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. 1997 Sep 1;25(17):3523–3531. doi: 10.1093/nar/25.17.3523

Competition between HMG-I(Y), HMG-1 and histone H1 on four-way junction DNA.

D A Hill 1, R Reeves 1
PMCID: PMC146912  PMID: 9254714

Abstract

High mobility group proteins HMG-I(Y) and HMG-1, as well as histone H1, all share the common property of binding to four-way junction DNA (4H), a synthetic substrate commonly used to study proteins involved in recognizing and resolving Holliday-type junctions formed during in vivo genetic recombination events. The structure of 4H has also been hypothesized to mimic the DNA crossovers occurring at, or near, the entrance and exit sites on the nucleosome. Furthermore, upon binding to either duplex DNA or chromatin, all three of these nuclear proteins share the ability to significantly alter the structure of bound substrates. In order to further elucidate their substrate binding abilities, electrophoretic mobility shift assays were employed to investigate the relative binding capabilities of HMG-I(Y), HMG-1 and H1 to 4H in vitro. Data indicate a definite hierarchy of binding preference by these proteins for 4H, with HMG-I(Y) having the highest affinity (Kd approximately 6.5 nM) when compared with either H1 (Kd approximately 16 nM) or HMG-1 (Kd approximately 80 nM). Competition/titration assays demonstrated that all three proteins bind most tightly to the same site on 4H. Hydroxyl radical footprinting identified the strongest site for binding of HMG-I(Y), and presumably for the other proteins as well, to be at the center of 4H. Together these in vitro results demonstrate that HMG-I(Y) and H1 are co-dominant over HMG-1 for binding to the central crossover region of 4H and suggest that in vivo both of these proteins may exert a dominant effect over HMG-1 in recognizing and binding to altered DNA structures, such as Holliday junctions, that have conformations similar to 4H.

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Selected References

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  1. Adachi Y., Mizuno S., Yoshida M. Efficient large-scale purification of non-histone chromosomal proteins HMG1 and HMG2 by using Polybuffer-exchanger PBE94. J Chromatogr. 1990 Aug 24;530(1):39–46. doi: 10.1016/s0378-4347(00)82300-2. [DOI] [PubMed] [Google Scholar]
  2. Agrawal A., Schatz D. G. RAG1 and RAG2 form a stable postcleavage synaptic complex with DNA containing signal ends in V(D)J recombination. Cell. 1997 Apr 4;89(1):43–53. doi: 10.1016/s0092-8674(00)80181-6. [DOI] [PubMed] [Google Scholar]
  3. Aiyar A., Hindmarsh P., Skalka A. M., Leis J. Concerted integration of linear retroviral DNA by the avian sarcoma virus integrase in vitro: dependence on both long terminal repeat termini. J Virol. 1996 Jun;70(6):3571–3580. doi: 10.1128/jvi.70.6.3571-3580.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Allan J., Hartman P. G., Crane-Robinson C., Aviles F. X. The structure of histone H1 and its location in chromatin. Nature. 1980 Dec 25;288(5792):675–679. doi: 10.1038/288675a0. [DOI] [PubMed] [Google Scholar]
  5. Bennett R. J., West S. C. RuvC protein resolves Holliday junctions via cleavage of the continuous (noncrossover) strands. Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5635–5639. doi: 10.1073/pnas.92.12.5635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bianchi M. E. Interaction of a protein from rat liver nuclei with cruciform DNA. EMBO J. 1988 Mar;7(3):843–849. doi: 10.1002/j.1460-2075.1988.tb02883.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Bonnefoy E., Takahashi M., Yaniv J. R. DNA-binding parameters of the HU protein of Escherichia coli to cruciform DNA. J Mol Biol. 1994 Sep 16;242(2):116–129. doi: 10.1006/jmbi.1994.1563. [DOI] [PubMed] [Google Scholar]
  8. Bouvet P., Dimitrov S., Wolffe A. P. Specific regulation of Xenopus chromosomal 5S rRNA gene transcription in vivo by histone H1. Genes Dev. 1994 May 15;8(10):1147–1159. doi: 10.1101/gad.8.10.1147. [DOI] [PubMed] [Google Scholar]
  9. 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]
  10. Bustin M., Reeves R. High-mobility-group chromosomal proteins: architectural components that facilitate chromatin function. Prog Nucleic Acid Res Mol Biol. 1996;54:35–100. doi: 10.1016/s0079-6603(08)60360-8. [DOI] [PubMed] [Google Scholar]
  11. 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]
  12. Evans J. N., Zajicek J., Nissen M. S., Munske G., Smith V., Reeves R. 1H and 13C NMR assignments and molecular modelling of a minor groove DNA-binding peptide from the HMG-I protein. Int J Pept Protein Res. 1995 Jun;45(6):554–560. doi: 10.1111/j.1399-3011.1995.tb01319.x. [DOI] [PubMed] [Google Scholar]
  13. 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]
  14. Fried M. G. Measurement of protein-DNA interaction parameters by electrophoresis mobility shift assay. Electrophoresis. 1989 May-Jun;10(5-6):366–376. doi: 10.1002/elps.1150100515. [DOI] [PubMed] [Google Scholar]
  15. Friedmann M., Holth L. T., Zoghbi H. Y., Reeves R. Organization, inducible-expression and chromosome localization of the human HMG-I(Y) nonhistone protein gene. Nucleic Acids Res. 1993 Sep 11;21(18):4259–4267. doi: 10.1093/nar/21.18.4259. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Giese K., Cox J., Grosschedl R. The HMG domain of lymphoid enhancer factor 1 bends DNA and facilitates assembly of functional nucleoprotein structures. Cell. 1992 Apr 3;69(1):185–195. doi: 10.1016/0092-8674(92)90129-z. [DOI] [PubMed] [Google Scholar]
  17. Goytisolo F. A., Gerchman S. E., Yu X., Rees C., Graziano V., Ramakrishnan V., Thomas J. O. Identification of two DNA-binding sites on the globular domain of histone H5. EMBO J. 1996 Jul 1;15(13):3421–3429. [PMC free article] [PubMed] [Google Scholar]
  18. Hayes J. J. Site-directed cleavage of DNA by a linker histone--Fe(II) EDTA conjugate: localization of a globular domain binding site within a nucleosome. Biochemistry. 1996 Sep 17;35(37):11931–11937. doi: 10.1021/bi961590+. [DOI] [PubMed] [Google Scholar]
  19. Hoess R., Wierzbicki A., Abremski K. Isolation and characterization of intermediates in site-specific recombination. Proc Natl Acad Sci U S A. 1987 Oct;84(19):6840–6844. doi: 10.1073/pnas.84.19.6840. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ivanchenko M., Hassan A., van Holde K., Zlatanova J. H1 binding unwinds DNA. Evidence from topological assays. J Biol Chem. 1996 Dec 20;271(51):32580–32585. doi: 10.1074/jbc.271.51.32580. [DOI] [PubMed] [Google Scholar]
  21. Ivanchenko M., Zlatanova J., Varga-Weisz P., Hassan A., van Holde K. Linker histones affect patterns of digestion of supercoiled plasmids by single-strand-specific nucleases. Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):6970–6974. doi: 10.1073/pnas.93.14.6970. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Iwasaki H., Takahagi M., Shiba T., Nakata A., Shinagawa H. Escherichia coli RuvC protein is an endonuclease that resolves the Holliday structure. EMBO J. 1991 Dec;10(13):4381–4389. doi: 10.1002/j.1460-2075.1991.tb05016.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Johnson K. R., Lehn D. A., Reeves R. Alternative processing of mRNAs encoding mammalian chromosomal high-mobility-group proteins HMG-I and HMG-Y. Mol Cell Biol. 1989 May;9(5):2114–2123. doi: 10.1128/mcb.9.5.2114. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Krylov D., Leuba S., van Holde K., Zlatanova J. Histones H1 and H5 interact preferentially with crossovers of double-helical DNA. Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5052–5056. doi: 10.1073/pnas.90.11.5052. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Lehn D. A., Elton T. S., Johnson K. R., Reeves R. A conformational study of the sequence specific binding of HMG-I (Y) with the bovine interleukin-2 cDNA. Biochem Int. 1988 May;16(5):963–971. [PubMed] [Google Scholar]
  26. Lilley D. M., Clegg R. M., Diekmann S., Seeman N. C., Von Kitzing E., Hagerman P. J. A nomenclature of junctions and branchpoints in nucleic acids. Nucleic Acids Res. 1995 Sep 11;23(17):3363–3364. doi: 10.1093/nar/23.17.3363. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Lilley D. M. DNA--protein interactions. HMG has DNA wrapped up. Nature. 1992 May 28;357(6376):282–283. doi: 10.1038/357282a0. [DOI] [PubMed] [Google Scholar]
  28. Lilley D. M. Molecular recognition of DNA structure by proteins that mediate genetic recombination. J Mol Recognit. 1994 Jun;7(2):71–78. doi: 10.1002/jmr.300070204. [DOI] [PubMed] [Google Scholar]
  29. Locker D., Decoville M., Maurizot J. C., Bianchi M. E., Leng M. Interaction between cisplatin-modified DNA and the HMG boxes of HMG 1: DNase I footprinting and circular dichroism. J Mol Biol. 1995 Feb 17;246(2):243–247. doi: 10.1006/jmbi.1994.0079. [DOI] [PubMed] [Google Scholar]
  30. Meyer-Leon L., Huang L. C., Umlauf S. W., Cox M. M., Inman R. B. Holliday intermediates and reaction by-products in FLP protein-promoted site-specific recombination. Mol Cell Biol. 1988 Sep;8(9):3784–3796. doi: 10.1128/mcb.8.9.3784. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Nightingale K. P., Pruss D., Wolffe A. P. A single high affinity binding site for histone H1 in a nucleosome containing the Xenopus borealis 5 S ribosomal RNA gene. J Biol Chem. 1996 Mar 22;271(12):7090–7094. doi: 10.1074/jbc.271.12.7090. [DOI] [PubMed] [Google Scholar]
  32. Nissen M. S., Langan T. A., Reeves R. Phosphorylation by cdc2 kinase modulates DNA binding activity of high mobility group I nonhistone chromatin protein. J Biol Chem. 1991 Oct 25;266(30):19945–19952. [PubMed] [Google Scholar]
  33. 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]
  34. Pennisi E. Linker histones, DNA's protein custodians, gain new respect. Science. 1996 Oct 25;274(5287):503–504. doi: 10.1126/science.274.5287.503. [DOI] [PubMed] [Google Scholar]
  35. Prunell A. Linker histones' role revisited. Biophys J. 1997 Mar;72(3):983–984. doi: 10.1016/S0006-3495(97)78747-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Pruss D., Bartholomew B., Persinger J., Hayes J., Arents G., Moudrianakis E. N., Wolffe A. P. An asymmetric model for the nucleosome: a binding site for linker histones inside the DNA gyres. Science. 1996 Oct 25;274(5287):614–617. doi: 10.1126/science.274.5287.614. [DOI] [PubMed] [Google Scholar]
  37. Radding C. M. Homologous pairing and strand exchange in genetic recombination. Annu Rev Genet. 1982;16:405–437. doi: 10.1146/annurev.ge.16.120182.002201. [DOI] [PubMed] [Google Scholar]
  38. Radic M. Z., Saghbini M., Elton T. S., Reeves R., Hamkalo B. A. Hoechst 33258, distamycin A, and high mobility group protein I (HMG-I) compete for binding to mouse satellite DNA. Chromosoma. 1992 Oct;101(10):602–608. doi: 10.1007/BF00360537. [DOI] [PubMed] [Google Scholar]
  39. Ramakrishnan V., Finch J. T., Graziano V., Lee P. L., Sweet R. M. Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature. 1993 Mar 18;362(6417):219–223. doi: 10.1038/362219a0. [DOI] [PubMed] [Google Scholar]
  40. Read C. M., Cary P. D., Crane-Robinson C., Driscoll P. C., Norman D. G. Solution structure of a DNA-binding domain from HMG1. Nucleic Acids Res. 1993 Jul 25;21(15):3427–3436. doi: 10.1093/nar/21.15.3427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Reeves R. Chromatin changes during the cell cycle. Curr Opin Cell Biol. 1992 Jun;4(3):413–423. doi: 10.1016/0955-0674(92)90006-x. [DOI] [PubMed] [Google Scholar]
  42. Reeves R., Nissen M. S. Interaction of high mobility group-I (Y) nonhistone proteins with nucleosome core particles. J Biol Chem. 1993 Oct 5;268(28):21137–21146. [PubMed] [Google Scholar]
  43. 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]
  44. Reeves R., Wolffe A. P. Substrate structure influences binding of the non-histone protein HMG-I(Y) to free nucleosomal DNA. Biochemistry. 1996 Apr 16;35(15):5063–5074. doi: 10.1021/bi952424p. [DOI] [PubMed] [Google Scholar]
  45. Saitoh Y., Laemmli U. K. From the chromosomal loops and the scaffold to the classic bands of metaphase chromosomes. Cold Spring Harb Symp Quant Biol. 1993;58:755–765. doi: 10.1101/sqb.1993.058.01.083. [DOI] [PubMed] [Google Scholar]
  46. Schild C., Claret F. X., Wahli W., Wolffe A. P. A nucleosome-dependent static loop potentiates estrogen-regulated transcription from the Xenopus vitellogenin B1 promoter in vitro. EMBO J. 1993 Feb;12(2):423–433. doi: 10.1002/j.1460-2075.1993.tb05674.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Sekiguchi J., Seeman N. C., Shuman S. Resolution of Holliday junctions by eukaryotic DNA topoisomerase I. Proc Natl Acad Sci U S A. 1996 Jan 23;93(2):785–789. doi: 10.1073/pnas.93.2.785. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Sharples G. J., Chan S. N., Mahdi A. A., Whitby M. C., Lloyd R. G. Processing of intermediates in recombination and DNA repair: identification of a new endonuclease that specifically cleaves Holliday junctions. EMBO J. 1994 Dec 15;13(24):6133–6142. doi: 10.1002/j.1460-2075.1994.tb06960.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Sheflin L. G., Spaulding S. W. High mobility group protein 1 preferentially conserves torsion in negatively supercoiled DNA. Biochemistry. 1989 Jun 27;28(13):5658–5664. doi: 10.1021/bi00439a048. [DOI] [PubMed] [Google Scholar]
  50. Shen X., Gorovsky M. A. Linker histone H1 regulates specific gene expression but not global transcription in vivo. Cell. 1996 Aug 9;86(3):475–483. doi: 10.1016/s0092-8674(00)80120-8. [DOI] [PubMed] [Google Scholar]
  51. 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]
  52. Staynov D. Z., Crane-Robinson C. Footprinting of linker histones H5 and H1 on the nucleosome. EMBO J. 1988 Dec 1;7(12):3685–3691. doi: 10.1002/j.1460-2075.1988.tb03250.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Strauss F., Varshavsky A. A protein binds to a satellite DNA repeat at three specific sites that would be brought into mutual proximity by DNA folding in the nucleosome. Cell. 1984 Jul;37(3):889–901. doi: 10.1016/0092-8674(84)90424-0. [DOI] [PubMed] [Google Scholar]
  54. Stros M., Reich J., Kolíbalová A. Calcium binding to HMG1 protein induces DNA looping by the HMG-box domains. FEBS Lett. 1994 May 16;344(2-3):201–206. doi: 10.1016/0014-5793(94)00364-5. [DOI] [PubMed] [Google Scholar]
  55. Takahagi M., Iwasaki H., Shinagawa H. Structural requirements of substrate DNA for binding to and cleavage by RuvC, a Holliday junction resolvase. J Biol Chem. 1994 May 27;269(21):15132–15139. [PubMed] [Google Scholar]
  56. Tullius T. D., Dombroski B. A., Churchill M. E., Kam L. Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol. 1987;155:537–558. doi: 10.1016/0076-6879(87)55035-2. [DOI] [PubMed] [Google Scholar]
  57. Ura K., Nightingale K., Wolffe A. P. Differential association of HMG1 and linker histones B4 and H1 with dinucleosomal DNA: structural transitions and transcriptional repression. EMBO J. 1996 Sep 16;15(18):4959–4969. [PMC free article] [PubMed] [Google Scholar]
  58. Varga-Weisz P., Zlatanova J., Leuba S. H., Schroth G. P., van Holde K. Binding of histones H1 and H5 and their globular domains to four-way junction DNA. Proc Natl Acad Sci U S A. 1994 Apr 26;91(9):3525–3529. doi: 10.1073/pnas.91.9.3525. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Varga-Weisz P., van Holde K., Zlatanova J. Competition between linker histones and HMG1 for binding to four-way junction DNA: implications for transcription. Biochem Biophys Res Commun. 1994 Sep 30;203(3):1904–1911. doi: 10.1006/bbrc.1994.2410. [DOI] [PubMed] [Google Scholar]
  60. Varga-Weisz P., van Holde K., Zlatanova J. Preferential binding of histone H1 to four-way helical junction DNA. J Biol Chem. 1993 Oct 5;268(28):20699–20700. [PubMed] [Google Scholar]
  61. Vogel T., Singer M. F. Interaction of f1 histone with superhelical DNA. Proc Natl Acad Sci U S A. 1975 Jul;72(7):2597–2600. doi: 10.1073/pnas.72.7.2597. [DOI] [PMC free article] [PubMed] [Google Scholar]
  62. Vogel T., Singer M. F. The effect of superhelicity on the interaction of histone f1 with closed circular duplex DNA. J Biol Chem. 1976 Apr 25;251(8):2334–2338. [PubMed] [Google Scholar]
  63. Weir H. M., Kraulis P. J., Hill C. S., Raine A. R., Laue E. D., Thomas J. O. Structure of the HMG box motif in the B-domain of HMG1. EMBO J. 1993 Apr;12(4):1311–1319. doi: 10.1002/j.1460-2075.1993.tb05776.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  64. Werner M. H., Huth J. R., Gronenborn A. M., Clore G. M. Molecular basis of human 46X,Y sex reversal revealed from the three-dimensional solution structure of the human SRY-DNA complex. Cell. 1995 Jun 2;81(5):705–714. doi: 10.1016/0092-8674(95)90532-4. [DOI] [PubMed] [Google Scholar]
  65. 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]
  66. Zlatanova J., van Holde K. The linker histones and chromatin structure: new twists. Prog Nucleic Acid Res Mol Biol. 1996;52:217–259. doi: 10.1016/s0079-6603(08)60968-x. [DOI] [PubMed] [Google Scholar]
  67. van de Wetering M., Clevers H. Sequence-specific interaction of the HMG box proteins TCF-1 and SRY occurs within the minor groove of a Watson-Crick double helix. EMBO J. 1992 Aug;11(8):3039–3044. doi: 10.1002/j.1460-2075.1992.tb05374.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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