-2075.1993.tb05993.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Zhou X., Benson K. F., Ashar H. R., Chada K. Mutation responsible for the mouse pygmy phenotype in the developmentally regulated factor HMGI-C. Nature. 1995 Aug 31;376(6543):771–774. doi: 10.1038/376771a0. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES