Human gamma-satellite DNA maintains open chromatin structure and protects a transgene from epigenetic silencing

Genome Research

Volumn 19, Issue 4, 2009, Pages 533-544

  Kim, Jung Hyun ^a   Ebersole, Thomas ^a   Kouprina, Natalay ^a   Noskov, Vladimir N ^a   Ohzeki, Jun Ichirou ^a   Masumoto, Hiroshi ^a   Mravinac, Brankica ^b   Sullivan, Beth A ^b   Pavlicek, Adam ^c   Dovat, Sinisa ^d   Pack, Svetlana D ^e   Kwon, Yoo Wook ^e   Flanagan, Patrick T ^e   Loukinov, Dmitri ^e   Lobanenkov, Victor ^e   Larionov, Vladimir ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

^b DUKE UNIVERSITY   (United States)

^c PFIZER INC   (United States)

^d UNIVERSITY OF WISCONSIN SCHOOL OF MEDICINE AND PUBLIC HEALTH   (United States)

^e NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

IKAROS TRANSCRIPTION FACTOR; SATELLITE DNA;

ANIMAL CELL; ARTICLE; CELL LEVEL; CHROMATIN STRUCTURE; CONTROLLED STUDY; DNA BINDING; DNA SEQUENCE; EPIGENETICS; ERYTHROLEUKEMIA; GENE CASSETTE; GENE MUTATION; GENE SILENCING; GENETIC TRANSCRIPTION; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN CONFORMATION; TRANSGENE;

ANIMALS; BINDING SITES; CENTROMERE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOMES, HUMAN; DNA, SATELLITE; DNA-BINDING PROTEINS; EPIGENESIS, GENETIC; GENE SILENCING; GENETIC VECTORS; HUMANS; IKAROS TRANSCRIPTION FACTOR; LEUKEMIA, ERYTHROBLASTIC, ACUTE; LUCIFERASES; MICE; PHYLOGENY; PROMOTER REGIONS, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; REPRESSOR PROTEINS; TRANSGENES; TUMOR CELLS, CULTURED;

EID: 63849152625     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.086496.108     Document Type: Article

References (37)

1. Basu, J. and Willard, H.F. 2005. Artificial and engineered chromosomes: Non-integrating vectors for gene therapy. Trends Mol. Med. 11:251-258.
2. Brown, K.E., Guest, S.S., Smale, S.T., Hahm, K., Merkenschlager, M., and Fisher, A.G. 1997. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91: 845-854.
3. Chen, Z.Y., He, C.Y., Meuse, L., and Kay, M.A. 2004. Silencing of episomal transgene expression by plasmid bacterial DNA elements in vivo. Gene Ther. 11: 856-864.
4. Chenna, R., Sugawara, H., Koike, T., Lopez, R., Gibson, T.J., Higgins, D.G., and Thompson, J.D. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31: 3497-3500.
5. Choo, K.H.A. 1997. The centromere. Oxford University Press, New York.
6. Chung, J.H., Whiteley, M., and Felsenfeld, G. 1993. A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 74:505-514.
7. Chung, J.H., Bell, A.C., and Felsenfeld, G. 1997. Characterization of the chicken beta-globin insulator. Proc. Natl. Acad. Sci. 94: 575-580.
8. Ebersole, T., Okamoto, Y., Noskov, V.N., Kouprina, N., Kim, J.-H., Leem, S.-H., Barrett, J., Masumoto, H., and Larionov, V. 2005. Rapid generation of long synthetic tandem repeats and its application for analysis in human artificial chromosome formation. Nucleic Acids Res. 33: e130. doi: 10.1093/nar/gni129.
9. Feng, Y.Q., Warin, R., Li, T., Olivier, E., Besse, A., Lobell, A., Fu, H., Lin, C.M., Aladjem, M.I., and Bouhassira, E.E. 2005. The human beta-globin locus control region can silence as well as activate gene expression. Mol. Cell. Biol. 25: 3864-3874.
10. Fu, H., Wang, L., Lin, C.M., Singhania, S., Bouhassira, E.E., and Aladjem, M.I. 2006. Preventing gene silencing with human replicators. Nat. Biotechnol. 24: 572-576.
11. Gaszner, M. and Felsenfeld, G. 2006. Insulators: Exploiting transcriptional and epigenetic mechanisms. Nat. Rev. Genet. 7: 703-713.
12. Georgopoulos, K. 2002. Haematopoietic cell-fate decisions, chromatin regulation and Ikaros. Nat. Rev. Immunol. 2: 162-174.
13. Katoh, K., Kuma, K., Toh, H., and Miyata, T. 2005. MAFFT version 5:Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
14. Kim, T.H., Abdullaev, Z.K., Smith, A.D., Ching, K.A., Loukinov, D.I., Green, R.D., Zhang, M.Q., Lobanenkov, V.V., and Ren, B. 2007. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128: 1231-1245.
15. Klenova, E.M., Morse III, H.C., 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.
16. Lam, A.L., Boivin, C.D., Bonney, C.F., Rudd, M.K., and Sullivan, B.A. 2006. Human centromeric chromatin is a dynamic chromosomal domain that can spread over noncentromeric DNA. Proc. Natl. Acad. Sci. 103: 4186-4191.
17. Lee, C., Wevrick, R., Fisher, R.B., Ferguson-Smith, M.A., and Lin, C.C. 1997. Human centromeric DNAs. Hum. Genet. 100: 291-304.
18. Lee, C., Critcher, R., Zhang, J.G., Mills, W., and Farr, C.J. 2000. Distribution of gamma-satellite DNA on the human X and Y chromosomes suggests that it is not required for mitotic centromere function. Chromosoma 109: 381-389.
19. Lin, C.C., Sasi, R., Lee, Y.S., and Court, D. 1993. Isolation and identification of a novel tandemly repeated DNA sequence in the centromeric region of human chromosome 8. Chromosoma 102: 333-339.
20. Molnár, A. and Georgopoulos, K. 1994. The Ikaros gene encodes a family of functionally diverse zinc finger DNA-binding proteins. Mol. Cell. Biol. 14: 8292-8303.
21. Ng, S.Y., Yoshida, T., and Georgopoulos, K. 2007. Ikaros and chromatin regulation in early hematopoiesis. Curr. Opin. Immunol. 19: 116-122.
22. 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.
23. Okada, T., Ohzeki, J.-I., Nakano, M., Yoda, Y., Brinkley, W.R., Larionov, V., and Masumoto, H. 2007. CENP-B controls centromere formation depending on the chromatin context. Cell 131: 1287-1300.
24. O'Neill, D.W., Schoetz, S.S., Lopez, R.A., Castle, M., Rabinowitz, L., Shor, E., Krawchuk, D., Goll, M.G., Renz, M., Seelig, H.P., et al. 2000. An Ikaros-containing chromatin-remodeling complex in adult-type erythroid cells. Mol. Cell. Biol. 20: 7572-7582.
25. Perdomo, J., Holmes, M., Chong, B., and Crossley, M. 2000. Eos and Pegasus, two members of the Ikaros family of proteins with distinct DNA binding activities. J. Biol. Chem. 275: 38347-38354.
26. Peters, A.H., Kubicek, K., Mechtler, R.J., O'Sullivan, A.A., Derijck, L., Perez- Burgos, A., Kohlmaier, S., Opravil, M., Tachibana, Y., Shinnkai, Y., et al. 2003. Partitioning and plasticity of repressive histone methylation states in mammalian chromatin. Mol. Cell 12: 1577-1589.
27. Ronni, T., Payne, K.J., Ho, S., Bradley, M.N., Dorsam, G., and Dovat, S. 2007. Human Ikaros function in activated T cells is regulated by coordinated expression of its largest isoforms. J. Biol. Chem. 282: 2538-2547.
28. Schueler, M.G. and Sullivan, B.A. 2006. Structural and functional dynamics of human centromeric chromatin. Annu. Rev. Genomics Hum. Genet. 7: 301-313.
29. Schueler, M.G., Dunn, J.M., Bird, C.P., Ross, M.T., Viggiano, L., Rocchi, M., Willard, H.F., and Green, E.D. 2005. Progressive proximal expansion of the primate X chromosome centromere. Proc. Natl. Acad. Sci. 102:10563-10568.
30. Scott, K.C., White, C.V., and Willard, H.F. 2007. An RNA polymerase III-dependent heterochromatin barrier at fission yeast centromere 1. PLoS One 10: e1099. doi: 10.1371/journal.pone.0001099.
31. Spence, J.M., Critcher, R., Ebersole, T.A., Valdivia, M.M., Earnshaw, W.C., Fukagawa, T., and Farr, C.J. 2002. Co-localization of centromere activity, proteins and topoisomerase II within a subdomain of the major human X alpha-satellite array. EMBO J. 21: 5269-5280.
32. Sullivan, B.A. and Karpen, G.H. 2004. Centromeric chromatin exhibits a histone modification pattern that is distinct from both euchromatin and heterochromatin. Nat. Struct. Mol. Biol. 11: 1076-1083.
33. Sun, F.L. and Elgin, S.C. 1999. Putting boundaries on silence. Cell 99: 459-462.
34. Suzuki, M., Kasai, K., and Saeki, Y. 2006. Plasmid DNA sequences present in conventional herpes simplex virus amplicon vectors cause rapid transgene silencing by forming inactive chromatin. J. Virol. 80: 3293-3300.
35. Swindle, S.C., Kim, H.G., and Klug, C.A. 2004. Mutation of CpGs in the murine stem cell viral retroviral vector long terminal repeat represses silencing in embryonic stem cells. J. Biol. Chem. 279: 34-41.
36. Valenzuela, L. and Kamakaka, R.T. 2006. Chromatin insulators. Annu. Rev. Genet. 40: 107-138.
37. Vissel, B., Nagy, A., and Choo, K.H. 1992. A satellite III sequence shared by human chromosomes 13, 14, and 21 that is contiguous with alpha satellite DNA. Cytogenet. Cell Genet. 61: 81-86.