The binding sites for the chromatin insulator protein CTCF map to DNA methylation-free domains genome-wide

Genome Research

Volumn 14, Issue 8, 2004, Pages 1594-1602

  Mukhopadhyay, Rituparna ^a   Yu, Wen Qiang ^a   Whitehead, Joanne ^a   Xu, Jun Wang ^a   Lezcano, Magda ^a   Pack, Svetlana ^b   Kanduri, Chandrasekhar ^a   Kanduri, Meena ^a   Ginjala, Vasudeva ^a   Vostrov, Alexander ^c   Quitschke, Wolfgang ^c   Chernukhin, Igor ^d   Klenova, Elena ^d   Lobanenkov, Victor ^b   Ohlsson, Rolf ^a  

^a UPPSALA UNIVERSITY   (Sweden)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

^c STONY BROOK UNIVERSITY   (United States)

^d UNIVERSITY OF ESSEX   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CTCF PROTEIN; DNA; NUCLEAR FACTOR; UNCLASSIFIED DRUG; ZINC FINGER PROTEIN;

ANIMAL CELL; APOPTOSIS; ARTICLE; BINDING SITE; CELL FUNCTION; CELL GROWTH; CELL METABOLISM; CHROMATIN; CONTROLLED STUDY; DNA DNA HYBRIDIZATION; DNA METHYLATION; DNA MICROARRAY; ENHANCER REGION; EPIGENETICS; GENE LOCUS; GENE SEQUENCE; GENE SILENCING; GENOME IMPRINTING; HETEROCHROMATIN; INSULATOR ELEMENT; MOLECULAR CLONING; MOUSE; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE; VERTEBRATE;

ANIMALS; BASE SEQUENCE; BINDING SITES; CHROMOSOME MAPPING; CPG ISLANDS; DNA METHYLATION; DNA PROBES; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; HYBRIDIZATION, GENETIC; LIVER; MICE; MOLECULAR SEQUENCE DATA; REPRESSOR PROTEINS;

VERTEBRATA;

EID: 4444261501     PISSN: 10889051     EISSN: None     Source Type: Journal    
DOI: 10.1101/gr.2408304     Document Type: Article

References (24)

1. Ballestar, E. and Wolffe, A. 2001. Methyl-CpG-binding proteins. Targeting specific gene repression. Eur. J. Biochem. 268: 1-6.
2. Bell, A.C. and Felsenfeld, G. 2000. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature 405: 482-485.
3. Bell, A.C., West, A.G., and Felsenfeld, G. 2001. Insulators and boundaries: Versatile regulatory elements in the eukaryotic genome. Science 291: 447-450.
4. Filippova, G., Fagerlie, S., Klenova, E., Myers, C., Dehner, Y., Goodwin, G., Neiman, P., Collins, S., and Lobanenkov, 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.
5. The Gene Ontology Consortium. 2000. Gene ontology: Tool for the unification of biology. Nature Genet. 25: 25-29.
6. 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 405: 486-489.
7. Holmgren, C., Kanduri, K., 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.
8. Horsthemke, B., Surani, M.A., James, T.C., and Ohlsson, R. 1999. The mechanisms of genomic imprinting. In Genomic imprinting. An interdisciplinary approach (ed. R. Ohlsson), pp. 91-118. Springer-Verlag, Berlin.
9. James, T.C. and Elgin, S.C. 1986. Identification of a nonhistone chromosomal protein associated with heterochromatin in Drosophila melanogaster and its gene. Mol. Cell Biol. 6: 3862-3872.
10. Kanduri, C., Holmgren, C., Franklin, G., Pilartz, M., Ullerås, E., Kanduri, M., Liu, L., Ginjala, V., Ulleras, E., Mattsson, R., et al. 2000a. The 5′-flank of the murine H19 gene in an unusual chromatin conformation unidirectionally blocks enhancer-promoter communication. Curr. Biol. 10: 449-457.
11. Kanduri, C., Pant, V., Loukinov, D., Pugacheva, E., Qi, C.-F., Wolffe, A., Ohlsson, R., and Lobanenkov, A. 2000b. Functional interaction of CTCF with the insulator upstream of the H19 gene is parent of origin-specific and methylation-sensitive. Curr. Biol. 10: 853-856.
12. Kanduri, C., Fitzpatrick, G., Mukhopadfhyay, R., Kanduri, M., Lobanenkov, V., Higgins, M., and Ohlsson, R. 2002. A differentially methylated imprinting control region within the Kcnq1 locus harbours a methylation-sensitive chromatin insulator. J. Biol. Chem. 277; 18106-18110.
13. Klenova, E., Chernukhin, I., El-Kady, A., Lee, R., Pugacheva, E., Loukinov, D., Goodwin, G., Delgado, D., Filippova, G., Leon, J., et al. 2001. Functional phosphorylation sites in the C-terminal region of the multivalent multifunctional transcriptional factor CTCF. Mol. Cell Biol. 21: 2221-2234.
14. Klenova, E., Morse, H., Ohlsson, R., and Lobanenkov, V.V. 2002. The novel Boris + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer. Sem. Cancer Biol. 12: 399-414.
15. Kuo, M. and Allis, C. 1999. In vivo cross-linking and immunoprecipitation for studying dynamic protein: DNA associations in a chromatin environment. Methods 19: 425-433.
16. Loukinov, D., Pugacheva, E., Vatolin, S., Pack, S., Moon, H., Chernukhin, I., Mannan, P., Larsson, E., Kanduri, C., Vostrov, A., et al. 2002. BORIS, a novel male germline-specific protein associated with epigenetic reprogramming events, shares the same 11 Zn-finger domain with CTCF, the insulator protein involved in reading imprinting marks in the soma. Proc. Natl. Acad. Sci. 99: 6806-6811.
17. The Mouse Genome Sequencing Consortium. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
18. Nikaido, L, Saito, C., Wakamoto, A., Tomaru, Y., Arakawa, T., Hayashizaki, Y., and Okazaki, Y. 2004. EICO (Expression-based Imprint Candidate Organizer): Finding disease-related imprinted genes. Nucleic Acids Res. 32: D548-D551.
19. 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.
20. Pant, V., Mariano, P., Kanduri, C., Mattsson, A., Lobanenkov, V., Heuchel, R., and Ohlsson, R. 2003. The nucleotides responsible for the direct physical contact between the chromatin insulator protein CTCF and the h19 imprinting control region manifest parent of origin-specific long-distance insulation and methylation-free domains. Genes & Dev. 17: 586-590.
21. Pant, V., Kurukuti, S., Pugacheva, E., Shamsuddin, S., Mariano, P., Renkawitz, R., Klenova, E., Lobanenkov, V., and Ohlsson, R. 2004. Mutation of a single CTCF target site within the H19 imprinting control region leads to loss of Igf2 imprinting and complex patterns of de novo methylation upon maternal inheritance. Mol. Cell Biol. 8: 3497-3504.
22. Quitschke, W.W., Taheny, M.J., Fochtmann, L.J., and Vostrov, A.A. 2000. Differential effect of zinc finger deletions on the binding of CTCF to the promoter of the amyloid precursor protein gene. Nucleic Acids Res. 28: 3370-3378.
23. Schoenherr, C., Levorse, J., and Tilghman, S. 2003. CTCF maintains differential methylation at the Igf2/H19 locus. Nat. Genet. 33: 66-69.
24. Yan, Q., Cho, E., Lockett, S., and Muegge, K. 2003. Association of Lsh, a regulator of DNA methylation, with pericentromeric heterochromatin is dependent on intact heterochromatin. Mol. Cell Biol. 23: 8416-8428.