The many roles of the transcriptional regulator CTCF

Biochemistry and Cell Biology

Volumn 81, Issue 3, 2003, Pages 161-167

  Dunn, Katherine L ^a   Davie, James R ^a  

^a UNIVERSITY OF MANITOBA   (Canada)

Author keywords

CTCF; Insulator; Transcription

Indexed keywords

BIOCHEMISTRY; CHEMICAL BONDS; GENES;

GENE REGULATION;

PROTEINS;

CCCTC BINDING FACTOR; DNA; NUCLEAR FACTOR; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

BINDING SITE; CONFERENCE PAPER; DNA BINDING; DNA SEQUENCE; GENE CONTROL; GENETIC CODE; GENETIC TRANSCRIPTION; NONHUMAN; ONCOGENE C MYC; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION;

ANIMALS; DNA; DNA-BINDING PROTEINS; GENES, MYC; HUMANS; INSULATOR ELEMENTS; MODELS, BIOLOGICAL; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC;

EUKARYOTA;

EID: 0041828248     PISSN: 08298211     EISSN: None     Source Type: Journal    
DOI: 10.1139/o03-052     Document Type: Conference Paper

References (62)

1. Alland, L., Muhle, R., Hou Jr., H., Potes, J., Chin, L., Schreiber-Agus, N., and DePinho, R.A. 1997. Role of N-CoR and histone deacetylase in Sin3-mediated transcriptional repression. Nature (London), 387: 49-55.
2. Antes, T.J., Namciu, S.J., Fournier, R.E., and Levy-Wilson, B. 2001. The 5′ boundary of the human apolipoprotein B chromatin domain in intestinal cells. Biochemistry, 40: 6731-6742.
3. Baniahmad, A., Steiner, C., Kohne, A.C., and Renkawitz, R. 1990a. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell, 61: 505-514.
4. Baniahmad, A., Steiner, C., Kohne, A.C., and Renkawitz, R. 1990b. Modular structure of a chicken lysozyme silencer: involvement of an unusual thyroid hormone receptor binding site. Cell, 61: 505-514.
5. Bell, A.C., and Felsenfeld, G. 1999a. Stopped at the border: boundaries and insulators. Curr. Opin. Genet. Dev. 9: 191-198.
6. Bell, A.C., and Felsenfeld, G. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature (London), 405: 482-485.
7. Bell, A.C., West, A.G., and Felsenfeld, G. 1999b. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell, 98: 387-396.
8. Bonifer, C., Hecht, A., Saueressig, H., Winter, D.M., and Sippel, A.E. 1991. Dynamic chromatin: the regulatory domain organization of eukaryotic gene loci. J. Cell Biochem. 47: 99-108.
9. Burcin, M., Arnold, R., Lutz, M., Kaiser, B., Runge, D., Lottspeich, F., Filippova, G.N., Lobanenkov, V.V., and Renkawitz, R. 1997. Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF. Mol. Cell. Biol. 17: 1281-1288.
10. Burton, T., Liang, B., Dibrov, A., and Amara, F. 2002. Transforming growth factor-beta-induced transcription of the Alzheimer beta-amyloid precursor protein gene involves interaction between the CTCF-complex and Smads. Biochem. Biophys. Res. Commun. 295: 713-723.
11. Cai, H.N., and Shen, P. 2001. Effects of cis arrangement of chromatin insulators on enhancer-blocking activity. Science (Washington, D.C.), 291: 493-495.
12. Chao, W., Huynh, K.D., Spencer, R.J., Davidow, L.S., and Lee, J.T. 2002. CTCF, a candidate trans-acting factor for X-inactivation choice. Science (Washington, D.C.), 295: 345-347.
13. Chernak, J.M. 1993. Structural features of the 5′ upstream regulatory region of the gene encoding rat amyloid precursor protein. Gene, 133: 255-260.
14. DePinho, R.A. 1998. Transcriptional repression. The cancer-chromatin connection. Nature (London), 391: 533-536.
15. Dunn, K.L., Zhao, H., and Davie, J.R. 2003. The insulator binding protein CTCF associates with the nuclear matrix. Exp. Cell Res. In press.
16. Elson, D.A., and Bartolomei, M.S. 1997. A 5′ differentially methylated sequence and the 3′-flanking region are necessary for H19 transgene imprinting. Mol. Cell. Biol. 17: 309-317.
17. Filippova, G.N., Fagerlie, S., Klenova, E.M., Myers, C., Dehner, Y., Goodwin, G., Neiman, P.E., Collins, S.J., and Lobanenkov, V.V. 1996. An exceptionally conserved transcriptional repressor, CTCF, employs different combinations of zinc fingers to bind diverged promoter sequences of avian and mammalian c-myc oncogenes. Mol. Cell. Biol. 16: 2802-2813.
18. Filippova, G.N., Lindblom, A., Meincke, L.J., Klenova, E.M., Neiman, P.E., Collins, S.J., Doggett, N.A., and Lobanenkov, V.V. 1998. A widely expressed transcription factor with multiple DNA sequence specificity, CTCF, is localized at chromosome segment 16q22.1 within one of the smallest regions of overlap for common deletions in breast and prostate cancers. Genes Chromosomes. Cancer, 22: 26-36.
19. Filippova, G.N., Qi, C.F., Ulmer, J.E., Moore, J.M., Ward, M.D., Hu, Y.J., Loukinov, D.I., Pugacheva, E.M., Klenova, E.M., Grundy, P.E., Feinberg, A.P., Cleton-Jansen, A.M., Moerland, E.W., Cornelisse, C.J., Suzuki, H., Komiya, A., Lindblom, A., Dorion-Bonnet, F., Neiman, P.E., Morse, H.C., III, Collins, S.J., and Lobanenkov, V.V. 2002. Tumor-associated zinc finger mutations in the CTCF transcription factor selectively alter tts DNA-binding specificity. Cancer Res. 62: 48-52.
20. Fischle, W., Dequiedt, F., Hendzel, M.J., Guenther, M.G., Lazar, M.A., Voelter, W., and Verdin, E. 2002. Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Mol. Cell, 9: 45-57.
21. Gaszner, M., Vazquez, J., and Schedl, P. 1999. The Zw5 protein, a component of the scs chromatin domain boundary, is able to block enhancer-promoter interaction. Genes Dev. 13: 2098-2107.
22. Glenner, G.G., and Wong, C.W. 1984. Alzheimer's disease and Down's syndrome: sharing of a unique cerebrovascular amyloid fibril protein. Biochem. Biophys. Res. Commun. 122: 1131-1135.
23. Hark, A.T., Schoenherr, C.J., Katz, D.J., Ingram, R.S., Levorse, J.M., and Tilghman, S.M. 2000. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature (London), 405: 486-489.
24. Holmgren, C., Kanduri, C., Dell, G., Ward, A., Mukhopadhya, R., Kanduri, M., Lobanenkov, V., and Ohlsson, R. 2001. CpG methylation regulates the Igf2/ H19 insulator. Curr. Biol. 11: 1128-1130.
25. Ishii, K., and Laemmli, U.K. 2003. Structural and dynamic functions establish chromatin domains. Mol. Cell, 11: 237-248.
26. Izumi, R., Yamada, T., Yoshikai, S., Sasaki, H., Hattori, M., and Sakaki, Y. 1992. Positive and negative regulatory elements for the expression of the Alzheimer's disease amyloid precursor-encoding gene in mouse. Gene, 112: 189-195.
27. Kanduri, C., Holmgren, C., Pilartz, M., Franklin, G., Kanduri, M., Liu, L., Ginjala, V., Ulleras, E., Mattsson, R., and Ohlsson, R. 2000. The 5′ flank of mouse H19 in an unusual chromatin conformation unidirectionally blocks enhancer-promoter communication. Curr. Biol. 10: 449-457.
28. Kanduri, C., Fitzpatrick, G., Mukhopadhyay, R., Kanduri, M., Lobanenkov, V., Higgins, M., and Ohlsson, R. 2002. A differentially methylated imprinting control region within the Kcnq1 locus harbors a methylation-sensitive chromatin insulator. J. Biol. Chem. 277: 18 106-18 110.
29. Kang, J., Lemaire, H.G., Unterbeck, A., Salbaum, J.M., Masters, C.L., Grzeschik, K.H., Multhaup, G., Beyreuther, K., and Muller-Hill, B. 1987. The precursor of Alzheimer's disease amyloid A4 protein resembles a cell-surface receptor. Nature (London), 325: 733-736.
30. Klenova, E.M., Nicolas, R.H., Paterson, H.F., Carne, A.F., Heath, C.M., Goodwin, G.H., Neiman, P.E., and Lobanenkov, V.V. 1993. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol. Cell Biol. 13: 7612-7624.
31. Klenova, E.M., Nicolas, R.H., U, S., Carne, A.F., Lee, R.E., Lobanenkov, V.V., and Goodwin, G.H. 1997. Molecular weight abnormalities of the CTCF transcription factor: CTCF migrates aberrantly in SDS-PAGE and the size of the expressed protein is affected by the UTRs and sequences within the coding region of the CTCF gene. Nucleic Acids Res. 25: 466-474.
32. Klenova, E.M., Chernukhin, I.V., El Kady, A., Lee, R.E., Pugacheva, E.M., Loukinov, D.I., Goodwin, G.H., Delgado, D., Filippova, G.N., Leon, J., Morse, H.C., III, Neiman, P.E., and Lobanenkov, V.V. 2001. Functional phosphorylation sites in the C-terminal region of the multivalent multifunctional transcriptional factor CTCF. Mol. Cell Biol. 21: 2221-2234.
33. Klenova, E.M., Morse, H.C., III, Ohlsson, R., and Lobanenkov, V.V. 2002. The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer. Semin. Cancer Biol. 12: 399-414.
34. Kohne, A.C., Baniahmad, A., and Renkawitz, R. 1993. NeP1. A ubiquitous transcription factor synergizes with v-ERBA in transcriptional silencing. J. Mol. Biol. 232: 747-755.
35. Levine, A.J. 1993. The tumor suppressor genes. Annu. Rev. Biochem. 62: 623-651.
36. Litt, M.D., Simpson, M., Gaszner, M., Allis, C.D., and Felsenfeld, G. 2001a. Correlation between histone lysine methylation and developmental changes at the chicken {beta}-globin locus. Science (Washington, D.C.), 293: 2453-2455.
37. Litt, M.D., Simpson, M., Recillas-Targa, F., Prioleau, M.N., and Felsenfeld, G. 2001b. Transitions in histone acetylation reveal boundaries of three separately regulated neighboring loci. EMBO J. 20: 2224-2235.
38. Lobanenkov, V.V., Nicolas, R.H., Adler, V.V., Paterson, H., Klenova, E.M., Polotskaja, A.V., and Goodwin, G.H. 1990. A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene. Oncogene, 5: 1743-1753.
39. Loukinov, D.I., Pugacheva, E., Vatolin, S., Pack, S.D., Moon, H., Chernukhin, I., Mannan, P., Larsson, E., Kanduri, C., Vostrov, A.A., Cui, H., Niemitz, E.L., Rasko, J.E., Docquier, F.M., Kistler, M., Breen, J.J., Zhuang, Z., Quitschke, W.W., Renkawitz, R., Klenova, E.M., Feinberg, A.P., Ohlsson, R., Morse, H.C., III, and Lobanenkov, V.V. 2002. BORIS, a novel male germ-line-specific protein associated with epigenetic reprogramming events, shares the same 11-zinc-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc. Natl. Acad. Sci. U.S.A. 99: 6806-6811.
40. Lutz, M., Burke, L.J., Barreto, G., Goeman, F., Greb, H., Arnold, R., Schultheiss, H., Brehm, A., Kouzarides, T., Lobanenkov, V., and Renkawitz, R. 2000. Transcriptional repression by the insulator protein CTCF involves histone deacetylases. Nucleic Acids Res. 28: 1707-1713.
41. Lutz, M., Burke, L.J., LeFevre, P., Myers, F.A., Thorne, A.W., Crane-Robinson, C., Bonifer, C., Filippova, G.N., Lobanenkov, V., and Renkawitz, R. 2003. Thyroid hormone-regulated enhancer blocking: cooperation of CTCF and thyroid hormone receptor. EMBO J. 22: 1579-1587.
42. Mann, D.M., Jones, D., Prinja, D., and Purkiss, M.S. 1990. The prevalence of amyloid (A4) protein deposits within the cerebral and cerebellar cortex in Down's syndrome and Alzheimer's disease. Acta Neuropathol. (Berl.), 80: 318-327.
43. Masters, C.L., Simms, G., Weinman, N.A., Multhaup, G., McDonald, B.L., and Beyreuther, K. 1985. Amyloid plaque core protein in Alzheimer disease and Down syndrome. Proc. Natl. Acad. Sci. U.S.A. 82: 4245-4249.
44. Muravyova, E., Golovnin, A., Gracheva, E., Parshikov, A., Belenkaya, T., Pirrotta, V., and Georgiev, P. 001. Loss of insulator activity by paired Su(Hw) chromatin insulators. Science (Washington, D.C.), 291: 495-498.
45. Mutskov, V.J., Farrell, C.M., Wade, P.A., Wolffe, A.P., and Felsenfeld, G. 2002. The barrier function of an insulator couples high histone acetylation levels with specific protection of promoter DNA from methylation. Genes Dev. 16: 1540-1554.
46. Ohlsson, R., Renkawitz, R., and Lobanenkov, V. 2001. CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease. Trends Genet. 17: 520-527.
47. Ohta, T., Gray, T.A., Rogan, P.K., Buiting, K., Gabriel, J.M., Saitoh, S., Muralidhar, B., Bilienska, B., Krajewska-Walasek, M., Driscoll, D.J., Horsthemke, B., Butler, M.G., and Nicholls, R.D. 1999. Imprinting-mutation mechanisms in Prader-Willi syndrome. Am. J. Hum. Genet. 64: 397-413.
48. Parkhurst, S.M., Harrison, D.A., Remington, M.P., Spana, C., Kelley, R.L., Coyne, R.S., and Corces, V.G. 1988. The Drosophila su(Hw) gene, which controls the phenotypic effect of the gypsy transposable element, encodes a putative DNA-binding protein. Genes Dev. 2: 1205-1215.
49. Paulsen, M., Takada, S., Youngson, N.A., Benchaib, M., Charlier, C., Segers, K., Georges, M., and Ferguson-Smith, A.C. 2001. Comparative sequence analysis of the imprinted Dlk1-Gt12 locus in three mammalian species reveals highly conserved genomic elements and refines comparison with the Igf2-H19 region. Genome Res. 11: 2085-2094.
50. Quitschke, W.W. 1994. Two nuclear factor binding domains activate expression from the human amyloid beta-protein precursor promoter. J. Biol. Chem. 269: 21 229-21 233.
51. Saitoh, N., Bell, A.C., Recillas-Targa, F., West, A.G., Simpson, M., Pikaart, M., and Felsenfeld, G. 2000. Structural and functional conservation at the boundaries of the chicken beta-globin domain. EMBO J. 19: 2315-2322.
52. Tilghman, S.M. 1999. The sins of the fathers and mothers: genomic imprinting in mammalian development. Cell, 96: 185-193.
53. Vostrov, A.A., and Quitschke, W.W. 1997. The zinc finger protein CTCF binds to the APBbeta domain of the amyloid beta-protein precursor promoter. Evidence for a role in transcriptional activation. J. Biol. Chem. 272: 33 353-33 359.
54. Vostrov, A.A., Taheny, M.J., and Quitschke, W.W. 2002. A region to the N-terminal side of the CTCF zinc finger domain is essential for activating transcription from the amyloid precursor protein promoter. J. Biol. Chem. 277: 1619-1627.
55. Weinberg, R. 1993. Tumor suppressor genes. Neuron, 11: 191-196.
56. West, A.G., Gaszner, M., and Felsenfeld, G. 2002. Insulators: many functions, many mechanisms. Genes Dev. 16: 271-288.
57. Wolffe, A.P. 2000. Transcriptional control: imprinting insulation. Curr. Biol. 10: R463-R465.
58. Wylie, A.A., Murphy, S.K., Orton, T.C., and Jirtle, R.L. 2000. Novel imprinted DLK1/GTL2 domain on human chromosome 14 contains motifs that mimic those implicated in IGF2/H19 regulation. Genome Res. 10: 1711-1718.
59. Yang, X.J., Ogryzko, V.V., Nishikawa, J., Howard, B.H., and Nakatani, Y. 1996. A p300/CBP-associated factor that competes with the adenoviral oncoprotein E1A. Nature (London), 382: 319-324.
60. Yeh, A., Wei, M., Golub, S.B., Yamashiro, D.J., Murty, V.V., and Tycko, B. 2002. Chromosome arm 16q in Wilms tumors: unbalanced chromosomal translocations, loss of heterozygosity, and assessment of the CTCF gene. Genes Chromosomes. Cancer, 35: 156-163.
61. Yoon, H.G., Chan, D.W., Huang, Z.Q., Li, J., Fondell, J.D., Qin, J., and Wong, J. 2003. Purification and functional characterization of the human N-CoR complex: the roles of HDAC3, TBL1 and TBLR1. EMBO J. 22: 1336-1346.
62. Zhao, K., Hart, C.M., and Laemmli, U.K. 1995. Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell, 81: 879-889.