Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations

PLoS Computational Biology

Volumn 9, Issue 11, 2013, Pages

  Portella, Guillem ^a   Battistini, Federica ^a   Orozco, Modesto ^a,b  

^a INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^b UNIVERSITY OF BARCELONA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ALKYLATION; BIOINFORMATICS; DNA; GENE EXPRESSION; MOLECULAR DYNAMICS; PROTEINS;

DNA METHYLATION; DYNAMICS SIMULATION; ELASTIC DEFORMATION MODELS; EPIGENETICS; GENES EXPRESSION; MINOR GROOVES; NUCLEOSOMES; REGULATORY PROTEIN; SIMPLE++; THEORETICAL CALCULATIONS;

METHYLATION;

DNA BINDING PROTEIN;

ARTICLE; BINDING AFFINITY; CALCULATION; CHROMATIN STRUCTURE; COMPUTER SIMULATION; DNA METHYLATION; DNA SEQUENCE; EPIGENETICS; GENE ACTIVITY; GENE EXPRESSION REGULATION; GENETIC ASSOCIATION; MOLECULAR DYNAMICS; NUCLEOSOME; PROTEIN BINDING;

COMPUTATIONAL BIOLOGY; CYTOSINE; DNA METHYLATION; EPIGENESIS, GENETIC; MODELS, GENETIC; MOLECULAR DYNAMICS SIMULATION; NUCLEOSOMES; THERMODYNAMICS;

EID: 84888223867     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003354     Document Type: Article

References (45)

1. Ng HH, Bird A, (1999) DNA methylation and chromatin modification. Current opinion in genetics & development 9: 158-163.
2. Ehrlich M, Gama-Sosa MA, Huang LH, Midgett RM, Kuo KC, et al. (1982) Amount and distribution of 5-methylcytosine in human DNA from different types of tissues of cells. Nucleic acids research 10: 2709-2721.
3. Jones PA, Baylin SB, (2002) The fundamental role of epigenetic events in cancer. Nature reviews Genetics 3: 415-428 doi:10.1038/nrg816.
4. Jones PA, Baylin SB, (2007) The epigenomics of cancer. Cell 128: 683-692 doi:10.1016/j.cell.2007.01.029.
5. Baylin S, (2005) DNA methylation and gene silencing in cancer. Nature Clinical Practice Oncology 2: S4-S11 Available: http://www.nature.com/nrclinonc/journal/v2/n12s/full/ncponc0354.html. Accessed 24 December 2012.
6. Jaenisch R, Bird A, (2003) Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals. Nature genetics 33 Suppl: 245-254 doi:10.1038/ng1089.
7. Jones PA, (2012) Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature reviews Genetics 13: 484-492 doi:10.1038/nrg3230.
8. Heyn H, Esteller M, (2012) DNA methylation profiling in the clinic: applications and challenges. Nature Reviews Genetics 13: 679-692 doi:10.1038/nrg3270.
9. Sandoval J, Esteller M, (2012) Cancer epigenomics: beyond genomics. Current opinion in genetics & development 22: 50-55 doi:10.1016/j.gde.2012.02.008.
10. Vestergaard EM, Nexø E, Tørring N, Borre M, Ørntoft TF, et al. (2010) Promoter hypomethylation and upregulation of trefoil factors in prostate cancer. International journal of cancer Journal international du cancer 127: 1857-1865 doi:10.1002/ijc.25209.
11. Kass SU, Landsberger N, Wolffe AP, (1997) DNA methylation directs a time-dependent repression of transcription initiation. Current Biology 7: 157-165 doi:10.1016/S0960-9822(97)70086-1.
12. Venolia L, Gartler SM, (1983) Comparison of transformation efficiency of human active and inactive X-chromosomal DNA. Nature 302: 82-83 doi:10.1038/302082a0.
13. Hashimshony T, Zhang J, Keshet I, Bustin M, Cedar H, (2003) The role of DNA methylation in setting up chromatin structure during development. Nature genetics 34: 187-192 doi:10.1038/ng1158.
14. Ponzielli R, Boutros PC, Katz S, Stojanova A, Hanley AP, et al. (2008) Optimization of experimental design parameters for high-throughput chromatin immunoprecipitation studies. Nucleic acids research 36: e144 doi:10.1093/nar/gkn735.
15. Kaminsky ZA, Tang T, Wang S-C, Ptak C, Oh GHT, et al. (2009) DNA methylation profiles in monozygotic and dizygotic twins. Nature genetics 41: 240-245 doi:10.1038/ng.286.
16. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, et al. (2005) Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nature genetics 37: 853-862 doi:10.1038/ng1598.
17. Weber M, Hellmann I, Stadler MB, Ramos L, Pääbo S, et al. (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nature genetics 39: 457-466 doi:10.1038/ng1990.
18. Novak P, Jensen T, Oshiro MM, Watts GS, Kim CJ, et al. (2008) Agglomerative epigenetic aberrations are a common event in human breast cancer. Cancer research 68: 8616-8625 doi:10.1158/0008-5472.CAN-08-1419.
19. Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, et al. (2008) Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454: 766-770 doi:10.1038/nature07107.
20. Gu H, Bock C, Mikkelsen TS, Jäger N, Smith ZD, et al. (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nature methods 7: 133-136 doi:10.1038/nmeth.1414.
21. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature 462: 315-322 doi:10.1038/nature08514.
22. Serre D, Lee BH, Ting AH, (2010) MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic acids research 38: 391-399 doi:10.1093/nar/gkp992.
23. Ruike Y, Imanaka Y, Sato F, Shimizu K, Tsujimoto G, (2010) Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing. BMC genomics 11: 137 doi:10.1186/1471-2164-11-137.
24. Collings CK, Waddell PJ, Anderson JN, (2013) Effects of DNA methylation on nucleosome stability. Nucleic acids research 41: 1-14 Available: http://www.ncbi.nlm.nih.gov/pubmed/23355616. Accessed 27 February 2013.
25. Laird PW, (2010) Principles and challenges of genomewide DNA methylation analysis. Nature reviews Genetics 11: 191-203 doi:10.1038/nrg2732.
26. Das PM, Singal R, (2004) DNA methylation and cancer. Journal of clinical oncology: official journal of the American Society of Clinical Oncology 22: 4632-4642 doi:10.1200/JCO.2004.07.151.
27. Sharma S, Kelly TK, Jones PA, (2010) Epigenetics in cancer. Carcinogenesis 31: 27-36 doi:10.1093/carcin/bgp220.
28. Choy JS, Wei S, Lee JY, Tan S, Chu S, et al. (2010) DNA methylation increases nucleosome compaction and rigidity. Journal of the American Chemical Society 132: 1782-1783 Available: http://www.ncbi.nlm.nih.gov/pubmed/20095602.
29. Lee JY, Lee T-H, (2012) Effects of DNA methylation on the structure of nucleosomes. Journal of the American Chemical Society 134: 173-175 Available: http://dx.doi.org/10.1021/ja210273w. Accessed 21 August 2012.
30. Jimenez-Useche I, Ke J, Tian Y, Shim D, Howell SC, et al. (2013) DNA methylation regulated nucleosome dynamics. Scientific reports 3: 2121 Available: http://www.nature.com/srep/2013/130702/srep02121/full/srep02121.html#. Accessed 10 July 2013.
31. Pérez A, Castellazzi CL, Battistini F, Collinet K, Flores O, et al. (2012) Impact of Methylation on the Physical Properties of DNA. Biophysical Journal 102: 2140-2148 Available: http://dx.doi.org/10.1016/j.bpj.2012.03.056 Accessed 14 July 2012.
32. Jessen WJ, Dhasarathy A, Hoose SA, Carvin CD, Risinger AL, et al. (2004) Mapping chromatin structure in vivo using DNA methyltransferases. Methods (San Diego, Calif) 33: 68-80 Available: http://pubget.com/paper/15039089/Mapping_chromatin_structure_in_vivo_using_DNA_methyltransferases. Accessed 2 August 2012.
33. Chodavarapu RK, Feng S, Bernatavichute Y V, Chen P-Y, Stroud H, et al. (2010) Relationship between nucleosome positioning and DNA methylation. Nature 466: 388-392 Available: http://dx.doi.org/10.1038/nature09147. Accessed 15 May 2011.
34. Davey CA, Sargent DF, Luger K, Maeder AW, Richmond TJ, (2002) Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. Journal of molecular biology 319: 1097-1113 Available: http://dx.doi.org/10.1016/S0022-2836(02)00386-8. Accessed 14 November 2012.
35. Kirkwood JG, (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3: 300-313.
36. Lankas F, Sponer J, Langowski J, Cheatham TE 3rd, (2003) DNA basepair step deformability inferred from molecular dynamics simulations. Biophysical Journal 85: 2872-2883.
37. Olson WK, Gorin AA, Lu XJ, Hock LM, Zhurkin VB, (1998) DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America 95: 11163-11168.
38. Lavery R, Zakrzewska K, Beveridge D, Bishop TC, Case DA, et al. (2010) A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucleic acids research 38: 299-313 Available: http://nar.oxfordjournals.org/content/38/1/299. Accessed 15 November 2012.
39. Richmond TJ, Davey CA, (2003) The structure of DNA in the nucleosome core. Nature 423: 145-150 Available: http://www.ncbi.nlm.nih.gov/pubmed/12736678. Accessed 21 July 2012.
40. Calladine CR, Drew HR, Luisi BF, Travers AA (2004) Undertanding DNA. The Molecule and how it works. Third. San Diego, California: Elsevier Academic Press.
41. Davey CS, Pennings S, Reilly C, Meehan RR, Allan J, (2004) A determining influence for CpG dinucleotides on nucleosome positioning in vitro. Nucleic acids research 32: 4322-4331 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=514372&tool=pmcentrez&rendertype=abstract. Accessed 20 October 2011.
42. Zhang Y, Jurkowska R, Soeroes S, Rajavelu A, Dhayalan A, et al. (2010) Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail. Nucleic acids research 38: 4246-4253 Available: http://nar.oxfordjournals.org/content/38/13/4246. Accessed 3 August 2012.
43. Felle M, Hoffmeister H, Rothammer J, Fuchs A, Exler JH, (2011) Nucleosomes protect DNA from DNA methylation in vivo and in vitro. Nucleic Acids Research 39 (16):: 6956-69 doi:10.1093/nar/gkr263.
44. Lavery R, Moakher M, Maddocks JH, Petkeviciute D, Zakrzewska K, (2009) Conformational analysis of nucleic acids revisited: Curves+. Nucleic acids research 37: 5917-5929 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2761274&tool=pmcentrez&rendertype=abstract. Accessed 7 August 2013.
45. Deniz O, Flores O, Battistini F, Pérez A, Soler-López M, et al. (2011) Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC genomics 12: 489 Available: http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3224377&tool=pmcentrez&rendertype=abstract. Accessed 18 March 2013.