Single-molecule analysis of chromatin: Changing the view of genomes one molecule at a time

Journal of Cellular Biochemistry

Volumn 105, Issue 2, 2008, Pages 330-337

  Pondugula, Santhi ^a   Kladde, Michael P ^a  

^a UNIVERSITY OF FLORIDA   (United States)

Author keywords

Chromatin remodeling; DNA methyltransferases; Positioned nucleosomes; Protein DNA interactions; Transcription

Indexed keywords

DNA METHYLTRANSFERASE;

CELL GROWTH; CELL MATURATION; CELL POPULATION; CHROMATIN STRUCTURE; EUKARYOTE; GENE CONTROL; GENOME; MOLECULAR MECHANICS; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; REVIEW;

CHROMATIN; DNA MODIFICATION METHYLASES; GENOME; MOLECULAR PROBE TECHNIQUES;

EUKARYOTA;

EID: 54849442676     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.21849     Document Type: Review

References (66)

1. Adkins MW, Howar SR, Tyler JK. 2004. Chromatin disassembly mediated by the histone chaperone Asf1 is essential for transcriptional activation of the yeast PHO5 and PHO8 genes. Mol Cell 14:657-666.
2. Adkins MW, Williams SK, Linger J, Tyler JK. 2007. Chromatin disassembly from the PHO5 promoter is essential for the recruitment of the general transcription machinery and coactivators. Mol Cell Biol 27:6372-6382.
3. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. 2007. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446:572-576.
4. Almer A, Hörz W. 1986. Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J 5:2681-2687.
5. Almer A, Rudolph H, Hinnen A, Hörz W. 1986. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J 5:2689-2696.
6. Anderson JD, Widom J. 2000. Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites. J Mol Biol 296:979-987.
7. Barbaric S, Fascher KD, Hörz W. 1992. Activation of the weakly regulated PHO8 promoter in S. cerevisiae: Chromatin transition and binding sites for the positive regulatory protein PHO4. Nucleic Acids Res 20:1031-1038.
8. Barbaric S, Reinke H, Hörz W. 2003. Multiple mechanistically distinct functions of SAGA at the PHO5 promoter. Mol Cell Biol 23:3468-3476.
9. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. 2007. High-resolution profiling of histone methylations in the human genome. Cell 129:823-837.
10. Becskei A, Seraphin B, Serrano L. 2001. Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J 20:2528-2535.
11. Bergman Y, Cedar H. 2004. A stepwise epigenetic process controls immunoglobulin allelic exclusion. Nat Rev Immunol 4:753-761.
12. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. 2004. Global nucleosome occupancy in yeast. Genome Biol 5:R62.
13. Biggar SR, Crabtree GR. 2001. Cell signaling can direct either binary or graded transcriptional responses. EMBO J 20:3167-3176.
14. Bird A. 2002. DNA methylation patterns and epigenetic memory. Genes Dev 16:6-21.
15. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. 2003. Nucleosomes unfold completely at a transcriptionally active promoter. Mol Cell 11:1587-1598.
16. Boeger H, Griesenbeck J, Strattan JS, Kornberg RD. 2004. Removal of promoter nucleosomes by disassembly rather than sliding in vivo. Mol Cell 14:667-673.
17. Bustamante C, Bryant Z, Smith SB. 2003. Ten years of tension: Single-molecule DNA mechanics. Nature 421:423-427.
18. Cairns BR. 2007. Chromatin remodeling: Insights and intrigue from single-molecule studies. Nat Struct Mol Biol 14:989-996.
19. Carvin CD, Dhasarathy A, Friesenhahn LB, Jessen WJ, Kladde MP. 2003. Targeted cytosine methylation for in vivo detection of protein-DNA interactions. Proc Natl Acad Sci USA 100:7743-7748.
20. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452:215-219.
21. Dhasarathy A, Kladde MP. 2005. Promoter occupancy is a major determinant of chromatin remodeling enzyme requirements. Mol Cell Biol 25:2698-2707.
22. Dong L, Wang W, Wang F, Stoner M, Reed JC, Harigai M, Samudio I, Kladde MP, Vyhlidal C, Safe S. 1999. Mechanisms of transcriptional activation of bcl-2 gene expression by 17b-estradiol in breast cancer cells. J Biol Chem 274:32099-32107.
23. Duan R, Porter W, Samudio I, Vyhlidal C, Kladde M, Safe S. 1999. Transcriptional activation of c-fos protooncogene by 17β-estradiol: Mechanism of aryl hydrocarbon receptor-mediated inhibition. Mol Endocrinol 13:1511-1521.
24. Fatemi M, Pao MM, Jeong S, Gal-Yam EN, Egger G, Weisenberger DJ, Jones PA. 2005. Footprinting of mammalian promoters: Use of a CpG DNA methyltransferase revealing nucleosome positions at a single molecule level. Nucleic Acids Res 33:e176.
25. Flick JT, Eissenberg JC, Elgin SC. 1986. Micrococcal nuclease as a DNA structural probe: Its recognition sequences, their genomic distribution and correlation with DNA structure determinants. J Mol Biol 190:619-633.
26. Fragoso G, John S, Roberts MS, Hager GL. 1995. Nucleosome positioning on the MMTV LTR results from the frequency-biased occupancy of multiple frames. Genes Dev 9:1933-1947.
27. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA 89:1827-1831.
28. Gal-Yam EN, Jeong S, Tanay A, Egger G, Lee AS, Jones PA. 2006. Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting. PLoS Genet 2:e160.
29. Gimelbrant A, Hutchinson JN, Thompson BR, Chess A. 2007. Widespread monoallelic expression on human autosomes. Science 318:1136-1140.
30. Hassan AH, Neely KE, Workman JL. 2001. Histone acetyltransferase complexes stabilize SWI/SNF binding to promoter nucleosomes. Cell 104:817-827.
31. Hassan AH, Prochasson P, Neely KE, Galasinski SC, Chandy M, Carrozza MJ, Workman JL. 2002. Function and selectivity of bromodomains in anchoring chromatin-modifying complexes to promoter nucleosomes. Cell 111:369-379.
32. Jessen WJ, Hoose SA, Kilgore JA, Kladde MP. 2006. Active PHO5 chromatin encompasses variable numbers of nucleosomes at individual promoters. Nat Struct Mol Biol 13:256-263.
33. Johnson DS, Mortazavi A, Myers RM, Wold B. 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science 316:1497-1502.
34. Jones PA, Baylin SB. 2007. The epigenomics of cancer. Cell 128:683-692.
35. Kilgore JA, Hoose SA, Gustafson TL, Porter W, Kladde MP. 2007. Single-molecule and population probing of chromatin structure using DNA methyltransferases. Methods 41:320-332.
36. Kladde MP, Simpson RT. 1994. Positioned nucleosomes inhibit Dam methylation in vivo. Proc Natl Acad Sci USA 91:1361-1365.
37. Kladde MP, Xu M, Simpson RT. 1996. Direct study of DNA-protein interactions in repressed and active chromatin in living cells. EMBO J 15:6290-6300.
38. Krueger C, Morison IM. 2008. Random monoallelic expression: Making a choice. Trends Genet.
39. Kuo MH, Zhou J, Jambeck P, Churchill ME, Allis CD. 1998. Histone acetyltransferase activity of yeast Gcn5p is required for the activation of target genes in vivo. Genes Dev 12:627-639.
40. Kusch T, Workman JL. 2007. Histone variants and complexes involved in their exchange. Subcell Biochem 41:91-109.
41. Lee CK, Shibata Y, Rao B, Strahl BD, Lieb JD. 2004. Evidence for nucleosome depletion at active regulatory regions genome-wide. Nat Genet 36:900-905.
42. Leuba SH, Bennink ML, Zlatanova J. 2004. Single-molecule analysis of chromatin. Methods Enzymol 376:73-105.
43. Li G, Levitus M, Bustamante C, Widom J. 2005. Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 12:46-53.
44. Lin JC, Jeong S, Liang G, Takai D, Fatemi M, Tsai YC, Egger G, Gal-Yam EN, Jones PA. 2007. Role of nucleosomal occupancy in the epigenetic silencing of the MLH1 CpG island. Cancer Cell 12:432-444.
45. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, Millar AH, Ecker JR. 2008. Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
46. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389:251-260.
47. Nourani A, Utley RT, Allard S, Côté J. 2004. Recruitment of the NuA4 complex poises the PHO5 promoter for chromatin remodeling and activation. EMBO J 23:2597-2607.
48. Pampin S, Rodriguez-Rey JC. 2007. Functional analysis of regulatory single-nucleotide polymorphisms. Curr Opin Lipidol 18:194-198.
49. Pennings S, Meersseman G, Bradbury EM. 1991. Mobility of positioned nucleosomes on 5 S rDNA. J Mol Biol 220:101-110.
50. Polach KJ, Widom J. 1995. Mechanism of protein access to specific DNA sequences in chromatin: A dynamic equilibrium model for gene regulation. J Mol Biol 254:130-149.
51. Raser JM, O'Shea EK. 2004. Control of stochasticity in eukaryotic gene expression. Science 304:1811-1814.
52. Reinke H, Hörz W. 2003. Histones are first hyperacetylated and then lose contact with the activated PHO5 promoter. Mol Cell 11:1599-1607.
53. Renbaum P, Abrahamove D, Fainsod A, Wilson G, Rottem S, Razin A. 1990. Cloning, characterization, and expression in Escherichia coli of the gene coding for the CpG DNA methylase from Spiroplasma sp. strain MQ1 (M.SssI). Nucleic Acids Res 18:1145-1152.
54. Robertson KD. 2005. DNA methylation and human disease. Nat Rev Genet 6:597-610.
55. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. 2007. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4:651-657.
56. Roh TY, Ngau WC, Cui K, Landsman D, Zhao K. 2004. High-resolution genome-wide mapping of histone modifications. Nat Biotechnol 22:1013-1016.
57. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. 2008. Dynamic regulation of nucleosome positioning in the human genome. Cell 132:887-898.
58. Simpson RT. 1998. Chromatin structure and analysis of mechanisms of activators and repressors. Methods 15:283-294.
59. Steger DJ, Haswell ES, Miller AL, Wente SR, O'Shea EK. 2003. Regulation of chromatin remodeling by inositol polyphosphates. Science 299:114-116.
60. Tse C, Sera T, Wolffe AP, Hansen JC. 1998. Disruption of higher-order folding by core histone acetylation dramatically enhances transcription of nucleosomal arrays by RNA polymerase III. Mol Cell Biol 18:4629-4638.
61. Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. 1995. Serial analysis of gene expression. Science 270:484-487.
62. Venter U, Svaren J, Schmitz J, Schmid A, Hörz W. 1994. A nucleosome precludes binding of the transcription factor Pho4 in vivo to a critical target site in the PHO5 promoter. EMBO J 13:4848-4855.
63. Xu M, Kladde MP, Van Etten JL, Simpson RT. 1998a. Cloning, characterization and expression of the gene coding for a cytosine-5-DNA methyltransferase recognizing GpC. Nucleic Acids Res 26:3961-3966.
64. Xu M, Simpson RT, Kladde MP. 1998b. Gal4p-mediated chromatin remodeling depends on binding site position in nucleosomes but does not require DNA replication. Mol Cell Biol 18:1201-1212.
65. Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309:626-630.
66. Zlatanova J, Leuba SH. 2003. Chromatin fibers, one-at-a-time. J Mol Biol 331:1-19.