Abstract
Using transient expression of the E. coli Dam methylase gene and analysis of the distribution of methylated GATC sites, we studied the distribution of open chromatin regions within a 140 kb long human genome segment in HEK-293 cells. Dam methylated sites were found in gene introns, exons, and intergenic regions, and their distribution along DNA was uneven. There were regions of high and low density of Dam methylated GATC sites, presumably corresponding to “open” and “closed” chromatin regions, respectively, and to the functional profile of the genomic locus under study. The Dam methylation profile was also generally in agreement with transcriptional activity of genes in the locus. Moreover, DNA regions accessible to Dam methylase apparently coincided with those hypersensitive to DNase I.
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Azhikina T, Gainetdinov I, Skvortsova Y, Batrak A, Dmitrieva N, Sverdlov E (2004) 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
Boivin A, Dura JM (1998) In vivo chromatin accessibility correlates with gene silencing in Drosophila. Genetics 150:1539–1549
Buryanov Y, Shevchuk T (2005) The use of prokaryotic DNA methyltransferases as experimental and analytical tools in modern biology. Anal Biochem 338:1–11
Chalaya TV, Akopov SB, Nikolaev LG, Sverdlov ED (2006) Tissue specificity of methylation of cytosines in regulatory regions of four genes located in the locus FXYD5-COX7A1 of human chromosome 19: correlation with their expression level. Biochemistry (Moscow) 71:371–377
Chernov IP, Akopov SB, Nikolaev LG, Sverdlov ED (2002) Identification and mapping of nuclear matrix attachment regions in a one megabase locus of human chromosome 19q13.12: long-range correlation of S/MARs and gene positions. J Cell Biochem 84:590–600
Dekker J (2003) A closer look at long-range chromosomal interactions. Trends Biochem Sci 28:277–280
Diatchenko L, Lau YF, Campbell AP, Chenchik A, Moqadam F, Huang B, Lukyanov S, Lukyanov K, Gurskaya N, Sverdlov ED et al (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc Natl Acad Sci USA 93:6025–6030
Felsenfeld G, Boyes J, Chung J, Clark D, Studitsky V (1996) Chromatin structure and gene expression. Proc Natl Acad Sci USA 93:9384–9388
Gilbert N, Gilchrist S, Bickmore WA (2005) Chromatin organization in the mammalian nucleus. Int Rev Cytol 242:283–336
Gottschling DE (1992) Telomere-proximal DNA in Saccharomyces cerevisiae is refractory to methyltransferase activity in vivo. Proc Natl Acad Sci USA 89:4062–4065
Green CM, Almouzni G (2002) When repair meets chromatin. First in series on chromatin dynamics. EMBO Rep 3:28–33
Hattman S, Kenny C, Berger L, Pratt K (1978) Comparative study of DNA methylation in three unicellular eukaryotes. J Bacteriol 135:1156–1157
Hebbes TR, Clayton AL, Thorne AW, Crane-Robinson C (1994) Core histone hyperacetylation co-maps with generalized DNase I sensitivity in the chicken beta-globin chromosomal domain. EMBO J 13:1823–1830
Hoekstra MF, Malone RE (1985) Expression of the Escherichia coli Dam methylase in Saccharomyces cerevisiae: effect of in vivo adenine methylation on genetic recombination and mutation. Mol Cell Biol 5:610–618
Kir’ianov GI, Smirnova TA, Isaeva LV, Vaniushin BF, Bur’ianov Ia I (1981) Limited accessibility of DNA methylation sites for bacterial methylases M. EcoR II and M.Eco dam in chromatin at different levels of organization. Biochemistry (Moscow) 46:1887–1895
Kudriashova IB, Kirnos MD, Vaniushin BF (1976) DNA-methylase activities from animal mitochondria and nuclei: different specificity of DNA methylation. Biochemistry (Moscow) 41:1968–1977
Lavrentieva I, Broude NE, Lebedev Y, Gottesman II, Lukyanov SA, Smith CL, Sverdlov ED (1999) High polymorphism level of genomic sequences flanking insertion sites of human endogenous retroviral long terminal repeats. FEBS Lett 443:341–347
Lipford JR, Bell SP (2001) Nucleosomes positioned by ORC facilitate the initiation of DNA replication. Mol Cell 7:21–30
McGhee JD, Felsenfeld G (1979) Reaction of nucleosome DNA with dimethyl sulfate. Proc Natl Acad Sci USA 76:2133–2137
Mymryk JS, Fryer CJ, Jung LA, Archer TK (1997) Analysis of chromatin structure in vivo. Methods 12:105–114
Nakai H, Storm TA, Kay MA (2000) Recruitment of single-stranded recombinant adeno-associated virus vector genomes and intermolecular recombination are responsible for stable transduction of liver in vivo. J Virol 74:9451–9463
Pfeifer GP, Tornaletti S (1997) Footprinting with UV irradiation and LMPCR. Methods 11:189–196
Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning : a laboratory manual. 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y
Simpson RT (1999) In vivo methods to analyze chromatin structure. Curr Opin Genet Dev 9:225–229
Singh J, Klar AJ (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
Vermaak D, Ahmad K, Henikoff S (2003) Maintenance of chromatin states: an open-and-shut case. Curr Opin Cell Biol 15:266–274
Wang X, Simpson RT (2001) Chromatin structure mapping in Saccharomyces cerevisiae in vivo with DNase I. Nucleic Acids Res 29:1943–1950
Wang S, Zhu J (2004) The hTERT gene is embedded in a nuclease-resistant chromatin domain. J Biol Chem 279:55401–55410
Wellinger RE, Sogo JM (1998) In vivo mapping of nucleosomes using psoralen-DNA crosslinking and primer extension. Nucleic Acids Res 26:1544–1545
Wines DR, Talbert PB, Clark DV, Henikoff S (1996) Introduction of a DNA methyltransferase into Drosophila to probe chromatin structure in vivo. Chromosoma 104:332–340
Wolffe A (1995) Chromatin : structure and function. 2nd edn. Academic Press, London; San Diego
Acknowledgements
The authors thank E.A. Stukacheva and S.B. Akopov for carrying out transfections, V.K. Potapov and N.V. Skaptsova for oligonucleotide synthesis, T.L. Azhikina and T.V. Vinogradova for critical remarks and advises, V.V. Ruda for assistance at several steps of the work, Anne Olsen for cosmid clones and N.I. Medvedeva for preparation of cosmids. We thank B.O. Glotov for critical reading of the manuscript. The work was supported by the Scientific School program of the Russian Federation President (project NSh 2006.2003.4), and the program of the Russian Academy of Sciences on Molecular and Cellular Biology.
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Bulanenkova, S., Snezhkov, E., Nikolaev, L. et al. 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 (2007). https://doi.org/10.1007/s10709-006-0026-1
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DOI: https://doi.org/10.1007/s10709-006-0026-1