Kaiso uses all three zinc fingers and adjacent sequence motifs for high affinity binding to sequence-specific and methyl-CpG DNA targets

FEBS Letters

Volumn 586, Issue 6, 2012, Pages 734-739

  Buck Koehntop, Bethany A ^a   Martinez Yamout, Maria A ^a   Jane Dyson, H ^a   Wright, Peter E ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Kaiso; Methyl CpG DNA binding protein; Methylated DNA; Zinc finger

Indexed keywords

DNA; KAISO; METHYL CPG DNA; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

AMINO TERMINAL SEQUENCE; ARTICLE; BINDING AFFINITY; CARBOXY TERMINAL SEQUENCE; DNA DETERMINATION; DNA SEQUENCE; DNA STRUCTURE; GENE TARGETING; MOLECULAR GENETICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS; TRANSCRIPTION REGULATION;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; CPG ISLANDS; DNA; HUMANS; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS; ZINC FINGERS;

EID: 84858701418     PISSN: 00145793     EISSN: 18733468     Source Type: Journal    
DOI: 10.1016/j.febslet.2012.01.045     Document Type: Article

References (30)

1. Robertson, K.D. and Wolffe, A.P. (2000) DNA methylation in health and disease. Nat. Rev. Genet. 1, 11-19.
2. Jones, P.A. and Baylin, S.B. (2002) The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 3, 415-428. (Pubitemid 34587077)
3. Esteller, M. (2005) Aberrant DNA methylation as a cancer-inducing mechanism. Annu. Rev. Pharmacol. Toxicol. 45, 629-656.
4. Klose, R.J. and Bird, A.P. (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci. 31, 89-97. (Pubitemid 43221841)
5. Clouaire, T. and Stancheva, I. (2008) Methyl-CpG binding proteins: specialized transcriptional repressors or structural components of chromatin? Cell. Mol. Life Sci. 65, 1509-1522.
6. Prokhortchouk, A., Hendrich, B., Jørgensen, H., Ruzov, A., Wilm, M., Georgiev, G., Bird, A. and Prokhortchouk, E. (2001) The p120 catenin partner Kaiso is a DNA methylation-dependent transcriptional repressor. Genes Dev. 15, 1613-1618. (Pubitemid 32702582)
7. Prokhortchouk, A.V., Aitkhozhina, D.S., Sablina, A.A., Ruzov, A.S. and Prokhortchouk, E.B. (2001) Kaiso, a New Protein of the BTB/POZ Family, Specifically Binds to Methylated DNA Sequences. Russ. J. Gene. 37, 603-609. (Pubitemid 33657048)
8. Yoon, H.G., Chan, D.W., Reynolds, A.B., Qin, J. and Wong, J. (2003) N-CoR mediates DNA methylation-dependent repression through a methyl CpG binding protein Kaiso. Mol. Cell 12, 723-734. (Pubitemid 37222492)
9. ctn-binding partner Kaiso is a bi-modal DNA-binding protein that recognizes both a sequence-specific consensus and methylated CpG dinucleotides. Nucleic Acids Res. 30, 2911-2919.
10. Kelly, K.F. and Daniel, J.M. (2006) POZ for effect - POZ-ZF transcription factors in cancer and development. Trends Cell Biol. 16, 578-587. (Pubitemid 44636217)
11. Sansom, O.J., Maddison, K. and Clarke, A.R. (2007) Mechanisms of disease: methyl-binding domain proteins as potential therapeutic targets in cancer. Nat. Clin. Pract. Oncol. 4, 305-315. (Pubitemid 46758788)
12. Lopes, E.C., Valls, E., Figueroa, M.E., Mazur, A., Meng, F.G., Chiosis, G., Laird, P.W., Schreiber-Agus, N., Greally, J.M., Prokhortchouk, E. and Melnick, A. (2008) Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines. Cancer Res. 68, 7258-7263.
13. Zhang B.Z., Gu L.K., and Deng D.J. (2007) Methylation specific binding activity of zinc finger protein Kaiso. Zhonghua. Yu. Fang Yi. Xue. Za. Zhi. [Chinese Journal Preventive Medicine] 41 Suppl, 43-46.
14. Delaglio, F., Grzesiek, S., Vuister, G.W., Guang, Z., Pfeifer, J. and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293.
15. Johnson, B.A. and Blevins, R.A. (1994) NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603-614.
16. Filion, G.J.P., Zhenilo, S., Salozhin, S., Yamada, D., Prokhortchouk, E. and Defossez, P.A. (2006) A family of human zinc finger proteins that bind methylated DNA and repress transcription. Mol. Cell Biol. 26, 169-181.
17. Nakaseko, Y., Neuhaus, D., Klug, A. and Rhodes, D. (1992) Adjacent zinc-finger motifs in multipe zinc-finger peptides from SWI5 form structurally independent, flexibly linked domains. J. Mol. Biol. 228, 619-636. (Pubitemid 23007579)
18. Dutnall, R.N., Neuhaus, D. and Rhodes, D. (1996) The solution structure of the first zinc finger domain of SW15: A novel structural extension to a common fold. Structure 4, 599-611. (Pubitemid 126657552)
19. Fairall, L., Schwabe, J.W.R., Chapman, L., Finch, J.T. and Rhodes, D. (1993) The crystal structure of a two zinc-finger peptide reveals an extension to the rules for zinc-finger/DNA recognition. Nature 366, 483-487. (Pubitemid 24013885)
20. Schoenmakers, E., Alen, P., Verrijdt, G., Peeters, B., Verhoeven, G., Rombauts, W. and Claessens, F. (1999) Differential DNA binding by the androgen and glucocorticoid receptors involves the second Zn-finger and a C-terminal extension of the DNA-binding domains. Biochem. J. 341, 515-521. (Pubitemid 29389179)
21. Gearhart, M.D., Holmbeck, S.M.A., Evans, R.M., Dyson, H.J. and Wright, P.E. (2003) Monomeric complex of human orphan estrogen related receptor-2 with DNA: A pseudo-dimer interface mediates extended half-site recognition. J. Mol. Biol. 327, 819-832. (Pubitemid 36315921)
22. Melvin, V.S., Harrell, C., Adelman, J.S., Kraus, W.L., Churchill, M. and Edwards, D.P. (2004) The role of the C-terminal extension (CTE) of the estrogen receptor alpha and beta DNA binding domain in DNA binding and interaction with HMGB. J. Biol. Chem. 279, 14763-14771. (Pubitemid 38647162)
23. Crane-Robinson, C., Dragan, A.I. and Privalov, P.L. (2006) The extended arms of DNA-binding domains: a tale of tails. Trends Biochem. Sci. 31, 547-552. (Pubitemid 44444875)
24. Sabogal, A., Lyubimov, A.Y., Corn, J.E., Berger, J.M. and Rio, D.C. (2010) THAP proteins target specific DNA sites through bipartite recognition of adjacent major and minor grooves. Nat. Struct. Mol. Biol. 17, 117-123.
25. Ohki, I., Shimotake, N., Fujita, N., Jee, J.G., Ikegami, T., Nakao, M. and Shirakawa, M. (2001) Solution structure of the methyl-CpG binding domain of human MBD1 in complex with methylated DNA. Cell 105, 487-497. (Pubitemid 32520854)
26. Ho, K.L., McNae, I.W., Schmiedeberg, L., Klose, R.J., Bird, A.P. and Walkinshaw, M.D. (2008) MeCP2 binding to DNA depends upon hydration at methyl-CpG. Mol. Cell 29, 525-531. (Pubitemid 351282541)
27. Ghosh, R.P., Nikitina, T., Horowitz-Scherer, R.A., Gierasch, L.M., Uversky, V.N., Hite, K., Hansen, J.C. and Woodcock, C.L. (2010) Unique physical properties and interactions of the domains of methylated DNA binding protein 2. Biochemistry 49, 4395-4410.
28. Klose, R.J., Sarraf, S.A., Schmiedeberg, L., McDermott, S.M., Stancheva, I. and Bird, A.P. (2005) DNA binding selectivity of MeCP2 due to a requirement for A/ T sequences adjacent to methyl-CpG. Mol. Cell 19, 667-678. (Pubitemid 41219442)
29. Clouaire, T., de Las Heras, J.I., Merusi, C. and Stancheva, I. (2010) Recruitment of MBD1 to target genes requires sequence-specific interaction of the MBD domain with methylated DNA. Nucleic Acids Res. 38, 4620-4634.
30. Sasai, N., Nakao, M. and Defossez, P.A. (2010) Sequence-specific recognition of methylated DNA by human zinc-finger proteins. Nucleic Acids Res. 38, 5015-5022.