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Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains

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Abstract

Cys2-His2 (C2H2) zinc finger domains (ZFs) were originally identified as DNA-binding domains, and uncharacterized domains are typically assumed to function in DNA binding. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. There are even examples of zinc fingers that support both DNA and protein interactions, which can be found in well-known DNA-binding proteins such as Sp1, Zif268, and Ying Yang 1 (YY1). C2H2 protein–protein interactions (PPIs) are proving to be more abundant than previously appreciated, more plastic than their DNA-binding counterparts, and more variable and complex in their interactions surfaces. Here we review the current knowledge of over 100 C2H2 zinc finger-mediated PPIs, focusing on what is known about the binding surface, contributions of individual fingers to the interaction, and function. An accurate understanding of zinc finger biology will likely require greater insights into the potential protein interaction capabilities of C2H2 ZFs.

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References

  1. Krishna, S. S., Majumdar, I., & Grishin, N. V. (2003). Structural classification of zinc fingers: Survey and summary. Nucleic Acids Research, 31, 532–550.

    PubMed  CAS  Google Scholar 

  2. Matthews, J. M., & Sunde, M. (2002). Zinc fingers–folds for many occasions. IUBMB Life, 54, 351–355.

    Article  PubMed  CAS  Google Scholar 

  3. Wolfe, S. A., Nekludova, L., & Pabo, C. O. (2000). DNA recognition by Cys2His2 zinc finger proteins. Annual Review of Biophysics and Biomolecular Structure, 29, 183–212.

    PubMed  CAS  Google Scholar 

  4. Frankel, A. D., Berg, J. M., & Pabo, C. O. (1987). Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proceedings of the National Academy of Sciences of the United States of America, 84, 4841–4845.

    PubMed  CAS  Google Scholar 

  5. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A., & Wright, P. E. (1989). Three-dimensional solution structure of a single zinc finger DNA-binding domain. Science, 245, 635–637.

    PubMed  CAS  Google Scholar 

  6. Parraga, G., Horvath, S. J., Eisen, A., Taylor, W. E., Hood, L., Young, E. T., & Klevit, R. E. (1988). Zinc-dependent structure of a single-finger domain of yeast ADR1. Science, 241, 1489–1492.

    PubMed  CAS  Google Scholar 

  7. Pavletich, N. P., & Pabo, C. O. (1991). Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A. Science, 252, 809–817.

    PubMed  CAS  Google Scholar 

  8. Liew, C. K., Kowalski, K., Fox, A. H., Newton, A., Sharpe, B. K., Crossley, M., & Mackay, J. P. (2000). Solution structures of two CCHC zinc fingers from the FOG family protein U-shaped that mediate protein–protein interactions. Structure, 8, 1157–1166.

    PubMed  CAS  Google Scholar 

  9. Miller, J., McLachlan, A. D., & Klug, A. (1985). Repetitive zinc-binding domains in the protein transcription factor IIIA from Xenopus oocytes. The EMBO Journal, 4, 1609–1614.

    PubMed  CAS  Google Scholar 

  10. Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A., Binns, D., Bork, P., Buillard, V., Cerutti, L., Copley, R., Courcelle, E., Das, U., Daugherty, L., Dibley, M., Finn, R., Fleischmann, W., Gough, J., Haft, D., Hulo, N., Hunter, S., Kahn, D., Kanapin, A., Kejariwal, A., Labarga, A., Langendijk-Genevaux, P.S., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McAnulla, C., McDowall, J., Mistry, J., Mitchell, A., Nikolskaya, A. N., Orchard, S., Orengo, C., Petryszak, R., Selengut, J. D., Sigrist, C. J., Thomas, P. D., Valentin, F., Wilson, D., Wu, C. H., & Yeats, C. (2007). New developments in the interpro database. Nucleic Acids Research, 35, D224–D228.

    PubMed  CAS  Google Scholar 

  11. Kersey, P., Bower, L., Morris, L., Horne, A., Petryszak, R., Kanz, C., Kanapin, A., Das, U., Michoud, K., Phan, I., Gattiker, A., Kulikova, T., Faruque, N., Duggan, K., McLaren, P., Reimholz, B., Duret, L., Penel, S., Reuter, I., & Apweiler, R. (2005). Integr8 and Genome Reviews: Integrated views of complete genomes and proteomes. Nucleic Acids Research, 33, D297–D302.

    PubMed  CAS  Google Scholar 

  12. Mackay, J. P., & Crossley, M. (1998). Zinc fingers are sticking together. Trends in Biochemical Sciences, 23, 1–4.

    PubMed  CAS  Google Scholar 

  13. Brown, R. S. (2005). Zinc finger proteins: Getting a grip on RNA. Current Opinion in Structural Biology, 15, 94–98.

    PubMed  CAS  Google Scholar 

  14. Hall, T. M. (2005). Multiple modes of RNA recognition by zinc finger proteins. Current Opinion in Structural Biology, 15, 367–373.

    PubMed  CAS  Google Scholar 

  15. Lee, B. M., Xu, J., Clarkson, B. K., Martinez-Yamout, M. A., Dyson, H. J., Case, D. A., Gottesfeld, J. M., & Wright, P. E. (2006). Induced fit and “lock and key” recognition of 5S RNA by zinc fingers of transcription factor IIIA. Journal of Molecular Biology, 357, 275–291.

    PubMed  CAS  Google Scholar 

  16. Lu, D., Searles, M. A., & Klug, A. (2003). Crystal structure of a zinc-finger-RNA complex reveals two modes of molecular recognition. Nature, 426, 96–100.

    PubMed  CAS  Google Scholar 

  17. Fox, A. H., Liew, C., Holmes, M., Kowalski, K., Mackay, J., & Crossley, M. (1999). Transcriptional cofactors of the FOG family interact with GATA proteins by means of multiple zinc fingers. The EMBO Journal, 18, 2812–2822.

    PubMed  CAS  Google Scholar 

  18. Honma, Y., Kiyosawa, H., Mori, T., Oguri, A., Nikaido, T., Kanazawa, K., Tojo, M., Takeda, J., Tanno, Y., Yokoya, S., Kawabata, I., Ikeda, H., & Wanaka, A. (1999). Eos: A novel member of the Ikaros gene family expressed predominantly in the developing nervous system. FEBS Letters, 447, 76–80.

    PubMed  CAS  Google Scholar 

  19. Kelley, C. M., Ikeda, T., Koipally, J., Avitahl, N., Wu, L., Georgopoulos, K., & Morgan, B. A. (1998). Helios, a novel dimerization partner of Ikaros expressed in the earliest hematopoietic progenitors. Current Biology, 8, 508–515.

    PubMed  CAS  Google Scholar 

  20. Morgan, B., Sun, L., Avitahl, N., Andrikopoulos, K., Ikeda, T., Gonzales, E., Wu, P., Neben, S., & Georgopoulos, K. (1997). Aiolos, a lymphoid restricted transcription factor that interacts with Ikaros to regulate lymphocyte differentiation. The EMBO Journal, 16, 2004–2013.

    PubMed  CAS  Google Scholar 

  21. Pelham, H. R., & Brown, D. D. (1980). A specific transcription factor that can bind either the 5S RNA gene or 5S RNA. Proceedings of the National Academy of Sciences of the United States of America, 77, 4170–4174.

    PubMed  CAS  Google Scholar 

  22. Perdomo, J., Holmes, M., Chong, B., & Crossley, M. (2000). Eos and pegasus, two members of the Ikaros family of proteins with distinct DNA binding activities. The Journal of Biological Chemistry, 275, 38347–38354.

    PubMed  CAS  Google Scholar 

  23. Simpson, R. J., Yi Lee, S. H., Bartle, N., Sum, E. Y., Visvader, J. E., Matthews, J. M., Mackay, J. P., & Crossley, M. (2004). A classic zinc finger from friend of GATA mediates an interaction with the coiled-coil of transforming acidic coiled-coil 3. The Journal of Biological Chemistry, 279, 39789–39797.

    PubMed  CAS  Google Scholar 

  24. Sun, L., Liu, A., & Georgopoulos, K. (1996). Zinc finger-mediated protein interactions modulate Ikaros activity, a molecular control of lymphocyte development. The EMBO Journal, 15, 5358–5369.

    PubMed  CAS  Google Scholar 

  25. Chapman, N. R., & Perkins, N. D. (2000). Inhibition of the RelA(p65) NF-kappaB subunit by Egr-1. The Journal of Biological Chemistry, 275, 4719–4725.

    PubMed  CAS  Google Scholar 

  26. Lee, J. S., Galvin, K. M., & Shi, Y. (1993). Evidence for physical interaction between the zinc-finger transcription factors YY1 and Sp1. Proceedings of the National Academy of Sciences of the United States of America, 90, 6145–6149.

    PubMed  CAS  Google Scholar 

  27. Seto, E., Lewis, B., & Shenk, T. (1993). Interaction between transcription factors Sp1 and YY1. Nature, 365, 462–464.

    PubMed  CAS  Google Scholar 

  28. Nardelli, J., Gibson, T. J., Vesque, C., & Charnay, P. (1991). Base sequence discrimination by zinc-finger DNA-binding domains. Nature, 349, 175–178.

    PubMed  CAS  Google Scholar 

  29. Rodriguez de la Vega, R. C., Merino, E., Becerril, B., & Possani, L. D. (2003). Novel interactions between K+ channels and scorpion toxins. Trends in Pharmacological Sciences, 24, 222–227.

    Google Scholar 

  30. Westman, B. J., Perdomo, J., Matthews, J. M., Crossley, M., & Mackay, J. P. (2004). Structural studies on a protein-binding zinc-finger domain of Eos reveal both similarities and differences to classical zinc fingers. Biochemistry, 43, 13318–13327.

    PubMed  CAS  Google Scholar 

  31. Pavletich, N. P., & Pabo, C. O. (1993). Crystal structure of a five-finger GLI-DNA complex: New perspectives on zinc fingers. Science, 261, 1701–1707.

    PubMed  CAS  Google Scholar 

  32. Wang, Z., Feng, L. S., Matskevich, V., Venkataraman, K., Parasuram, P., & Laity, J. H. (2006). Solution structure of a Zap1 zinc-responsive domain provides insights into metalloregulatory transcriptional repression in Saccharomyces cerevisiae. Journal of Molecular Biology, 357, 1167–1183.

    PubMed  CAS  Google Scholar 

  33. Merithew, E., Stone, C., Eathiraj, S., & Lambright, D. G. (2003). Determinants of Rab5 interaction with the N terminus of early endosome antigen 1. The Journal of Biological Chemistry, 278, 8494–8500.

    PubMed  CAS  Google Scholar 

  34. Hoffmann, A., Ciani, E., Boeckardt, J., Holsboer, F., Journot, L., & Spengler, D. (2003). Transcriptional activities of the zinc finger protein Zac are differentially controlled by DNA binding. Molecular and Cellular Biology, 23, 988–1003.

    PubMed  CAS  Google Scholar 

  35. Omichinski, J. G., Clore, G. M., Robien, M., Sakaguchi, K., Appella, E., & Gronenborn, A. M. (1992). High-resolution solution structure of the double Cys2His2 zinc finger from the human enhancer binding protein MBP-1. Biochemistry, 31, 3907–3917.

    PubMed  CAS  Google Scholar 

  36. Tsang, A. P., Visvader, J. E., Turner, C. A., Fujiwara, Y., Yu, C., Weiss, M. J., Crossley, M., & Orkin, S. H. (1997). FOG, a multitype zinc finger protein, acts as a cofactor for transcription factor GATA-1 in erythroid and megakaryocytic differentiation. Cell, 90, 109–119.

    PubMed  CAS  Google Scholar 

  37. Liew, C. K., Simpson, R. J., Kwan, A. H., Crofts, L. A., Loughlin, F. E., Matthews, J. M., Crossley, M., & Mackay, J. P. (2005). Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/friend of GATA interaction. Proceedings of the National Academy of Sciences of the United States of America, 102, 583–588.

    PubMed  CAS  Google Scholar 

  38. Morellet, N., Jullian, N., De Rocquigny, H., Maigret, B., Darlix, J. L., & Roques, B. P. (1992). Determination of the structure of the nucleocapsid protein NCp7 from the human immunodeficiency virus type 1 by 1H NMR. The EMBO Journal, 11, 3059–3065.

    PubMed  CAS  Google Scholar 

  39. Matthews, J. M., Kowalski, K., Liew, C. K., Sharpe, B. K., Fox, A. H., Crossley, M., & MacKay, J. P. (2000). A class of zinc fingers involved in protein–protein interactions biophysical characterization of CCHC fingers from fog and U-shaped. European Journal of Biochemistry, 267, 1030–1038.

    PubMed  CAS  Google Scholar 

  40. Kwan, A. H., Czolij, R., Mackay, J. P., & Crossley, M. (2003). Pentaprobe: A comprehensive sequence for the one-step detection of DNA-binding activities. Nucleic Acids Research, 31, e124.

    PubMed  Google Scholar 

  41. Tsai, R. Y., & Reed, R. R. (1998). Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Molecular and Cellular Biology, 18, 6447–6456.

    PubMed  CAS  Google Scholar 

  42. Hata, A., Seoane, J., Lagna, G., Montalvo, E., Hemmati-Brivanlou, A., & Massague, J. (2000). OAZ uses distinct DNA- and protein-binding zinc fingers in separate BMP-smad and olf signaling pathways. Cell, 100, 229–240.

    PubMed  CAS  Google Scholar 

  43. Martin, P. J., Delmotte, M. H., Formstecher, P., & Lefebvre, P. (2003). PLZF is a negative regulator of retinoic acid receptor transcriptional activity. Nuclear Receptor, 1, 6.

    PubMed  Google Scholar 

  44. Tsuzuki, S., & Enver, T. (2002). Interactions of GATA-2 with the promyelocytic leukemia zinc finger (PLZF) protein, its homologue FAZF, and the t(11;17)-generated PLZF-retinoic acid receptor alpha oncoprotein. Blood, 99, 3404–3410.

    PubMed  CAS  Google Scholar 

  45. Dhordain, P., Albagli, O., Honore, N., Guidez, F., Lantoine, D., Schmid, M., The, H. D., Zelent, A., & Koken, M. H. (2000). Colocalization and heteromerization between the two human oncogene POZ/zinc finger proteins, LAZ3 (BCL6) and PLZF. Oncogene, 19, 6240–6250.

    PubMed  CAS  Google Scholar 

  46. Nanba, D., Mammoto, A., Hashimoto, K., & Higashiyama, S. (2003). Proteolytic release of the carboxy-terminal fragment of proHB-EGF causes nuclear export of PLZF. The Journal of Cell Biology, 163, 489–502.

    PubMed  CAS  Google Scholar 

  47. Lee, J. A., Suh, D. C., Kang, J. E., Kim, M. H., Park, H., Lee, M. N., Kim, J. M., Jeon, B. N., Roh, H. E., Yu, M. Y., Choi, K. Y., Kim, K. Y., & Hur, M. W. (2005). Transcriptional activity of Sp1 is regulated by molecular interactions between the zinc finger DNA binding domain and the inhibitory domain with corepressors, and this interaction is modulated by MEK. The Journal of Biological Chemistry, 280, 28061–28071.

    PubMed  CAS  Google Scholar 

  48. Suzuki, T., Kimura, A., Nagai, R., & Horikoshi, M. (2000). Regulation of interaction of the acetyltransferase region of p300 and the DNA-binding domain of Sp1 on and through DNA binding. Genes Cells, 5, 29–41.

    PubMed  CAS  Google Scholar 

  49. Kadam, S., McAlpine, G. S., Phelan, M. L., Kingston, R. E., Jones, K. A., & Emerson, B. M. (2000). Functional selectivity of recombinant mammalian SWI/SNF subunits. Genes & Development, 14, 2441–2451.

    CAS  Google Scholar 

  50. Suzuki, T., Muto, S., Miyamoto, S., Aizawa, K., Horikoshi, M., & Nagai, R. (2003). Functional interaction of the DNA-binding transcription factor Sp1 through its DNA-binding domain with the histone chaperone TAF-I. The Journal of Biological Chemistry, 278, 28758–28764.

    PubMed  CAS  Google Scholar 

  51. Rotheneder, H., Geymayer, S., & Haidweger, E. (1999). Transcription factors of the Sp1 family: Interaction with E2F and regulation of the murine thymidine kinase promoter. Journal of Molecular Biology, 293, 1005–1015.

    PubMed  CAS  Google Scholar 

  52. Zhou, Q., Gedrich, R. W., & Engel, D. A. (1995). Transcriptional repression of the c-fos gene by YY1 is mediated by a direct interaction with ATF/CREB. Journal of Virology, 69, 4323–4330.

    PubMed  CAS  Google Scholar 

  53. Kalenik, J. L., Chen, D., Bradley, M. E., Chen, S. J., & Lee, T. C. (1997). Yeast two-hybrid cloning of a novel zinc finger protein that interacts with the multifunctional transcription factor YY1. Nucleic Acids Research, 25, 843–849.

    PubMed  CAS  Google Scholar 

  54. Kurisaki, K., Kurisaki, A., Valcourt, U., Terentiev, A. A., Pardali, K., Ten Dijke, P., Heldin, C. H., Ericsson, J., & Moustakas, A. (2003). Nuclear factor YY1 inhibits transforming growth factor beta- and bone morphogenetic protein-induced cell differentiation. Molecular and Cellular Biology, 23, 4494–4510.

    PubMed  CAS  Google Scholar 

  55. Rodgers, K. K., Bu, Z., Fleming, K. G., Schatz, D. G., Engelman, D. M., & Coleman, J. E. (1996). A zinc-binding domain involved in the dimerization of RAG1. Journal of Molecular Biology, 260, 70–84.

    PubMed  CAS  Google Scholar 

  56. Aidinis, V., Dias, D. C., Gomez, C. A., Bhattacharyya, D., Spanopoulou, E., & Santagata, S. (2000). Definition of minimal domains of interaction within the recombination-activating genes 1 and 2 recombinase complex. Journal of Immunology, 164, 5826–5832.

    CAS  Google Scholar 

  57. Hoffmann, A., Barz, T., & Spengler, D. (2006). Multitasking C2H2 zinc fingers link Zac DNA binding to coordinated regulation of p300-histone acetyltransferase activity. Molecular and Cellular Biology, 26, 5544–5557.

    PubMed  CAS  Google Scholar 

  58. Hahm, K., Cobb, B. S., McCarty, A. S., Brown, K. E., Klug, C. A., Lee, R., Akashi, K., Weissman, I. L., Fisher, A. G., & Smale, S. T. (1998). Helios, a T cell-restricted Ikaros family member that quantitatively associates with Ikaros at centromeric heterochromatin. Genes & Development, 12, 782–796.

    CAS  Google Scholar 

  59. Molnar, A., & Georgopoulos, K. (1994). The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins. Molecular and Cellular Biology, 14, 8292–8303.

    PubMed  CAS  Google Scholar 

  60. Momeni, P., Glockner, G., Schmidt, O., von Holtum, D., Albrecht, B., Gillessen-Kaesbach, G., Hennekam, R., Meinecke, P., Zabel, B., Rosenthal, A., Horsthemke, B., & Ludecke, H. J. (2000). Mutations in a new gene, encoding a zinc-finger protein, cause tricho-rhino-phalangeal syndrome type I. Nature Genetics, 24, 71–74.

    PubMed  CAS  Google Scholar 

  61. Westman, B. J., Perdomo, J., Sunde, M., Crossley, M., & Mackay, J. P. (2003). The C-terminal domain of Eos forms a high order complex in solution. The Journal of Biological Chemistry, 278, 42419–42426.

    PubMed  CAS  Google Scholar 

  62. Nojiri, S., Joh, T., Miura, Y., Sakata, N., Nomura, T., Nakao, H., Sobue, S., Ohara, H., Asai, K., & Ito, M. (2004). ATBF1 enhances the suppression of STAT3 signaling by interaction with PIAS3. Biochemical and Biophysical Research Communications Links, 314, 97–103.

    CAS  Google Scholar 

  63. Avram, D., Fields, A., Pretty On Top, K., Nevrivy, D. J., Ishmael, J. E., & Leid, M. (2000). Isolation of a novel family of C(2)H(2) zinc finger proteins implicated in transcriptional repression mediated by chicken ovalbumin upstream promoter transcription factor (COUP-TF) orphan nuclear receptors. The Journal of Biological Chemistry, 275, 10315–10332.

    PubMed  CAS  Google Scholar 

  64. Avram, D., Fields, A., Senawong, T., Topark-Ngarm, A., & Leid, M. (2002). COUP-TF (chicken ovalbumin upstream promoter transcription factor)-interacting protein 1 (CTIP1) is a sequence-specific DNA binding protein. The Biochemical Journal, 368, 555–563.

    PubMed  CAS  Google Scholar 

  65. Rohr, O., Lecestre, D., Chasserot-Golaz, S., Marban, C., Avram, D., Aunis, D., Leid, M., & Schaeffer, E. (2003). Recruitment of Tat to heterochromatin protein HP1 via interaction with CTIP2 inhibits human immunodeficiency virus type 1 replication in microglial cells. Journal of Virology, 77, 5415–5427.

    PubMed  CAS  Google Scholar 

  66. Mascle, X., Albagli, O., & Lemercier, C. (2003). Point mutations in BCL6 DNA-binding domain reveal distinct roles for the six zinc fingers. Biochemical and Biophysical Research Communications Links, 300, 391–396.

    CAS  Google Scholar 

  67. Lemercier, C., Brocard, M. P., Puvion-Dutilleul, F., Kao, H. Y., Albagli, O., & Khochbin, S. (2002). Class II histone deacetylases are directly recruited by BCL6 transcriptional repressor. The Journal of Biological Chemistry, 277, 22045–22052.

    PubMed  CAS  Google Scholar 

  68. Chevallier, N., Corcoran, C. M., Lennon, C., Hyjek, E., Chadburn, A., Bardwell, V. J., Licht, J. D., & Melnick, A. (2004). ETO protein of t(8;21) AML is a corepressor for Bcl-6 B-cell lymphoma oncoprotein. Blood, 103, 1454–1463.

    PubMed  CAS  Google Scholar 

  69. Davies, M. A., Koul, D., Dhesi, H., Berman, R., McDonnell, T. J., McConkey, D., Yung, W. K., & Steck, P. A. (1999). Regulation of Akt/PKB activity, cellular growth, and apoptosis in prostate carcinoma cells by MMAC/PTEN. Cancer Research, 59, 2551–2556.

    PubMed  CAS  Google Scholar 

  70. Phan, R. T., Saito, M., Basso, K., Niu, H., & Dalla-Favera, R. (2005). BCL6 interacts with the transcription factor Miz-1 to suppress the cyclin-dependent kinase inhibitor p21 and cell cycle arrest in germinal center B cells. Nature Immunology, 6, 1054–1060.

    PubMed  CAS  Google Scholar 

  71. Vasanwala, F. H., Kusam, S., Toney, L. M., & Dent, A. L. (2002). Repression of AP-1 function: A mechanism for the regulation of Blimp-1 expression and B lymphocyte differentiation by the B cell lymphoma-6 protooncogene. Journal of Immunology, 169, 1922–1929.

    CAS  Google Scholar 

  72. Lee, T. H., Lwu, S., Kim, J., & Pelletier, J. (2002). Inhibition of Wilms tumor 1 transactivation by bone marrow zinc finger 2, a novel transcriptional repressor. The Journal of Biological Chemistry, 277, 44826–44837.

    PubMed  CAS  Google Scholar 

  73. Chernukhin, I. V., Shamsuddin, S., Robinson, A. F., Carne, A. F., Paul, A., El-Kady, A.I., Lobanenkov, V. V., & Klenova, E. M. (2000). Physical and functional interaction between two pluripotent proteins, the Y-box DNA/RNA-binding factor, YB-1, and the multivalent zinc finger factor, CTCF. The Journal of Biological Chemistry, 275, 29915–29921.

    PubMed  CAS  Google Scholar 

  74. Donohoe, M. E., Zhang, L. F., Xu, N., Shi, Y., & Lee, J. T. (2007). Identification of a Ctcf cofactor, Yy1, for the X chromosome binary switch. Molecular Cell, 25, 43–56.

    PubMed  CAS  Google Scholar 

  75. Moore, F. L., Jaruzelska, J., Dorfman, D. M., & Reijo-Pera, R.A. (2004). Identification of a novel gene, DZIP (DAZ-interacting protein), that encodes a protein that interacts with DAZ (deleted in azoospermia) and is expressed in embryonic stem cells and germ cells. Genomics, 83, 834–843.

    PubMed  CAS  Google Scholar 

  76. Bond, H. M., Mesuraca, M., Carbone, E., Bonelli, P., Agosti, V., Amodio, N., De Rosa, G., Di Nicola, M., Gianni, A. M., Moore, M. A., Hata, A., Grieco, M., Morrone, G., & Venuta, S. (2004). Early hematopoietic zinc finger protein (EHZF), the human homolog to mouse Evi3, is highly expressed in primitive human hematopoietic cells. Blood, 103, 2062–2070.

    PubMed  CAS  Google Scholar 

  77. Laricchia-Robbio, L., Fazzina, R., Li, D., Rinaldi, C. R., Sinha, K. K., Chakraborty, S., & Nucifora, G. (2006). Point mutations in two EVI1 Zn fingers abolish EVI1-GATA1 interaction and allow erythroid differentiation of murine bone marrow cells. Molecular and Cellular Biology, 26, 7658–7666.

    PubMed  CAS  Google Scholar 

  78. Wolf, I., & Rohrschneider, L. R. (1999). Fiz1, a novel zinc finger protein interacting with the receptor tyrosine kinase Flt3. The Journal of Biological Chemistry, 274, 21478–21484.

    PubMed  CAS  Google Scholar 

  79. Liu, F., Massague, J., & Ruiz i Altaba, A. (1998). Carboxy-terminally truncated Gli3 proteins associate with Smads. Nature Genetics, 20, 325–326.

    PubMed  CAS  Google Scholar 

  80. Koyabu, Y., Nakata, K., Mizugishi, K., Aruga, J., & Mikoshiba, K. (2001). Physical and functional interactions between Zic and Gli proteins. The Journal of Biological Chemistry, 276, 6889–6892.

    PubMed  CAS  Google Scholar 

  81. Dahl, R., Iyer, S. R., Owens, K. S., Cuylear, D. D., & Simon, M. C. (2007). The transcriptional repressor GFI-1 antagonizes PU.1 activity through protein–protein interaction. The Journal of Biological Chemistry, 282, 6473–6483.

    PubMed  CAS  Google Scholar 

  82. McGhee, L., Bryan, J., Elliott, L., Grimes, H. L., Kazanjian, A., Davis, J. N., & Meyers, S. (2003). Gfi-1 attaches to the nuclear matrix, associates with ETO (MTG8) and histone deacetylase proteins, and represses transcription using a TSA-sensitive mechanism. Journal of Cellular Biochemistry, 89, 1005–1018.

    PubMed  CAS  Google Scholar 

  83. McCarty, A. S., Kleiger, G., Eisenberg, D., & Smale, S. T. (2003). Selective dimerization of a C2H2 zinc finger subfamily. Molecular Cell, 11, 459–470.

    PubMed  CAS  Google Scholar 

  84. Hennemann, H., Vassen, L., Geisen, C., Eilers, M., & Moroy, T. (2003). Identification of a novel Kruppel-associated box domain protein, Krim-1, that interacts with c-Myc and inhibits its oncogenic activity. The Journal of Biological Chemistry, 278, 28799–28811.

    PubMed  CAS  Google Scholar 

  85. Starck, J., Cohet, N., Gonnet, C., Sarrazin, S., Doubeikovskaia, Z., Doubeikovski, A., Verger, A., Duterque-Coquillaud, M., & Morle, F. (2003). Functional cross-antagonism between transcription factors FLI-1 and EKLF. Molecular and Cellular Biology, 23, 1390–1402.

    PubMed  CAS  Google Scholar 

  86. Song, C. Z., Keller, K., Murata, K., Asano, H., & Stamatoyannopoulos, G. (2002). Functional interaction between coactivators CBP/p300, PCAF, and transcription factor FKLF2. The Journal of Biological Chemistry, 277, 7029–7036.

    PubMed  CAS  Google Scholar 

  87. Zhang, W., Wang, Y., Long, J., Girton, J., Johansen, J., & Johansen, K. M. (2003). A developmentally regulated splice variant from the complex lola locus encoding multiple different zinc finger domain proteins interacts with the chromosomal kinase JIL-1. The Journal of Biological Chemistry, 278, 11696–11704.

    PubMed  CAS  Google Scholar 

  88. Morii, E., Oboki, K., Kataoka, T. R., Igarashi, K., & Kitamura, Y. (2002). Interaction and cooperation of mi transcription factor (MITF) and myc-associated zinc-finger protein-related factor (MAZR) for transcription of mouse mast cell protease 6 gene. The Journal of Biological Chemistry, 277, 8566–8571.

    PubMed  CAS  Google Scholar 

  89. Mahajan, M. A., Murray, A., & Samuels, H. H. (2002). NRC-interacting factor 1 is a novel cotransducer that interacts with and regulates the activity of the nuclear hormone receptor coactivator NRC. Molecular and Cellular Biology, 22, 6883–6894.

    PubMed  CAS  Google Scholar 

  90. Bomar, M. G., Pai, M. T., Tzeng, S. R., Li, S. S., & Zhou, P. (2007). Structure of the ubiquitin-binding zinc finger domain of human DNA Y-polymerase eta. EMBO Reports, 8, 247–251.

    PubMed  CAS  Google Scholar 

  91. Andres, M. E., Burger, C., Peral-Rubio, M.J., Battaglioli, E., Anderson, M. E., Grimes, J., Dallman, J., Ballas, N., & Mandel, G. (1999). CoREST: A functional corepressor required for regulation of neural-specific gene expression. Proceedings of the National Academy of Sciences of the United States of America, 96, 9873–9878.

    PubMed  CAS  Google Scholar 

  92. Dai, H., Hogan, C., Gopalakrishnan, B., Torres-Vazquez, J., Nguyen, M., Park, S., Raftery, L. A., Warrior, R., & Arora, K. (2000). The zinc finger protein schnurri acts as a Smad partner in mediating the transcriptional response to decapentaplegic. Developmental Biology, 227, 373–387.

    PubMed  CAS  Google Scholar 

  93. Acar, M., Jafar-Nejad, H., Giagtzoglou, N., Yallampalli, S., David, G., He, Y., Delidakis, C., & Bellen, H. J. (2006). Senseless physically interacts with proneural proteins and functions as a transcriptional co-activator. Development, 133, 1979–1989.

    PubMed  CAS  Google Scholar 

  94. Formstecher, E., Aresta, S., Collura, V., Hamburger, A., Meil, A., Trehin, A., Reverdy, C., Betin, V., Maire, S., Brun, C., Jacq, B., Arpin, M., Bellaiche, Y., Bellusci, S., Benaroch, P., Bornens, M., Chanet, R., Chavrier, P., Delattre, O., Doye, V., Fehon, R., Faye, G., Galli, T., Girault, J. A., Goud, B., de Gunzburg, J., Johannes, L., Junier, M. P., Mirouse, V., Mukherjee, A., Papadopoulo, D., Perez, F., Plessis, A., Rosse, C., Saule, S., Stoppa-Lyonnet, D., Vincent, A., White, M., Legrain, P., Wojcik, J., Camonis, J., & Daviet, L. (2005). Protein interaction mapping: A Drosophila case study. Genome Research, 15, 376–384.

    PubMed  CAS  Google Scholar 

  95. Payre, F., Buono, P., Vanzo, N., & Vincent, A. (1997). Two types of zinc fingers are required for dimerization of the serendipity delta transcriptional activator. Molecular and Cellular Biology, 17, 3137–3145.

    PubMed  CAS  Google Scholar 

  96. Karlseder, J., Rotheneder, H., & Wintersberger, E. (1996). Interaction of Sp1 with the growth- and cell cycle-regulated transcription factor E2F. Molecular and Cellular Biology, 16, 1659–1667.

    PubMed  CAS  Google Scholar 

  97. Li, S. H., Cheng, A. L., Zhou, H., Lam, S., Rao, M., Li, H., & Li, X. J. (2002). Interaction of Huntington disease protein with transcriptional activator Sp1. Molecular and Cellular Biology, 22, 1277–1287.

    PubMed  CAS  Google Scholar 

  98. Gartel, A. L., Ye, X., Goufman, E., Shianov, P., Hay, N., Najmabadi, F., & Tyner, A. L. (2001). Myc represses the p21(WAF1/CIP1) promoter and interacts with Sp1/Sp3. Proceedings of the National Academy of Sciences of the United States of America, 98, 4510–4515.

    PubMed  CAS  Google Scholar 

  99. Smith, G. E., & Darling, D. S. (2003). Combination of a zinc finger and homeodomain required for protein-interaction. Molecular Biology Reports, 30, 199–206.

    PubMed  CAS  Google Scholar 

  100. Mercer, K. B., Flaherty, D. B., Miller, R. K., Qadota, H., Tinley, T. L., Moerman, D. G., & Benian, G. M. (2003). Caenorhabditis elegans UNC-98, a C2H2 Zn finger protein, is a novel partner of UNC-97/PINCH in muscle adhesion complexes. Molecular Biology of the Cell, 14, 2492–2507.

    PubMed  CAS  Google Scholar 

  101. Little, N. A., Hastie, N. D., & Davies, R. C. (2000). Identification of WTAP, a novel Wilms’ tumour 1-associating protein. Human Molecular Genetics, 9, 2231–2239.

    PubMed  CAS  Google Scholar 

  102. Lee, S. B., & Haber, D. A. (2001). Wilms tumor and the WT1 gene. Experimental Cell Research, 264, 74–99.

    PubMed  CAS  Google Scholar 

  103. Spraggon, L., Dudnakova, T., Slight, J., Lustig-Yariv, O., Cotterell, J., Hastie, N., & Miles, C. (2007). hnRNP-U directly interacts with WT1 and modulates WT1 transcriptional activation. Oncogene, 26, 1484–1491.

    PubMed  CAS  Google Scholar 

  104. Davies, R. C., Calvio, C., Bratt, E., Larsson, S. H., Lamond, A. I., & Hastie, N. D. (1998). WT1 interacts with the splicing factor U2AF65 in an isoform-dependent manner and can be incorporated into spliceosomes. Genes & Development, 12, 3217–3225.

    CAS  Google Scholar 

  105. Austen, M., Luscher, B., & Luscher-Firzlaff, J.M. (1997). Characterization of the transcriptional regulator YY1. The bipartite transactivation domain is independent of interaction with the TATA box-binding protein, transcription factor IIB, TAFII55, or cAMP-responsive element-binding protein (CPB)-binding protein. The Journal of Biological Chemistry, 272, 1709–1717.

    PubMed  CAS  Google Scholar 

  106. Lee, J. S., See, R. H., Galvin, K. M., Wang, J., & Shi, Y. (1995). Functional interactions between YY1 and adenovirus E1A. Nucleic Acids Research, 23, 925–931.

    PubMed  CAS  Google Scholar 

  107. Lewis, B. A., Tullis, G., Seto, E., Horikoshi, N., Weinmann, R., & Shenk, T. (1995). Adenovirus E1A proteins interact with the cellular YY1 transcription factor. Journal of Virology, 69, 1628–1636.

    PubMed  CAS  Google Scholar 

  108. Austen, M., Cerni, C., Luscher-Firzlaff, J.M., & Luscher, B. (1998). YY1 can inhibit c-Myc function through a mechanism requiring DNA binding of YY1 but neither its transactivation domain nor direct interaction with c-Myc. Oncogene, 17, 511–520.

    PubMed  CAS  Google Scholar 

  109. Ishiguro, A., Ideta, M., Mikoshiba, K., Chen, D. J., & Aruga, J. (2007). ZIC2-dependent transcriptional regulation is mediated by DNA-dependent protein kinase, poly(ADP-ribose) polymerase, and RNA helicase A. The Journal of Biological Chemistry, 282, 9983–9995.

    PubMed  CAS  Google Scholar 

  110. Bai, L., & Merchant, J. L. (2001). ZBP-89 promotes growth arrest through stabilization of p53. Molecular and Cellular Biology, 21, 4670–4683.

    PubMed  CAS  Google Scholar 

  111. Tan, W., Zheng, L., Lee, W. H., & Boyer, T. G. (2004). Functional dissection of transcription factor ZBRK1 reveals zinc fingers with dual roles in DNA-binding and BRCA1-dependent transcriptional repression. The Journal of Biological Chemistry, 279, 6576–6587.

    PubMed  CAS  Google Scholar 

  112. Numoto, M., Yokoro, K., & Koshi, J. (1999). ZF5, which is a Kruppel-type transcriptional repressor, requires the zinc finger domain for self-association. Biochemical and Biophysical Research Communications Links, 256, 573–578.

    CAS  Google Scholar 

  113. Paces-Fessy, M., Boucher, D., Petit, E., Paute-Briand, S., & Blanchet-Tournier, M.F. (2004). The negative regulator of Gli, Suppressor of fused (Sufu), interacts with SAP18, Galectin3 and other nuclear proteins. The Biochemical Journal, 378, 353–362.

    PubMed  CAS  Google Scholar 

  114. Colland, F., Jacq, X., Trouplin, V., Mougin, C., Groizeleau, C., Hamburger, A., Meil, A., Wojcik, J., Legrain, P., & Gauthier, J. M. (2004). Functional proteomics mapping of a human signaling pathway. Genome Research, 14, 1324–1332.

    PubMed  CAS  Google Scholar 

  115. Wang, J., Kudoh, J., Takayanagi, A., & Shimizu, N. (2005). Novel human BTB/POZ domain-containing zinc finger protein ZNF295 is directly associated with ZFP161. Biochemical and Biophysical Research Communications Links, 327, 615–627.

    CAS  Google Scholar 

  116. Al-Kandari, W., Koneni, R., Navalgund, V., Aleksandrova, A., Jambunathan, S., & Fontes, J. D. (2007). The zinc finger proteins ZXDA and ZXDC form a complex that binds CIITA and regulates MHC II gene transcription. Journal of Molecular Biology, 369, 1175–1187.

    PubMed  CAS  Google Scholar 

  117. Mysliwiec, M. R., Kim, T. G., & Lee, Y. (2007). Characterization of zinc finger protein 496 that interacts with Jumonji/Jarid2. FEBS Letters, 581, 2633–2640. .

    PubMed  CAS  Google Scholar 

  118. Spengler, D., Villalba, M., Hoffmann, A., Pantaloni, C., Houssami, S., Bockaert, J., & Journot, L. (1997). Regulation of apoptosis and cell cycle arrest by Zac1, a novel zinc finger protein expressed in the pituitary gland and the brain. The EMBO Journal, 16, 2814–2825.

    PubMed  CAS  Google Scholar 

  119. Varrault, A., Ciani, E., Apiou, F., Bilanges, B., Hoffmann, A., Pantaloni, C., Bockaert, J., Spengler, D., & Journot, L. (1998). hZAC encodes a zinc finger protein with antiproliferative properties and maps to a chromosomal region frequently lost in cancer. Proceedings of the National Academy of Sciences of the United States of America, 95, 8835–8840.

    PubMed  CAS  Google Scholar 

  120. Baldwin, A. S. Jr., LeClair, K. P., Singh, H., & Sharp, P. A. (1990). A large protein containing zinc finger domains binds to related sequence elements in the enhancers of the class I major histocompatibility complex and kappa immunoglobulin genes. Molecular and Cellular Biology, 10, 1406–1414.

    PubMed  CAS  Google Scholar 

  121. Clark, L., Matthews, J. R., & Hay, R. T. (1990). Interaction of enhancer-binding protein EBP1 (NF-kappa B) with the human immunodeficiency virus type 1 enhancer. Journal of Virology, 64, 1335–1344.

    PubMed  CAS  Google Scholar 

  122. Fan, C. M., & Maniatis, T. (1990). A DNA-binding protein containing two widely separated zinc finger motifs that recognize the same DNA sequence. Genes & Development, 4, 29–42.

    CAS  Google Scholar 

  123. Maekawa, T., Sakura, H., Sudo, T., & Ishii, S. (1989). Putative metal finger structure of the human immunodeficiency virus type 1 enhancer binding protein HIV-EP1. The Journal of Biological Chemistry, 264, 14591–14593.

    PubMed  CAS  Google Scholar 

  124. Tsai, R. Y., & Reed, R. R. (1997). Cloning and functional characterization of Roaz, a zinc finger protein that interacts with O/E-1 to regulate gene expression: Implications for olfactory neuronal development. The Journal of Neuroscience, 17, 4159–4169.

    PubMed  CAS  Google Scholar 

  125. de The, H., Lavau, C., Marchio, A., Chomienne, C., Degos, L., & Dejean, A. (1991). The PML-RAR alpha fusion mRNA generated by the t(15;17) translocation in acute promyelocytic leukemia encodes a functionally altered RAR. Cell, 66, 675–684.

    PubMed  Google Scholar 

  126. Kakizuka, A., Miller, W. H. Jr., Umesono, K., Warrell, R. P. Jr., Frankel, S. R., Murty, V. V., Dmitrovsky, E., & Evans, R. M. (1991). Chromosomal translocation t(15;17) in human acute promyelocytic leukemia fuses RAR alpha with a novel putative transcription factor, PML. Cell, 66, 663–674.

    PubMed  CAS  Google Scholar 

  127. Sitterlin, D., Tiollais, P., & Transy, C. (1997). The RAR alpha-PLZF chimera associated with Acute Promyelocytic Leukemia has retained a sequence-specific DNA-binding domain. Oncogene, 14, 1067–1074.

    PubMed  CAS  Google Scholar 

  128. Ward, J. O., McConnell, M. J., Carlile, G. W., Pandolfi, P. P., Licht, J. D., & Freedman, L. P. (2001). The acute promyelocytic leukemia-associated protein, promyelocytic leukemia zinc finger, regulates 1,25-dihydroxyvitamin D(3)-induced monocytic differentiation of U937 cells through a physical interaction with vitamin D(3) receptor. Blood, 98, 3290–3300.

    PubMed  CAS  Google Scholar 

  129. Prenzel, N., Zwick, E., Daub, H., Leserer, M., Abraham, R., Wallasch, C., & Ullrich, A. (1999). EGF receptor transactivation by G-protein-coupled receptors requires metalloproteinase cleavage of proHB-EGF. Nature, 402, 884–888.

    PubMed  CAS  Google Scholar 

  130. Armstrong, S. A., Barry, D. A., Leggett, R. W., & Mueller, C. R. (1997). Casein kinase II-mediated phosphorylation of the C terminus of Sp1 decreases its DNA binding activity. The Journal of Biological Chemistry, 272, 13489–13495.

    PubMed  CAS  Google Scholar 

  131. Briggs, M. R., Kadonaga, J. T., Bell, S. P., & Tjian, R. (1986). Purification and biochemical characterization of the promoter-specific transcription factor, Sp1. Science, 234, 47–52.

    PubMed  CAS  Google Scholar 

  132. Dennig, J., Hagen, G., Beato, M., & Suske, G. (1995). Members of the Sp transcription factor family control transcription from the uteroglobin promoter. The Journal of Biological Chemistry, 270, 12737–12744.

    PubMed  CAS  Google Scholar 

  133. Hagen, G., Muller, S., Beato, M., & Suske, G. (1994). Sp1-mediated transcriptional activation is repressed by Sp3. The EMBO Journal, 13, 3843–3851.

    PubMed  CAS  Google Scholar 

  134. Kadonaga, J. T., Carner, K. R., Masiarz, F. R., & Tjian, R. (1987). Isolation of cDNA encoding transcription factor Sp1 and functional analysis of the DNA binding domain. Cell, 51, 1079–1090.

    PubMed  CAS  Google Scholar 

  135. Kwon, H. S., Kim, M. S., Edenberg, H. J., & Hur, M. W. (1999). Sp3 and Sp4 can repress transcription by competing with Sp1 for the core cis-elements on the human ADH5/FDH minimal promoter. The Journal of Biological Chemistry, 274, 20–28.

    PubMed  CAS  Google Scholar 

  136. Li, N., Seetharam, S., & Seetharam, B. (1998). Characterization of the human transcobalamin II promoter. A proximal GC/GT box is a dominant negative element. The Journal of Biological Chemistry, 273, 16104–16111.

    PubMed  CAS  Google Scholar 

  137. Murata, Y., Kim, H. G., Rogers, K. T., Udvadia, A. J., & Horowitz, J. M. (1994). Negative regulation of Sp1 trans-activation is correlated with the binding of cellular proteins to the amino terminus of the Sp1 trans-activation domain. The Journal of Biological Chemistry, 269, 20674–20681.

    PubMed  CAS  Google Scholar 

  138. Ogra, Y., Suzuki, K., Gong, P., Otsuka, F., & Koizumi, S. (2001). Negative regulatory role of Sp1 in metal responsive element-mediated transcriptional activation. The Journal of Biological Chemistry, 276, 16534–16539.

    PubMed  CAS  Google Scholar 

  139. Shou, Y., Baron, S., & Poncz, M. (1998). An Sp1-binding silencer element is a critical negative regulator of the megakaryocyte-specific alphaIIb gene. The Journal of Biological Chemistry, 273, 5716–5726.

    PubMed  CAS  Google Scholar 

  140. Zaid, A., Hodny, Z., Li, R., & Nelson, B. D. (2001). Sp1 acts as a repressor of the human adenine nucleotide translocase-2 (ANT2) promoter. European Journal of Biochemistry, 268, 5497–5503.

    PubMed  CAS  Google Scholar 

  141. Hyde-DeRuyscher, RP, Jennings, E., & Shenk, T. (1995). DNA binding sites for the transcriptional activator/repressor YY1. Nucleic Acids Research, 23, 4457–4465.

    PubMed  CAS  Google Scholar 

  142. Shi, Y., Lee, J. S., & Galvin, K. M. (1997). Everything you have ever wanted to know about Yin Yang 1. Biochim Biophys Acta, 1332, F49–F66.

    PubMed  CAS  Google Scholar 

  143. Thomas, M. J., & Seto, E. (1999). Unlocking the mechanisms of transcription factor YY1: Are chromatin modifying enzymes the key? Gene, 236, 197–208.

    PubMed  CAS  Google Scholar 

  144. Sander, T. L., Stringer, K. F., Maki, J. L., Szauter, P., Stone, J. R., & Collins, T. (2003). The SCAN domain defines a large family of zinc finger transcription factors. Gene, 310, 29–38.

    PubMed  CAS  Google Scholar 

  145. Bellon, S. F., Rodgers, K. K., Schatz, D. G., Coleman, J. E., & Steitz, T. A. (1997). Crystal structure of the RAG1 dimerization domain reveals multiple zinc-binding motifs including a novel zinc binuclear cluster. Nature Structural Biology, 4, 586–591.

    PubMed  CAS  Google Scholar 

  146. Dean, A. B., Stanger, M. J., Dansereau, J. T., Van Roey, P., Derbyshire, V., & Belfort, M. (2002). Zinc finger as distance determinant in the flexible linker of intron endonuclease I-TevI. Proceedings of the National Academy of Sciences of the United States of America, 99, 8554–8561.

    PubMed  CAS  Google Scholar 

  147. Ko, J. E., Kim, C. W., & Kim, D. R. (2004). Amino acid residues in RAG1 responsible for the interaction with RAG2 during the V(D)J recombination process. The Journal of Biological Chemistry, 279, 7715–7720.

    PubMed  CAS  Google Scholar 

  148. Swanson, P. C., & Desiderio, S. (1999). RAG-2 promotes heptamer occupancy by RAG-1 in the assembly of a V(D)J initiation complex. Molecular and Cellular Biology, 19, 3674–3683.

    PubMed  CAS  Google Scholar 

  149. Chang, C. C., Ye, B. H., Chaganti, R. S., & Dalla-Favera, R. (1996). BCL-6, a POZ/zinc-finger protein, is a sequence-specific transcriptional repressor. Proceedings of the National Academy of Sciences of the United States of America, 93, 6947–6952.

    PubMed  CAS  Google Scholar 

  150. Lossos, I. S., Czerwinski, D. K., Alizadeh, A. A., Wechser, M. A., Tibshirani, R., Botstein, D., & Levy, R. (2004). Prediction of survival in diffuse large-B-cell lymphoma based on the expression of six genes. The New England Journal of Medicine, 350, 1828–1837.

    PubMed  CAS  Google Scholar 

  151. Phan, R. T., & Dalla-Favera, R. (2004). The BCL6 proto-oncogene suppresses p53 expression in germinal-centre B cells. Nature, 432, 635–639.

    PubMed  CAS  Google Scholar 

  152. Segal, D., & Barbas, C. F. III (2001). Custom DNA-binding proteins come of age: Polydactyl zinc-finger proteins. Current Opinion in Biotechnology, 12, 632–637.

    PubMed  CAS  Google Scholar 

  153. Ghosh, I., Stains, C. I., Ooi, A. T., & Segal, D. J. (2006). Direct detection of double-stranded DNA: Molecular methods and applications for DNA diagnostics. Molecular BioSystems, 2, 551–560.

    PubMed  CAS  Google Scholar 

  154. Jamieson, A. C., Miller, J. C., & Pabo, C. O. (2003). Drug discovery with engineered zinc-finger proteins. Nature Reviews. Drug Discovery, 2, 361–368.

    PubMed  CAS  Google Scholar 

  155. Porteus, M. H., & Carroll, D. (2005). Gene targeting using zinc finger nucleases. Nature Biotechnology, 23, 967–973.

    PubMed  CAS  Google Scholar 

  156. Bae, K. H., Kwon, Y. D., Shin, H. C., Hwang, M. S., Ryu, E. H., Park, K. S., Yang, H. Y., Lee, D. K., Lee, Y., Park, J., Kwon, H. S., Kim, H. W., Yeh, B. I., Lee, H. W., Sohn, S. H., Yoon, J., Seol, W., & Kim, J. S. (2003). Human zinc fingers as building blocks in the construction of artificial transcription factors. Nature Biotechnology, 21, 275–280.

    PubMed  CAS  Google Scholar 

  157. Giesecke, A. V., Fang, R., & Joung, J. K. (2006). Synthetic protein–protein interaction domains created by shuffling Cys2His2 zinc-fingers. Molecular Systems Biology, 2, 2006 2011.

    PubMed  Google Scholar 

  158. Laity, J. H., Dyson, H. J., & Wright, P. E. (2000). DNA-induced alpha-helix capping in conserved linker sequences is a determinant of binding affinity in Cys(2)-His(2) zinc fingers. Journal of Molecular Biology, 295, 719–727.

    PubMed  CAS  Google Scholar 

  159. Ryan, R. F., & Darby, M. K. (1998). The role of zinc finger linkers in p43 and TFIIIA binding to 5S rRNA and DNA. Nucleic Acids Research, 26, 703–709.

    PubMed  CAS  Google Scholar 

  160. Fairall, L., Harrison, S. D., Travers, A. A., & Rhodes, D. (1992). Sequence-specific DNA binding by a two zinc-finger peptide from the Drosophila melanogaster Tramtrack protein. Journal of Molecular Biology, 226, 349–366.

    PubMed  CAS  Google Scholar 

  161. Houbaviy, H. B., Usheva, A., Shenk, T., & Burley, S. K. (1996). Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator. Proceedings of the National Academy of Sciences of the United States of America, 93, 13577–13582.

    PubMed  CAS  Google Scholar 

  162. Brayer, K. J., & Segal, D. J. The protein binding potential of C2H2 zinc finger domains. Cell Biochemistry and Biophysics, doi:10.1007/s12013-008-9007-6.

  163. Del Rio, S., & Setzer, D. R. (1993). The role of zinc fingers in transcriptional activation by transcription factor IIIA. Proceedings of the National Academy of Sciences of the United States of America, 90, 168–172.

    PubMed  Google Scholar 

  164. Friesen, W. J., & Darby, M. K. (1997). Phage display of RNA binding zinc fingers from transcription factor IIIA. The Journal of Biological Chemistry, 272, 10994–10997.

    PubMed  CAS  Google Scholar 

  165. Theunissen, O., Rudt, F., & Pieler, T. (1998). Structural determinants in 5S RNA and TFIIIA for 7S RNP formation. European Journal of Biochemistry, 258, 758–767.

    PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported in part by Contract 9016 from the Arizona Disease Control Research Committee. KJB received support from an NSF IGERT-Genomics award.

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  1. Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA

    Kathryn J. Brayer

  2. Genome Center and Department of Pharmacology, University of California, Davis, Genome Center/Pharmacology, 4513 GBSF, 451 Health Sciences Dr, Davis, CA, 95616, USA

    David J. Segal

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Brayer, K.J., Segal, D.J. Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains. Cell Biochem Biophys 50, 111–131 (2008). https://doi.org/10.1007/s12013-008-9008-5

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