Экспериментальные подходы к идентификации и картированию ЦИС-регуляторных элементов в протяженных областях генома человека

Список литературы

1. Акопов, С.Б., Николаев, Л.Г., Тырсин, О., Рузов, А.С., and Свердлов, Е.Д. 1997.
2. Идентификация и характеристики 14 последовательностей генома китайского хомячка, предпочтительно связывающихся с ядерным матриксом. Биоорганич. химия 23: 727−731.
3. Чернов, И.П., Акопов, С.Б., and Николаев, Л.Г. 2004. Структура и функции участковприкрепления ДНК к ядерному матриксу (S/MARs). Биоорганич. химия 30: 1−11.
4. Николаев, Л.Г., Акопов, С.Б., Чернов, И.П., Глотов, Б.О., Эшворт, Л.К., and Свердлов, Е.Д. 1998. Расположение 19 участков связывания ДНК с ядерным матриксом (MARs) на хромосоме 19 человека. Доклады РАН361: 409−411.
5. Рогаев, Е.И. 1999. Генетические факторы и полигенная модель болезни Альцгеймера. Генетика 35: 1558−1571
6. Adachi, Y., Kas, Е., and Laemmli, U.K. 1989. Preferential, cooperative binding of DNA topoisomerase II to scaffold- associated regions. Embo J8: 3997−4006.
7. Adorjan, P., Distler, J., Lipscher, E., Model, F., Muller, J., Pelet, C., Braun, A., Florl, A.R., Gutig, D., Grabs, G. et al. 2002. Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res 30: e21.
8. Allen, G.C., Hall, G., Jr., Michalowski, S., Newman, W., Spiker, S., Weissinger, A.K., and
9. Thompson, W.F. 1996. High-level transgene expression in plant cells: effects of a strong scaffold attachment region from tobacco. Plant Cell 8: 899−913.
10. Allen, G.C., Hall, G.E., Jr., Childs, L.C., Weissinger, A.K., Spiker, S., and Thompson, W.F. 1993. Scaffold attachment regions increase reporter gene expression in stably transformed plant cells. Plant Cell 5: 603−613.
11. Allen, G.C., Spiker, S., and Thompson, W.F. 2000. Use of matrix attachment regions (MARs) to minimize transgene silencing. Plant Mol Biol 43: 361−376.
12. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389−3402.
13. Alvarez, J.D., Yasui, D.H., Niida, H., Joh, Т., Loh, D.Y., and Kohwi-Shigematsu, T. 2000. The MAR-binding protein SATB1 orchestrates temporal and spatial expression of multiple genes during T-cell development. Genes Dev 14: 521−535.
14. Antes, T.J., Chen, J., Cooper, A.D., and Levy-Wilson, B. 2000. The nuclear matrix protein CDP represses hepatic transcription of the human cholesterol-7alpha hydroxylase gene. J Biol Chem 275: 26 649−26 660.
15. 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.
16. Ashworth, L.K., Batzer, M.A., Brandriff, B., Branscomb, E., de Jong, P., Garcia, E., Games, J.A., Gordon, L.A., Lamerdin, J.E., Lennon, G. et al. 1995. An integrated metric physical map of human chromosome 19. Nat Genet 11: 422−427.
17. Avramova, Z., SanMiguel, P., Georgieva, E., and Bennetzen, J.L. 1995. Matrix attachment regions and transcribed sequences within a long chromosomal continuum containing maize Adhl. Plant Cell 7: 1667−1680.
18. Avramova, Z., Tikhonov, A., Chen, M., and Bennetzen, J.L. 1998. Matrix attachment regions and structural colinearity in the genomes of two grass species. Nucleic Acids Res 26: 761−767.
19. Azhikina, T., Gainetdinov, I., Skvortsova, Y., Batrak, A., Dmitrieva, N., and Sverdlov, E. 2004.
20. Non-methylated Genomic Sites Coincidence Cloning (NGSCC): an approach to large scale analysis of hypomethylated CpG patterns at predetermined genomic loci. Mol Genet Genomics 271: 22−32.
21. Balint, B.L., Gabor, P., and Nagy, L. 2005. Genome-wide localization of histone 4 arginine 3 methylation in a differentiation primed myeloid leukemia cell line. Immunobiology 210: 141−152.
22. Barbashov, S.F., Glotov, B.O., and Nikolaev, L.G. 1982. Interphase chromatin at the sites of attachment to the nuclear matrix has a nucleosome nature. Dokl AkadNauk SSSR 266: 1274−1277.
23. Barski, A., Cuddapah, S., Cui, K., Roh, T.Y., Schones, D.E., Wang, Z., Wei, G., Chepelev, I., and Zhao, K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129: 823−837.
24. Bayer, T.A., Cappai, R., Masters, C.L., Beyreuther, K., and Multhaup, G. 1999. It all stickstogether—the APP-related family of proteins and Alzheimer’s disease. Mol Psychiatry 4: 524−528.
25. Bell, A.C. and Felsenfeld, G. 1999. Stopped at the border: boundaries and insulators. Curr Opin Genet Dev 9: 191−198.
26. Bell, A.C., West, A.G., and Felsenfeld, G. 1999. The protein CTCF is required for the enhancer blocking activity of vertebrate insulators. Cell 98: 387−396.
27. Bell, A.C., West, A.G., and Felsenfeld, G. 2001. Insulators and boundaries: versatile regulatory elements in the eukaryotic genome. Science 291: 447−450.
28. Benham, C., Kohwi-Shigematsu, T., and Bode, J. 1997. Stress-induced duplex DNA destabilization in scaffold/matrix attachment regions. J Mol Biol 274: 181−196.
29. Bentley, D.R. 2006. Whole-genome re-sequencing. Curr Opin Genet Dev 16: 545−552.
30. Berezney, R. and Coffey, D.S. 1974. Identification of a nuclear protein matrix. Biochem Biophys Res Commun 60: 1410−1417.
31. Berezney, R. and Coffey, D.S. 1977. Nuclear matrix. Isolation and characterization of a framework structure from rat liver nuclei. J Cell Biol 73: 616−637.
32. Berezney, R., Mortillaro, M.J., Ma, H., Wei, X., and Samarabandu, J. 1995. The nuclear matrix: a structural milieu for genomic function. Int Rev Cytol: 1−65.
33. Bibikova, M., Lin, Z., Zhou, L., Chudin, E., Garcia, E.W., Wu, B., Doucet, D., Thomas, N.J., Wang, Y., Vollmer, E. et al. 2006. High-throughput DNA methylation profiling using universal bead arrays. Genome Res 16: 383−393.
34. Birch-Machin, I., Gao, S., Huen, D., McGirr, R., White, R.A., and Russell, S. 2005. Genomic analysis of heat-shock factor targets in Drosophila. Genome Biol 6: R63.
35. Bird, A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16: 6−21.
36. Blasquez, V.C., Sperry, A.O., Cockerill, P.N., and Garrard, W.T. 1989. Protein: DNA interactions at chromosomal loop attachment sites. Genome 31: 503−509.
37. Bode, J., Bartsch, J., Boulikas, T., Iber, M., Mielke, C., Schubeler, D., Seibler, J., and Benham, C. 1998. Transcription-promoting genomic sites in mammalia: their elucidation and architectural principles. Gene Therapy Mol Biol 1: 551−580.
38. Bode, J., Benham, C., Knopp, A., and Mielke, C. 2000a. Transcriptional augmentation: modulation of gene expression by scaffold/matrix-attached regions (S/MAR elements). Crit Rev Eukaryot Gene Expr 10: 73−90.
39. Bode, J., Kohwi, Y., Dickinson, L., Joh, T., Klehr, D., Mielke, C., and Kohwi-Shigematsu, T. 1992. Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255: 195−197.
40. Bode, J. and Maass, K. 1988. Chromatin domain surrounding the human interferon-beta gene as defined by scaffold-attached regions. Biochemistry 27: 4706−4711.
41. Bode, J., Schlake, T., Iber, M., Schubeler, D., Seibler, J., Snezhkov, E., and Nikolaev, L. 2000b. The transgeneticist’s toolbox: novel methods for the targeted modification of eukaryotic genomes. Biol Chem 381: 801−813.
42. Bode, J., Schlake, T., Rios-Ramirez, M., Mielke, C., Stengert, M., Kay, V., and Klehr-Wirth, D. 1995. Scaffold/matrix-attached regions: structural properties creating transcriptionally active loci. Int Rev Cytoh 389−454.
43. Bode, J., Stengert-Iber, M., Kay, V., Schlake, T., and Dietz-Pfeilstetter, A. 1996. Scaffold/matrix-attached regions: topological switches with multiple regulatory functions. Crit Rev Eukaryot Gene Expr 6: 115−138.
44. Bode, J., Winkelmann, S., Gotze, S., Spiker, S., Tsutsui, K., Bi, C., A, K.P., and Benham, C. 2006. Correlations between scaffold/matrix attachment region (S/MAR) binding activity and DNA duplex destabilization energy. J Mol Biol 358: 597−613.
45. Bondarenko, V.A., Liu, Y.V., Jiang, Y.I., and Studitsky, V.M. 2003. Communication over a large distance: enhancers and insulators. Biochem Cell Biol 81: 241−251.
46. Borrelli, E., Heyman, R., Hsi, M., and Evans, R.M. 1988. Targeting of an inducible toxic phenotype in animal cells. Proc Natl Acad Sci U SA 85: 7572−7576.
47. Boulikas, T. 1993a. Homeodomain protein binding sites, inverted repeats, and nuclear matrixattachment regions along the human beta-globin gene complex. J Cell Biochem 52: 23−36.
48. Boulikas, T. 1993b. Nature of DNA sequences at the attachment regions of genes to the nuclear matrix. J Cell Biochem 52: 14−22.
49. Boulikas, T. 1995. Chromatin domains and prediction of MAR sequences. Int Rev Cytolx 279−388.
50. Boulikas, T. and Kong, C.F. 1993. Multitude of inverted repeats characterizes a class of anchorage sites of chromatin loops to the nuclear matrix. J Cell Biochem 53: 1−12.
51. Brand, A.H., Breeden, L., Abraham, J, Sternglanz, R., and Nasmyth, K. 1985. Characterization of a «silencer» in yeast: a DNA sequence with properties opposite to those of a transcriptional, enhancer. Cell 41: 41−48.
52. Brotherton, T., Zenk, D., Kahanic, S., and Reneker, J. 1991. Avian nuclear matrix proteins bind very tightly to cellular DNA of the beta-globin gene enhancer in a tissue-specific fashion. Biochemistry 30: 5845−5850.
53. Buhrmester, H., von Kries, J.P., and Stratling, W.H. 1995. Nuclear matrix protein ARBP recognizes a novel DNA sequence motif with high affinity. Biochemistry 34: 4108−4117.
54. Bulanenkova, S., Snezhkov, E., Nikolaev, L., and Sverdlov, E. 2007. Identification and mapping of open chromatin regions within a 140 kb polygenic locus of human chromosome 19 using E. coli Dam methylase. Genetica 130: 83−92.
55. Buzdin, A.A. 2004. Retroelements and formation of chimeric retrogenes. Cell Mol Life Sci 61: 2046−2059.
56. Cai, S. and Kohwi-Shigematsu, T. 1999. Intranuclear relocalization of matrix binding sites during T cell activation detected by amplified fluorescence in situ hybridization. Methods 19: 394 402.
57. Carninci, P. 2006. Tagging mammalian transcription complexity. Trends Genet 22: 501−510.
58. Carrano, A.V., de Jong, P.J., Branscomb, E., Slezak, T., and Watkins, B.W. 1989. Constructing chromosome- and region-specific cosmid maps of the human genome. Genome 31: 10 591 065.
59. Carrero-Valenzuela, R.D., Quan, F., Lightowlers, R., Kennaway, N.G., Litt, M., and Forte, M. 1991. Human cytochrome c oxidase subunit VIb: characterization and mapping of a multigene family. Gene 102: 229−236.
60. Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A.,
61. Sementchenko, V., Cheng, J., Williams, A.J. et al. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499−509.
62. Charron, G., Julien, J.P., and Bibor-Hardy, V. 1995. Neuron specificity of the neurofilament light promoter in transgenic mice requires the presence of DNA unwinding elements. J Biol Chem 270: 25 739−25 745.
63. Chattopadhyay, S., Kaul, R., Charest, A., Housman, D., and Chen, J. 2000. SMAR1, a novel, alternatively spliced gene product, binds the Scaffold/Matrix-associated region at the T cell receptor beta locus. Genomics 68: 93−96.
64. 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.
65. Chernov, I.P., Akopov, S.B., Nikolaev, L.G., and Sverdlov, E.D. 2006. Identification and mapping of DNA binding proteins target sequences in long genomic regions by two-dimensional EMSA. BioTechniques 41: 90−96.
66. Chernov, I.P., Timchenko, K.A., Akopov, S.B., Nikolaev, L.G., and Sverdlov, E.D. 2007.1.entification of tissue-specific DNA-protein binding sites by means of two-dimensional electrophoretic mobility shift assay display. Anal Biochem 364: 60−66.
67. Chimera, J.A. and Musich, P.R. 1985. The association of the interspersed repetitive Kpnl sequences with the nuclear matrix. J Biol Chem 260: 9373−9379.
68. Cockerill, P.N. 1990. Nuclear matrix attachment occurs in several regions of the IgH locus. Nucleic Acids Res 18: 2643−2648.
69. Cockerill, P.N. and Garrard, W.T. 1986. Chromosomal loop anchorage of the kappaimmunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44: 273−282.
70. Cockerill, P.N., Yuen, M.H., and Garrard, W.T. 1987. The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage elements. J Biol Chem 262: 5394−5397. -
71. Cook, P.R. and Brazell, I. A. 1980. Mapping sequences in loops of nuclear DNA by their progressive detachment from the nuclear cage. Nucleic Acids Res 8: 2895−2906.
72. Cooper, S.J., Trinklein, N.D., Anton, E.D., Nguyen, L., and Myers, R.M. 2006. Comprehensive analysis of transcriptional promoter structure and function in 1% of the human genome. Genome Res 16: 1−10.
73. Crawford, G.E., Holt, I.E., Mullikin, J.C., Tai, D., Blakesley, R., Bouffard, G., Young, A.,
74. Masiello, C., Green, E.D., Wolfsberg, T.G. et al. 2004. Identifying gene regulatory elements by genome-wide recovery of DNase hypersensitive sites. Proc Natl Acad Sci USA 101: 992−997.
75. Dahl, C. and Guldberg, P. 2003. DNA methylation analysis techniques. Biogerontology 4: 233−250.
76. Dang, Q., Auten, J., and Plavec, I. 2000. Human beta interferon scaffold attachment region inhibits de novo methylation and confers long-term, copy number-dependent expression to a retroviral vector. J Virol 74: 2671−2678.
77. Dickinson, L.A., Dickinson, C.D., and Kohwi-Shigematsu, T. 1997. An atypical homeodomain in S ATB1 promotes specific recognition of the key structural element in a matrix attachment region. J Biol Chem 272: 11 463−11 470.
78. Dickinson, L.A., Joh, T., Kohwi, Y., and Kohwi-Shigematsu, T. 1992. A tissue-specific MAR7SAR DNA-binding protein with unusual binding site recognition. Cell 70: 631−645.
79. Dignam, J.D., Lebovitz, R.M., and Roeder, R.G. 1983. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucleic Acids Res 11: 1475−1489.
80. Dobreva, G., Chahrour, M., Dautzenberg, M., Chirivella, L., Kanzler, B., Farinas, I., Karsenty, G., and Grosschedl, R. 2006. S ATB2 is a multifunctional determinant of craniofacial patterning and osteoblast differentiation. Cell 125: 971−986.
81. Dorion-Bonnet, F., Mautalen, S., Hostein, I., and Longy, M. 1995. Allelic imbalance study of 16q in human primary breast carcinomas using microsatellite markers. Genes Chromosomes Cancer 14: 171−181.
82. Dunaway, M., Hwang, J.Y., Xiong, M., and Yuen, H.L. 1997. The activity of the scs and scs’insulator elements is not dependent on chromosomal context. Mol Cell Biol 17: 182−189.
83. ENCODE consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 306: 636−640.
84. Euskirchen, G., Royce, T.E., Bertone, P., Martone, R., Rinn, J.L., Nelson, F.K., Sayward, F., Luscombe, N.M., Miller, P., Gerstein, M. et al. 2004. CREB binds to multiple loci on human chromosome 22. Mol Cell Biol 24: 3804−3814.
85. Fackelmayer, F.O., Dahm, K., Renz, A., Ramsperger, U., and Richter, A. 1994. Nucleic-acid-binding properties of hnRNP-U/SAF-A, a nuclear-matrix protein which binds DNA and RNA in vivo and in vitro. Eur JBiochem 221: 749−757.
86. Fackelmayer, F.O. and Richter, A. 1994. hnRnp-U/Saf-a is encoded by two differentially polyadenylated mRnas in human cells. Biochim Biophys Acta 1217: 232−234.
87. Feigner, P.L., Gadek, T.R., Holm, M., Roman, R., Chan, H.W., Wenz, M., Northrop, J.P., Ringold, G.M., and Danielsen, M. 1987. Lipofection: a highly efficient, lipid-mediated DNA-transfection procedure. Proc Natl Acad Sci USA 84: 7413−7417.
88. Felsenfeld, G. and Groudine, M. 2003. Controlling the double helix. Nature 421: 448−453.
89. Fernandez, L.A., Winkler, M., and Grosschedl, R. 2001. Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy. Mol Cell Biol 21: 196−208.
90. Finch, J.T. and Klug, A. 1976. Solenoidal model for superstructure in chromatin. Proc Natl Acad Sci USAl^: 1897−1901.
91. Fischer, D.F., van Drunen, C.M., Winkler, G.S., van de Putte, P., and Backendorf, C. 1998. Involvement of a nuclear matrix association region in the regulation of the SPRR2A keratinocyte terminal differentiation marker. Nucleic Acids Res 26: 5288−5294.
92. FitzPatrick, D.R., Carr, I.M., McLaren, L., Leek, J.P., Wightman, P., Williamson, K., Gautier, P., McGill, N. Hayward, C., Firth, H. et al. 2003. Identification of SATB2 as the cleft palate gene on 2q32-q33. Hum Mol Genet 12: 2491−2501.
93. Forrester, W.C., Fernandez, L.A., and Grosschedl, R. 1999. Nuclear matrix attachment regionsantagonize methylation-dependent repression of long-range enhancer-promoter interactions. Genes Dev 13: 3003−3014.
94. Forrester, W.C., van Genderen, C., Jenuwein, T., and Grosschedl, R. 1994. Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science 265: 1221−1225.
95. Fraga, M.F. and Esteller, M. 2002. DNA methylation: a profile of methods and applications. Biotechniques 33: 632, 634, 636−649.
96. Frisch, M., Freeh, K., Klingenhoff, A., Cartharius, K., Liebich, I., and Werner, T. 2002. In silico prediction of scaffold/matrix attachment regions in large genomic sequences. Genome Res 12: 349−354.
97. Gasser, S.M. and Laemmli, U.K. 1986. Cohabitation of scaffold binding regions withupstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46: 521−530.
98. Gaszner, M. and Felsenfeld, G. 2006. Insulators: exploiting transcriptional and epigenetic mechanisms. Nat Rev Genet 7: 703−713.
99. Gaubatz, S., Meichle, A., and Eilers, M. 1994. An E-box element localized in the first intronmediates regulation of the prothymosin alpha gene by c-myc. Mol Cell Biol 14: 3853−3862.
100. Gerdes, M.G., Carter, K.C., Moen, P.T., Jr., and Lawrence, J.B. 1994. Dynamic changes in thehigher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J Cell Biol 126: 289−304.
101. Geyer, P.K. 1997. The role of insulator elements in defining domains of gene expression. Curr Opin Genet Dev 7: 242−248.
102. Gilbert, N., Boyle, S., Fiegler, H., Woodfine, K., Carter, N.P., and Bickmore, W.A. 2004.
103. Chromatin architecture of the human genome: gene-rich domains are enriched in open chromatin fibers. Cell 118: 555−566.
104. Gindullis, F. and Meier, I. 1999. Matrix attachment region binding protein MFP1 is localized in discrete domains at the nuclear envelope. Plant Cell 11: 1117−1128.
105. Gitan, R.S., Shi, H., Chen, C.M., Yan, P. S., and Huang, T.H. 2002. Methylation-specificoligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res 12: 158−164.
106. Glazko, G.V., Rogozin, I.B., and Glazkov, M.V. 2001. Comparative study and prediction of DNA fragments associated with various elements of the nuclear matrix. Biochim Biophys Acta 1517: 351−364.
107. Grandori, C., Cowley, S.M., James, L.P., and Eisenman, R.N. 2000. The Myc/Max/Mad network and the transcriptional control of cell behavior. Annu Rev Cell Dev Biol 16: 653−699.
108. Gray, C.E. and Coates, C.J. 2005. Cloning and characterization of cDNAs encoding putative
109. CTCFs in the mosquitoes, Aedes aegypti and Anopheles gambiae. BMC Mol Biol 6: 16.
110. Greasley, P.J., Bonnard, C., and Amati, B. 2000. Myc induces the nucleolin and BN51 genes: possible implications in ribosome biogenesis. Nucleic Acids Res 28: 446−453.
111. Hale, M.A. and Garrard, W.T. 1998. A targeted kappa immunoglobulin gene containing a deletion of the nuclear matrix association region exhibits spontaneous hyper-recombination in pre-B cells. Mol Immunol 35: 609−620.
112. Hallikas, O., Palin, K., Sinjushina, N., Rautiainen, R., Partanen, J., Ukkonen, E., and Taipale, J.2006. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124: 47−59.
113. Hammarstrom, S. 1999. The carcinoembryonic antigen (CEA) family: structures, suggestedfunctions and expression in normal and malignant tissues. Semin Cancer Biol 9: 67−81.
114. Hancock, R. and Boulikas, T. 1982. Functional organization in the nucleus. Int Rev Cytol 79: 165 214.
115. Hayashizaki, Y., Hirotsune, S., Okazaki, Y., Hatada, I., Shibata, H., Kawai, J., Hirose, K.,
116. Watanabe, S., Fushiki, S., Wada, S. et al. 1993. Restriction landmark genomic scanning method and its various applications. Electrophoresis 14: 251−258.
117. Heng, H.H., Goetze, S., Ye, C.J., Liu, G., Stevens, J.B., Bremer, S.W., Wykes, S.M., Bode, J., and Krawetz, S.A. 2004. Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J Cell Sci 117: 999−1008.
118. Heng, H.H., Krawetz, S.A., Lu, W., Bremer, S., Liu, G., and Ye, C.J. 2001. Re-defining the chromatin loop domain. Cytogenet Cell Genet 93: 155−161.
119. Henriksson, M. and Luscher, B. 1996. Proteins of the Myc network: essential regulators of cell growth and differentiation. Adv Cancer Res 68: 109−182.
120. Homberger, H.P. 1989. Bent DNA is a structural feature of scaffold-attached regions in Drosophila melanogaster interphase nuclei. Chromosoma 98: 99−104.
121. Horikawa, I., Cable, P.L., Afshari, C., and Barrett, J.C. 1999. Cloning and characterization of the promoter region of human telomerase reverse transcriptase gene. Cancer Res 59: 826−830.
122. Jack, R.S. andEggert, H. 1992. The elusive nuclear matrix. Eur J Biochem 209: 503−509.
123. Jackson, D.A., Bartlett, J., and Cook, P.R. 1996. Sequences attaching loops of nuclear andmitochondrial DNA to underlying structures in human cells: the role of transcription units. Nucleic Acids Res 24: 1212−1219.
124. Jackson, D.A., Dickinson, P., and Cook, P.R. 1990a. Attachment of DNA to the nucleoskeleton of HeLa cells examined using physiological conditions. Nucleic Acids Res 18: 4385−4393.
125. Jackson, D.A., Dickinson, P., and Cook, P.R. 1990b. The size of chromatin loops in HeLa cells. EmboJ9: 567−571.
126. Jackson, D.A., Dolle, A., Robertson, G., and Cook, P.R. 1992. The attachments of chromatin loops to the nucleoskeleton. Cell Biol Int Rep 16: 687−696.
127. Jaenisch, R. and Bird, A. 2003. Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nat Genet 33 Suppl: 245−254.
128. Jarman, A.P. and Higgs, D.R. 1988. Nuclear scaffold attachment sites in the human globin gene complexes. EmboJl: 3337−3344.
129. Jenuwein, T. and Allis, C.D. 2001. Translating the histone code. Science 293: 1074−1080.
130. Jenuwein, T., Forrester, W.C., Fernandez-Herrero, L.A., Laible, G., Dull, M., and Grosschedl, R. 1997. Extension of chromatin accessibility by nuclear matrix attachment regions. Nature 385: 269−272.
131. Jurka, J., Kapitonov, V.Y., Pavlicek, A., Klonowski, P., Kohany, O., and Walichiewicz, J. 2005.
132. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res 110: 462−467.
133. Jurka, J., Kaplan, D.J., Duncan, C.H., Walichiewicz, J., Milosavljevic, A., Murali, G., and Solus, J.F. 1993. Identification and characterization of new human medium reiteration frequency repeats. Nucleic Acids Res 21: 1273−1279.
134. Kadonaga, J.T. 2004. Regulation of RNA polymerase II transcription by sequence-specific DNA binding factors. Cell 116: 247−257.
135. Kalos, M. and Fournier, R.E. 1995. Position-independent transgene expression mediated byboundary elements from the apolipoprotein B chromatin domain. Mol Cell Biol 15: 198 207.
136. Kaneda, A., Takai, D., Kaminishi, M., Okochi, E., and Ushijima, T. 2003. Methylation-sensitiverepresentational difference analysis and its application to cancer research. Ann N Y AcadSci 983: 131−141.
137. Kas, E. and Chasin, L.A. 1987. Anchorage of the Chinese hamster dihydrofolate reductase gene to the nuclear scaffold occurs in an intragenic region. J Mol Biol 198: 677−692.
138. Kaul-Ghanekar, R., Jalota, A., Pavithra, L., Tucker, P., and Chattopadhyay, S. 2004. SMAR1 and Cux/CDP modulate chromatin and act as negative regulators of the TCRbeta enhancer (Ebeta). Nucleic Acids Res 32: 4862−4875.
139. Kawabata, Y., Katunuma, N., and Sanada, Y. 1980. Characteristics of proline oxidase in rat tissues. JBiochem (Tokyo) 88: 281−283.
140. Kazazian, H.H., Jr. and Goodier, J.L. 2002. LINE drive, retrotransposition and genome instability. Cell 110: 277−280.
141. Kellum, R. and Schedl, P. 1992. A group of scs elements function as domain boundaries in an enhancer-blocking assay. Mol Cell Biol 12: 2424−2431.
142. Kent, W.J., Sugnet, C.W., Furey, T.S., Roskin, K.M., Pringle, T.H., Zahler, A.M., and Haussler, D. 2002. The human genome browser at UCSC. Genome Res 12: 996−1006.
143. 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.
144. Kim, T.H., Barrera, L.O., Qu, C., Van Calcar, S., Trinklein, N.D., Cooper, S.J., Luna, R.M., Glass, C.K., Rosenfeld, M.G., Myers, R.M. et al. 2005a. Direct isolation and identification of promoters in the human genome. Genome Res 15: 830−839.
145. Kim, T.H., Barrera, L.O., Zheng, M., Qu, C., Singer, M.A., Richmond, T.A., Wu, Y., Green, R.D., and Ren, B. 2005b. A high-resolution map of active promoters in the human genome. Nature 436: 876−880.
146. Kipp, M., Gohring, F., Ostendorp, T., van Drunen, C.M., van Driel, R., Przybylski, M., and Fackelmayer, F.O. 2000a. SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA. Mol Cell Biol 20: 7480−7489.
147. Kipp, M., Schwab, B.L., Przybylski, M., Nicotera, P., and Fackelmayer, F.O. 2000b. Apoptotic cleavage of scaffold attachment factor A (SAF-A) by caspase-3 occurs at a noncanonical cleavage site. J Biol Chem 275: 5031−5036.
148. Kirillov, A., Kistler, B., Mostoslavsky, R., Cedar, H., Wirth, T., and Bergman, Y. 1996. A role for nuclear NF-kappaB in B-cell-specific demethylation of the Igkappa locus. Nat Genet 13: 435−441.
149. Kiryanov, G.I., Smirnova, T.A., and Polyakov, V. 1982. Nucleomeric organization of chromatin. Eur JBiochem 124: 331−338.
150. Klehr, D., Maass, K., and Bode, J. 1991. Scaffold-attached regions from the human interferon beta domain can be used to enhance the stable expression of genes under the control of various promoters. Biochemistry 30: 1264−1270.
151. Kohwi-Shigematsu, T., Maass, K., and Bode, J. 1997. A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry 36: 12 005−12 010.
152. Kolosha, V.O. and Martin, S.L. 1997. In vitro properties of the first ORF protein from mouse
153. NE-1 support its role in ribonucleoprotein particle formation during retrotransposition. Proc Natl Acad Sci USA 94: 10 155−10 160.
154. Konat, G.W. 1996. Chromatin structure and transcriptional activity of MAG gene. Acta Neurobiol Exp 56: 281−285.
155. Kondo, Y., Shen, L., Yan, P. S., Huang, T.H., and Issa, J.P. 2004. Chromatin immunoprecipitation microarrays for identification of genes silenced by histone H3 lysine 9 methylation. Proc Natl Acad Sci USA 101: 7398−7403.
156. Krogh, S., Mortensen, U.H., Westergaard, O., and Bonven, B.J. 1991. Eukaryotic topoisomerase I-DNA interaction is stabilized by helix curvature. Nucleic Acids Res 19: 1235−1241.
157. Magdinier, F., Yusufzai, T.M., and Felsenfeld, G. 2004. Both CTCF-dependent and -independent insulators are found between the mouse T cell receptor alpha and Dadl genes. J Biol Chem 279: 25 381−25 389.
158. Marais, G., Nouvellet, P., Keightley, P.D., and Charlesworth, B. 2005. Intron size and exon evolution in Drosophila. Genetics 170: 481−485.
159. Marie, C. and Hyrien, O. 1998. Remodeling of chromatin loops does not account for specification of replication origins during Xenopus development. Chromosoma 107: 155−165.
160. Marsden, M.P. and Laemmli, U.K. 1979. Metaphase chromosome structure: evidence for a radial. loop model. Cell 17: 849−858.
161. Maston, G.A., Evans, S.K., and Green, M.R. 2006. Transcriptional Regulatory Elements in the Human Genome. Annu Rev Genomics Hum Genet 7: 29−59.
162. Meier, I., Phelan, T., Gruissem, W., Spiker, S., and Schneider, D. 1996. MFP1, a novel plantfilament-like protein with affinity for matrix attachment region DNA. Plant Cell 8: 21 052 115.
163. Meissner, A., Gnirke, A., Bell, G.W., Ramsahoye, B., Lander, E.S., and Jaenisch, R. 2005. Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res 33: 5868−5877.
164. Mesner, L.D., Crawford, E.L., and Hamlin, J.L. 2006. Isolating apparently pure libraries of replication origins from complex genomes. Mol Cell 21: 719−726.
165. Miao, F. and Natarajan, R. 2005. Mapping global histone methylation patterns in the coding regions of human genes. Mol Cell Biol 25: 4650−4661.
166. Miassod, R., Razin, S.V., and Hancock, R. 1997. Distribution of topoisomerase II-mediatedcleavage sites and relation to structural and functional landmarks in 830 kb of Drosophila DNA. Nucleic Acids Res 25: 2041−2046.
167. Michalowski, S.M., Allen, G.C., Hall, G.E., Jr., Thompson, W.F., and Spiker, S. 1999.
168. Characterization of randomly-obtained matrix attachment regions (MARs) from higher plants. Biochemistry 38: 12 795−12 804.
169. Mielke, C., Kohwi, Y., Kohwi-Shigematsu, T., and Bode, J. 1990. Hierarchical binding of DNA fragments derived from scaffold-attached regions: correlation of properties in vitro and function in vivo. Biochemistry 29: 7475−7485.
170. Mielke, C., Maass, K., Tummler, M., and Bode, J. 1996. Anatomy of highly expressing chromosomal sites targeted by retroviral vectors. Biochemistry 35: 2239−2252.
171. Mirkovitch, J., Gasser, S.M., and Laemmli, U.K. 1988. Scaffold attachment of DNA loops in metaphase chromosomes. J Mol Biol 200: 101−109.
172. Mirkovitch, J., Mirault, M.E., and Laemmli, U.K. 1984. Organization of the higher-order chromatin loop: specific DNA attachment sites on nuclear scaffold. Cell 39: 223−232.
173. Mirkovitch, J., Spierer, P., and Laemmli, U.K. 1986. Genes and loops in 320,000 base-pairs of the Drosophila melanogaster chromosome. J Mol Biol 190: 255−258.
174. Miyamoto, Y., Yamauchi, J., Sanbe, A., and Tanoue, A. 2006. Dock6, a Dock-C subfamily guanine nucleotide exchanger, has the dual specificity for Racl and Cdc42 and regulates neurite outgrowth. Exp Cell Res 313: 791−804.
175. Mlynarova, L., Jansen, R.C., Conner, A.J., Stiekema, W.J., and Nap, J.P. 1995. The MAR
176. Mediated Reduction in Position Effect Can Be Uncoupled from Copy Number-Dependent Expression in Transgenic Plants. Plant Cell 7: 599−609.
177. Mockler, T.C., Chan, S., Sundaresan, A., Chen, H., Jacobsen, S.E., and Ecker, J.R. 2005. Applications of DNA tiling arrays for whole-genome analysis. Genomics 85: 1−15.
178. Morisawa, G., Han-Yama, A., Moda, I., Tamai, A., Iwabuchi, M., and Meshi, T. 2000. AHM1, a novel type of nuclear matrix-localized, MAR binding protein with a single AT hook and a J domain-homologous region. Plant Cell 12: 1903−1916.
179. Morse, R.H. 2003. Getting into chromatin: how do transcription factors get past the histones? Biochem Cell Biol 81: 101−112.
180. Myslinski, E., Gerard, M.A., Krol, A., and Carbon, P. 2006. A genome scale location analysis of human Staf/ZNF143-binding sites suggests a widespread role for human Staf/ZNF143 in mammalian promoters. J Biol Chem 281: 39 953−39 962.
181. Nabirochkin, S., Ossokina, M., and Heidmann, T. 1998. A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J Biol Chem 273: 2473−2479.
182. Nakagomi, K., Kohwi, Y., Dickinson, L.A., and Kohwi-Shigematsu, T. 1994. A novel DNAbinding motif in the nuclear matrix attachment DNA-binding protein S ATB1. Mol Cell Biol 14: 1852−1860.
183. Namciu, S.J., Blochlinger, K.B., and Fournier, R.E. 1998. Human matrix attachment regions insulate transgene expression from chromosomal position effects in Drosophila melanogaster. Mol Cell Biol 18: 2382−2391.
184. Nikolaev, L.G., Tsevegiyn, T., Akopov, S.B., Ashworth, L.K., and Sverdlov, E.D. 1996.
185. Construction of a chromosome specific library of human MARs and mapping of matrix attachment regions on human chromosome 19. Nucleic Acids Res 24: 1330−1336.
186. Nikolaev, L.G., Tsogtkhishig, T., Akopov, S.B., and Sverdlov, E.D. 1995. Mapping the sequences, preferentially bound with the nuclear matrix, on human chromosome 19. Bioorg Khim 21: 954−958.
187. Oancea, A.E., Berru, M., and Shulman, M.J. 1997. Expression of the (recombinant) endogenous immunoglobulin heavy-chain locus requires the intronic matrix attachment regions. Mol Cell Biol 17: 2658−2668.
188. Oesterreich, S., Lee, A.V., Sullivan, T.M., Samuel, S.K., Davie, J.R., and Fuqua, S.A. 1997. Novel nuclear matrix protein HET binds to and influences activity of the HSP27 promoter in human breast cancer cells. J Cell Biochem 67: 275−286.
189. Ogbourne, S. and Antalis, T.M. 1998. Transcriptional control and the role of silencers in transcriptional regulation in eukaryotes. Biochem J331 (Pt 1): 1−14.
190. 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.
191. Olsen, A.S., Combs, J., Garcia, E., Elliott, J., Amemiya, C., de Jong, P., and Threadgill, G. 1993. Automated production of high density cosmid and YAC colony filters using a robotic workstation. Biotechniques 14: 116−117, 120−113.
192. Opstelten, R.J., Clement, J.M., and Wanka, F. 1989. Direct repeats at nuclear matrix-associated DNA regions and their putative control function in the replicating eukaryotic genome. Chromosoma 98: 422−427.
193. Orian, A. 2006. Chromatin profiling, DamID and the emerging landscape of gene expression. Curr Opin Genet Dev 16: 157−164.
194. Orian, A., van Steensel, B., Delrow, J., Bussemaker, H.J., Li, L., Sawado, T., Williams, E., Loo, L.W., Cowley, S.M., Yost, C. et al. 2003. Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network. Genes Dev 17: 1101−1114.
195. Orlando, V. 2000. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 25: 99−104.
196. Oshiman, K., Motojima, K., Mahmood, S., Shimada, A., Tamura, S., Maeda, M., and Futai, M. 1991. Control region and gastric specific transcription of the rat H+, K (+)-ATPase alpha subunit gene. FEBS Lett 281: 250−254.
197. Paul, A.L. and Ferl, R.J. 1998. Higher order chromatin structures in maize and Arabidopsis. Plant Cell 10: 1349−1359.
198. Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M.,
199. Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D. et al. 2006. In vivo enhancer analysis of human conserved non-coding sequences. Nature 444: 499−502.
200. Pennacchio, L.A., Loots, G.G., Nobrega, M.A., and Ovcharenko, I. 2007. Predicting tissue-specific enhancers in the human genome. Genome Res 17: 201−211.
201. Pennisi, E. 2004. Searching for the genome’s second code. Science 306: 632−635.
202. Phi-Van, L. and Stratling, W.H. 1990. Association of DNA with nuclear matrix. Progr Mol Subcell Biol 11: 1−11.
203. Phi-Van, L. and Stratling, W.H. 1996. Dissection of the ability of the chicken lysozyme gene 5'matrix attachment region to stimulate transgene expression and to dampen position effects. Biochemistry 35: 10 735−10 742.
204. Pienta, K.J. and Coffey, D.S. 1984. A structural analysis of the role of the nuclear matrix and DNA loops in the organization of the nucleus and chromosome. J Cell Sci Suppl 1: 123−135.
205. Pienta, K.J., Partin, A.W., and Coffey, D.S. 1989. Cancer as a disease of DNA organization and dynamic cell structure. Cancer Res 49: 2525−2532.
206. Poljak, L., Seum, C., Mattioni, T., and Laemmli, U.K. 1994. SARs stimulate but do not confer position independent gene expression. Nucleic Acids Res 22: 4386−4394.
207. Pommier, Y., Cockerill, P.N., Kohn, K.W., and Garrard, W.T. 1990. Identification within thesimian virus 40 genome of a chromosomal loop attachment site that contains topoisomerase II cleavage sites. J Virol 64: 419−423.
208. Porter, S.D., Hu, J., and Gilks, C.B. 1999. Distal upstream tyrosinase S/MAR-containing sequence has regulatory properties specific to subsets of melanocytes. Dev Genet 25: 40−48.
209. Purbowasito, W., Suda, C., Yokomine, T., Zubair, M., Sado, T., Tsutsui, K., and Sasaki, H. 2004. Large-scale identification and mapping of nuclear matrix-attachment regions in the distal imprinted domain of mouse chromosome 7. DNA Res 11: 391−407.
210. Quarles, R.H. 2007. Myelin-associated glycoprotein (MAG): past, present and beyond. J Neurochem 100: 1431−1448.
211. Rauch, T. and Pfeifer, G.P. 2005. Methylated-CpG island recovery assay: a new technique for the rapid detection of methylated-CpG islands in cancer. Lab Invest 85: 1172−1180.
212. Razin, S.V. and Vassetzky, Y.S. 1992. Domain organization of eukaryotic genome. Cell Biol Int Rep 16: 697−708.
213. Recillas-Targa, F., Bell, A.C., and Felsenfeld, G. 1999. Positional enhancer-blocking activity of the chicken beta-globin insulator in transiently transfected cells. Proc Natl Acad Sci USA 96: 14 354−14 359.
214. Recillas-Targa, F., Valadez-Graham, V., and Farrell, C.M. 2004. Prospects and implications of using chromatin insulators in gene therapy and transgenesis. Bioessays 26: 796−807.
215. Renan, M.J. and Reeves, B.R. 1987. Chromosomal localization of human endogenous retroviralelement ERV1 to 18q22—q23 by in situ hybridization. Cytogenet Cell Genet 44: 167−170.
216. Renz, A. and Fackelmayer, F.O. 1996. Purification and molecular cloning of the scaffoldattachment factor B (SAF-B), a novel human nuclear protein that specifically binds to S/MAR-DNA. Nucleic Acids Res 24: 843−849.
217. Roh, T.Y., Cuddapah, S., and Zhao, K. 2005. Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev 19: 542−552.
218. Roh, T.Y., Wei, G., Farrell, C.M., and Zhao, K. 2007. Genome-wide prediction of conserved and nonconserved enhancers by histone acetylation patterns. Genome Res 17: 74−81.
219. Rollini, P., Namciu, S.J., Marsden, M.D., and Fournier, R.E. 1999. Identification andcharacterization of nuclear matrix-attachment regions in the human serpin gene cluster at 14q32.1. Nucleic Acids Res 27: 3779−3791.
220. Romig, H., Fackelmayer, F.O., Renz, A., Ramsperger, U., and Richter, A. 1992. Characterization of SAF-A, a novel nuclear DNA binding protein from HeLa cells with high affinity for nuclear matrix/scaffold attachment DNA elements. Embo J11: 3431−3440.
221. Romig, H., Ruff, J., Fackelmayer, F.O., Patil, M.S., and Richter, A. 1994. Characterisation of two intronic nuclear-matrix-attachment regions in the human DNA topoisomerase I gene. Eur J Biochem 221: 411−419.
222. Rosen, S. and Skaletsky, H. 2000. Primer3 on the WWW for general users and for biologistprogrammers. In Bioinformatics Methods and Protocols: Methods in Molecular Biology. (eds. S. Krawetz and S. Misener), pp. 365−386. Humana Press, Totowa, NJ.
223. Roti Roti, J.L., Wright, W.D., and VanderWaal, R. 1997. The nuclear matrix: a target for heatshock effects and a determinant for stress response. Crit Rev Eukaryot Gene Expr 7: 343 360.
224. Sabo, P.J., Humbert, R., Hawrylycz, M., Wallace, J.C., Dorschner, M.O., McArthur, M., and
225. Stamatoyannopoulos, J.A. 2004. Genome-wide identification of DNasel hypersensitive sites using active chromatin sequence libraries. Proc Natl Acad Sci USA 101: 4537−4542.
226. Sabo, P.J., Kuehn, M.S., Thurman, R., Johnson, B.E., Johnson, E.M., Cao, H., Yu, M., Rosenzweig, E., Goldy, J., Haydock, A. et al. 2006. Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nat Methods 3:511−518.
227. Sakkers, R.J., Brunsting, J.F., Filon, A.R., Kampinga, H.H., Konings, A.W., and Mullenders, L.H. 1999. Altered association of transcriptionally active DNA with the nuclear-matrix after heat shock. Int JRadiat Biol 75: 875−883.
228. Sambrook, J. and Russell, D.W. 2001. Molecular Cloning. A laboratory Manual. CSHL Press, Cold Spring Harbor.
229. Schachner, M. and Bartsch, U. 2000. Multiple functions of the myelin-associated glycoprotein MAG (siglec- 4a) in formation and maintenance of myelin. Glia 29: 154−165.
230. Schatz, P., Distler, J., Berlin, K., and Schuster, M. 2006. Novel method for high throughput DNA methylation marker evaluation using PNA-probe library hybridization and MALDI-TOF detection. Nucleic Acids Res 34: e59.
231. Scheuermann, R.H. and Chen, U. 1989. A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer. Genes Dev 3: 1255−1266.
232. Schreiber-Agus, N. and DePinho, R.A. 1998. Repression by the Mad (Mxil)-Sin3 complex. Bioessays 20: 808−818.
233. Schubeler, D., Mielke, C., Maass, K., and Bode, J. 1996. Scaffold/matrix-attached regions act upon transcription in a context-dependent manner. Biochemistry 35: 11 160−11 169.
234. Scott, K.C., Taubman, A.D., and Geyer, P.K. 1999. Enhancer blocking by the Drosophila gypsy insulator depends upon insulator anatomy and enhancer strength. Genetics 153: 787−798.
235. Senga, T., Iwamoto, S., Yoshida, T., Yokota, T., Adachi, K., Azuma, E., Hamaguchi, M., and1. amoto, T. 2003. LSSIG is a novel murine leukocyte-specific GPCR that is induced by the activation of STAT3. Blood 101: 1185−1187.
236. Shi, H., Maier, S., Nimmrich, I., Yan, P. S., Caldwell, C.W., Olek, A., and Huang, T.H. 2003. Oligonucleotide-based microarray for DNA methylation analysis: principles and applications. JCellBiochem 88: 138−143.
237. Shields, R. 2006. The emperor’s new clothes revisited. Trends Genet 22: 463.
238. Singh, G.B., Kramer, J.A., and Krawetz, S.A. 1997. Mathematical model to predict regions of chromatin attachment to the nuclear matrix. Nucleic Acids Res 25: 1419−1425.
239. Singh, J. and Klar, A.J. 1992. Active genes in budding yeast display enhanced in vivo accessibility to foreign DNA methylases: a novel in vivo probe for chromatin structure of yeast. Genes Dev 6: 186−196.
240. Smit, A.F., Toth, G., Riggs, A.D., and Jurka, J. 1995. Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. JMol Biol 246: 401−417.
241. Sommer, A., Bousset, K., Kremmer, E., Austen, M., and Luscher, B. 1998. Identification and characterization of specific DNA-binding complexes containing members of the Myc/Max/Mad network of transcriptional regulators. J Biol Chem 273: 6632−6642.
242. Stief, A., Winter, D.M., Stratling, W.H., and Sippel, A.E. 1989. A nuclear DNA attachmentelement mediates elevated and position-independent gene activity. Nature 341: 343−345.
243. Stratling, W.H. and Yu, F. 1999. Origin and roles of nuclear matrix proteins. Specific functions of the MAR-binding protein MeCP2/ARBP. Crit Rev Eukaryot Gene Expr 9: 311−318.
244. Streydio, C., Swillens, S., Georges, M., Szpirer, C., and Vassart, G. 1990. Structure, evolution and chromosomal localization of the human pregnancy-specific beta 1 glycoprotein gene family. Genomics 6: 579−592.
245. Strissel, P.L., Dann, H.A., Pomykala, H.M., Diaz, M.O., Rowley, J.D., and Olopade, O.I. 1998.
246. Scaffold-associated regions in the human type I interferon gene cluster on the short arm of chromosome 9. Genomics 47: 217−229.
247. Subirana, J.A., Munoz-Guerra, S., Aymami, J., Radermacher, M., and Frank, J. 1985. The layered organization of nucleosomes in 30 nm chromatin fibers. Chromosoma 91: 377−390.
248. Sun, T.T., Zhao, H., Provet, J., Aebi, U., and Wu, X.R. 1996. Formation of asymmetric unit membrane during urothelial differentiation. Mol Biol Rep 23: 3−11.
249. Surdej, P., Got, C., and Miassod, R. 1990a. Developmental expression pattern of a 800 kb DNAcontinuum cloned from the Drosophila X chromosome 14B-15B region. Biol Cell 68: 105 118.
250. Thomas, J.O. 1984. The higher order structure of chromatin and histone HI. J Cell Sci Suppl 1:120.
251. Thompson, J.D., Higgins, D.G., and Gibson, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673−4680.
252. Tikhonov, A.P., Bennetzen, J.L., and Avramova, Z.V. 2000. Structural domains and matrixattachment regions along colinear chromosomal segments of maize and sorghum. Plant Cell 12: 249−264.
253. Tremethick, D.J. 2007. Higher-order structures of chromatin: the elusive 30 nm fiber. Cell 128: 651−654.
254. Trinklein, N.D., Aldred, S.F., Hartman, S.J., Schroeder, D.I., Otillar, R.P., and Myers, R.M. 2004. An abundance of bidirectional promoters in the human genome. Genome Res 14: 62−66.
255. Tsongalis, G.J., Coleman, W.B., Smith, G.J., and Kaufman, D.G. 1992. Partial characterization of nuclear matrix attachment regions from human fibroblast DNA using Alu-polymerase chain reaction. Cancer Res 52: 3807−3810.
256. Tsuda, H., Callen, D.F., Fukutomi, T., Nakamura, Y., and Hirohashi, S. 1994. Allele loss onchromosome 16q24.2-qter occurs frequently in breast cancers irrespectively of differences in phenotype and extent of spread. Cancer Res 54: 513−517.
257. Tsuneoka, M., Nakano, F., Ohgusu, H., and Mekada, E. 1997. c-myc activates RCC1 gene expression through E-box elements. Oncogene 14: 2301−2311.
258. Tsutsui, K., Tsutsui, K., Okada, S., Watarai, S., Seki, S., Yasuda, T., and Shohmori, T. 1993. Identification and characterization of a nuclear scaffold protein that binds the matrix attachment region DNA. J Biol Chem 268: 12 886−12 894.
259. Tybulewicz, V.L., Crawford, C.E., Jackson, P.K., Branson, R.T., and Mulligan, R.C. 1991.
260. Neonatal lethality and lymphopenia in mice with a homozygous disruption of the c-abl proto-oncogene. Cell 65: 1153−1163.
261. Unsinger, J. 2001. Entwicklung regulierbarer retro- und adenoviraler Vektoren fur die Gentherapie. Ph. D. Thesis. Technische Universitat Braunschweig, Braunschweig.
262. Valenzuela, L. and Kamakaka, R.T. 2006. Chromatin insulators. Annu Rev Genet 40: 107−138.
263. Venter, J.C. Adams, M.D. Myers, E.W. Li, P.W. Mural, R.J. Sutton, G.G. Smith, H.O. Yandell, M. Evans, C.A. Holt, R.A. et al. 2001. The sequence of the human genome. Science 291: 13 041 351.
264. 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.
265. Wahlstrom, T. and Henriksson, M. 2007. Mnt takes control as key regulator of the myc/max/mxd network. Adv Cancer Res 97: 61−80.
266. Walhout, A.J., Gubbels, J.M., Bernards, R., van der Vliet, P.C., and Timmers, H.T. 1997. c
267. Myc/Max heterodimers bind cooperatively to the E-box sequences located in the first intron of the rat ornithine decarboxylase (ODC) gene. Nucleic Acids Res 25: 1493−1501.
268. Wang, D.M., Taylor, S., and Levy-Wilson, B. 1996. Evaluation of the function of the humanapolipoprotein B gene nuclear matrix association regions in transgenic mice. J Lipid Res 37: 2117−2124.
269. Waterston, R.H. Lindblad-Toh, K. Birney, E. Rogers, J. Abril, J.F. Agarwal, P. Agarwala, R.
270. Ainscough, R. Alexandersson, M. An, P. et al. 2002. Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520−562.
271. Weber, M., Davies, J.J., Wittig, D., Oakeley, E.J., Haase, M., Lam, W.L., and Schubeler, D. 2005. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 37: 853−862.
272. Weil, M.R., Widlak, P., Minna, J.D., and Garner, H.R. 2004. Global survey of chromatin accessibility using DNA microarrays. Genome Res 14: 1374−1381.
273. Weitzel, J.M., Buhrmester, H., and Stratling, W.H. 1997. Chicken MAR-binding protein ARBP is homologous to rat methyl-CpG- binding protein MeCP2. Mol Cell Biol 17: 5656−5666.
274. West, A.G. and Fraser, P. 2005. Remote control of gene transcription. Hum Mol Genet 14 Spec No 1: R101−111.
275. Willoughby, D.A., Vilalta, A., and Oshima, R.G. 2000. An Alu element from the K18 gene confers position-independent expression in transgenic mice. J Biol Chem 275: 759−768.
276. Woodcock, C.L. 2006. Chromatin architecture. Curr Opin Struct Biol 16: 213−220.
277. Woodcock, C.L., Grigoryev, S.A., Horowitz, R.A., and Whitaker, N. 1993. A chromatin folding model that incorporates linker variability generates fibers resembling the native structures. Proc Natl Acad Sci USA 90: 9021−9025.
278. Yamamura, J. and Nomura, K. 2001. Analysis of sequence-dependent curvature in matrixattachment regions. FEBS Lett 489: 166−170.
279. Yang, A.S., Estecio, M.R., Doshi, K., Kondo, Y., Tajara, E.H., and Issa, J.P. 2004. A simple method for estimating global DNA methylation using bisulfite PCR of repetitive DNA elements. Nucleic Acids Res 32: e38.
280. Yen, F.T., Masson, M., Clossais-Besnard, N., Andre, P., Grosset, J.M., Bougueleret, L., Dumas,
281. J.B., Guerassimenko, O., and Bihain, B.E. 1999. Molecular cloning of a lipolysis-stimulated remnant receptor expressed in the liver. J Biol Chem 274: 13 390−13 398.
282. Yi, M., Wu, P., Trevorrow, K.W., Claflin, L., and Garrard, W.T. 1999. Evidence that the Igkappa, gene MAR regulates the probability of premature V-J joining and somatic hypermutation. J Immunol 162: 6029−6039.
283. Yu, W., Ginjala, V., Pant, V., Chernukhin, I., Whitehead, J., Docquier, F., Farrar, D., Tavoosidana, G., Mukhopadhyay, R., Kanduri, C. et al. 2004. Poly (ADP-ribosyl)ation regulates CTCF-dependent chromatin insulation. Nat Genet 36: 1105−1110.
284. Zahn-Zabal, M., Kobr, M., Girod, P.A., Imhof, M., Chatellard, P., de Jesus, M., Wurm, F., and
285. Mermod, N. 2001. Development of stable cell lines for production or regulated expression using matrix attachment regions. JBiotechnol 87: 29−42.
286. Zeller, K.I., Zhao, X., Lee, C.W., Chiu, K.P., Yao, F., Yustein, J.T., Ooi, H.S., Orlov, Y.L., Shahab, A., Yong, H.C. et al. 2006. Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc Natl Acad Sci USA 103: 17 834−17 839.
287. Zhong, X.P., Carabana, J., and Krangel, M.S. 1999. Flanking nuclear matrix attachment regions synergize with the T cell receptor delta enhancer to promote V (D)J recombination. Proc Natl Acad Sci USA 96: 11 970−11 975.
288. Zlatanova, J., Leuba, S.H., and van Holde, K. 1998. Chromatin fiber structure: morphology, molecular determinants, structural transitions. Biophys J 74: 2554−2566.
289. Zong, R.T., Das, C., and Tucker, P.W. 2000. Regulation of matrix attachment region-dependent, lymphocyte-restricted transcription through differential localization within promyelocytic leukemia nuclear bodies. EmboJ 19: 4123−4133.