Modeling, simulation and analysis of methylation profiles from reduced representation bisulfite sequencing experiments

Statistical Applications in Genetics and Molecular Biology

Volumn 12, Issue 6, 2013, Pages 723-742

  Lacey, Michelle R ^a,b   Baribault, Carl ^b   Ehrlich, Melanie ^b,c  

^a Tulane University   (United States)

^b TULANE UNIVERSITY SCHOOL OF MEDICINE   (United States)

^c TULANE UNIVERSITY HEALTH SCIENCES CENTER   (United States)

Author keywords

DMR detection; DNA methylation; RRBS; Simulation; Statistical methods

Indexed keywords

BISULFITE;

ARTICLE; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; HUMAN; MUSCLE CELL; MUSCLE DEVELOPMENT; REDUCED REPRESENTATION BISULFITE SEQUENCING;

CELLS, CULTURED; COMPUTER SIMULATION; CPG ISLANDS; DNA METHYLATION; GENE ONTOLOGY; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; MUSCLE DEVELOPMENT; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84888168160     PISSN: None     EISSN: 15446115     Source Type: Journal    
DOI: 10.1515/sagmb-2013-0027     Document Type: Article

References (43)

1. Akalin, A., F. Garrett-Bakelman, M. Kormaksson, J. Busuttil, L. Zhang, I. Khrebtukova, T. Milne, Y. Huang, D. Biswas, J. Hess, C. Allis, R. Roeder, P. Valk, B. Löwenberg, R. Delwel, H. Fernandez, E. Paietta, M. Tallman, G. Schroth, C. Mason, A. Melnick and M. Figueroa (2012a): "Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia," PLoS Genet., 8, e1002781.
2. Akalin, A., M. Kormaksson, S. Li, F. Garrett-Bakelman, M. Figueroa, A. Melnick and C. Mason (2012b): "Methylkit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles," Genome Biol., 13, R87.
3. Benjamini, Y. and Y. Hochberg (1995): "Controlling the false discovery rate: a practical and powerful approach to multiple testing," J. Roy. Stat. Soc. B., 57, 289-300.
4. Berman, B., D. Weisenberger, J. Aman, T. Hinoue, Z. Ramjan, Y. Liu, H. Noushmehr, C. Lange, C. van Dijk, R. Tollenaar, D. V. D. Berg and P. Laird (2012): "Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains," Nat. Genet., 44, 40-46.
5. Bock, C., E. Tomazou, A. Brinkman, F. Müller, F. Simmer, H. Gu, N. Jäger, A. Gnirke, H. Stunnenberg and A. Meissner (2010): "Quantitative comparison of genome-wide DNA methylation mapping technologies," Nat. Biotechnol., 28, 1106-1114.
6. Chou, R. H., Y. L. Yu and M. C. Hung (2011): "The roles of EZH2 in cell lineage commitment," Am. J. Transl. Res., 3, 243-250.
7. Coulombe, Y., M. Lemieux, J. Moreau, J. Aubin, M. Joksimovic, F. A. Berube-Simard, S. Tabaries, O. Boucherat, F. Guillou, C. Larochelle, C. K. Tuggle and L. Jeannotte (2010): "Multiple promoters and alternative splicing: Hoxa5 transcriptional complexity in the mouse embryo," PLoS One, 5, e10600.
8. Fong, A. P., Z. Yao, J. W. Zhong, Y. Cao, W. L. Ruzzo, R. C. Gentleman and S. J. Tapscott (2012): "Genetic and epigenetic determinants of neurogenesis and myogenesis," Dev. Cell, 22, 721-735.
9. Gentleman, R. C., V. J. Carey, D. M. Bates and others (2004): "Bioconductor: Open software development for computational biology and bioinformatics," Genome Biol., 5, R80. URL http://genomebiology.com/2004/5/ 10/R80.
10. Hansen, K., B. Langmead and R. Irizarry (2012): "Bsmooth: from whole genome bisulfite sequencing reads to differentially methylated regions," Genome Biol., 13, R83.
11. Harte, D. (2012): HiddenMarkov: Hidden Markov Models, Statistics Research Associates, Wellington. URL http://cran.at.r-project.org/web/packages/ HiddenMarkov, R package version 1.7-0.
12. Hartung, T., L. Zhang, R. Kanwar, I. Khrebtukova, M. Reinhardt, C. Wang, T. Therneau, M. Banck, G. Schroth and A. Beutler (2012): "Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue," Epigenetics, 7, 421-428.
13. Hebestreit, K., M. Dugas and H. U. Klein (2013): "Detection of significantly differentially methylated regions in targeted bisulfite sequencing data," Bioinformatics, 29, 1647-1653.
14. Hofert, M., I. Kojadinovic, M. Maechler and J. Yan (2012): Copula: Multivariate Dependence with Copulas. URL http://CRAN.Rproject.org/package= copula, R package version 0.999-5.
15. Huang, D., B. Sherman and R. Lempicki (2009a): "Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists," Nucleic Acids Res., 37, 1-13.
16. Huang, D., B. Sherman and R. Lempicki (2009b): "Systematic and integrative analysis of large gene lists using DAVID Bioinformatics resources," Nat. Protocols, 4, 44-57.
17. Hupkes, M., M. K. Jonsson, W. J. Scheenen, W. van Rotterdam, A. M. Sotoca, E. P. van Someren, M. A. van der Heyden, T. A. van Veen, R. I. van Ravestein-van Os, S. Bauerschmidt, E. Piek, D. L. Ypey, E. J. van Zoelen and K. J. Dechering (2011): "Epigenetics: DNA demethylation promotes skeletal myotube maturation," FASEB J., 25, 3861-3872.
18. Inose, H., H. Ochi, A. Kimura, K. Fujita, R. Xu, S. Sato, M. Iwasaki, S. Sunamura, Y. Takeuchi, S. Fukumoto, K. Saito, T. Nakamura, H. Siomi, H. Ito, Y. Arai, K. Shinomiya and S. Takeda (2009): "A microRNA regulatory mechanism of osteoblast differentiation," Proc. Natl. Acad. Sci. USA, 106, 20794-20799.
19. Kane, M. J. and J. W. Emerson (2011): Bigmemory: Manage massive matrices with shared memory and memory-mapped files. URL http://CRAN.R-project.org/ package=bigmemory, R package version 4.2.11.
20. Kojadinovic, I. and J. Yan (2010): "Modeling multivariate distributions with continuous margins using the copula R package," J. Stat. Software, 34, 1-20, URL http://www.jstatsoft.org/v34/i09/.
21. Laird, P. (2010): "Principles and challenges of genomewide DNA methylation analysis," Nat. Rev. Genet., 11, 191-203.
22. Lawrence, M., R. Gentleman and V. Carey (2009): "rtracklayer: an R package for interfacing with genome browsers," Bioinformatics, 25, 1841-1842, URL http://bioinformatics.oxfordjournals.org/content/25/14/1841. abstract.
23. Li, S., F. E. Garrett-Bakelman, A. Akalin, P. Zumbo, R. Levine, B. L. To, I. D. Lewis, A. L. Brown, R. J. D'Andrea, A. Melnick and C. E. Mason (2013): "An optimized algorithm for detecting and annotating regional differential methylation," BMC Bioinformatics, 14 Suppl 5, S10.
24. Lister, R., M. Pelizzola, R. Dowen, R. Hawkins, G. Hon, J. Tonti-Filippini, J. Nery, L. Lee, Z. Ye, Q. Ngo, L. Edsall, J. Antosiewicz-Bourget, R. Stewart, V. Ruotti, A. Millar, J. Thomson, B. Ren and J. Ecker (2009): "Human DNA methylomes at base resolution show widespread epigenomic differences," Nature, 462, 315-322.
25. Maconochie, M., S. Nonchev, A. Morrison and R. Krumlauf (1996): "Paralogous Hox genes: function and regulation," Annu. Rev. Genet., 30, 529-556.
26. Meissner, A., T. Mikkelsen, H. Gu, M. Wernig, J. Hanna, A. Sivachenko, X. Zhang, B. Bernstein, C. Nusbaum, D. Jaffe, A. Gnirke, R. Jaenisch and E. Lander (2007): "Genome-scale DNA methylation maps of pluripotent and differentiated cells," Nature, 454, 766-770.
27. Mercer, T. R., D. J. Gerhardt, M. E. Dinger, J. Crawford, C. Trapnell, J. A. Jeddeloh, J. S. Mattick and J. L. Rinn (2012): "Targeted RNA sequencing reveals the deep complexity of the human transcriptome," Nat. Biotechnol., 30, 99-104.
28. Nelsen, R. B. (1999): An Introduction to Copulas, Lecture Notes in Statistics, vol. 139, Springer: New York, USA.
29. Ng, C., F. Yildirim, Y. Yap, S. Dalin, B. Matthews, P. Velez, A. Labadorf, D. Housman and E. Fraenkel (2013): "Extensive changes in DNA methylation are associated with expression of mutant huntingtin," Proc. Natl. Acad. Sci. USA, 110, 2354-2359.
30. Pedersen, B. S., D. A. Schwartz, I. V. Yang and K. J. Kechris (2012): "Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values," Bioinformatics, 28, 2986-2988.
31. Ramachandrareddy, H., A. Bouska, Y. Shen, M. Ji, A. Rizzino, W. C. Chan and T. W. McKeithan (2010): "BCL6 promoter interacts with far upstream sequences with greatly enhanced activating histone modifications in germinal center B cells," Proc. Natl. Acad. Sci. USA, 107, 11930-11935.
32. R Core Team (2012): R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing, Vienna, Austria, URL http://www.R-project.org/, ISBN 3-900051-07-0.
33. Rosca, A. M. and A. Burlacu (2011): "Effect of 5-azacytidine: evidence for alteration of the multipotent ability of mesenchymal stem cells," Stem Cells Dev., 20, 1213-1221.
34. Schlather, M., P. Menck, R. Singleton, B. Pfaff and R. C. team (2013): RandomFields: simulation and analysis of random fields, URL http://CRAN.R- project.org/package=RandomFields, R package version 2.0.66.
35. Schoofs, T., C. Rohde, K. Hebestreit, H. U. Klein, S. Gollner, I. Schulze, M. Lerdrup, N. Dietrich, S. Agrawal-Singh, A. Witten, M. Stoll, E. Lengfelder, W. K. Hofmann, P. Schlenke, T. Buchner, K. Hansen, W. E. Berdel, F. Rosenbauer, M. Dugas and C. Muller-Tidow (2013): "DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding," Blood, 121, 178-187.
36. Sessa, L., A. Breiling, G. Lavorgna, L. Silvestri, G. Casari and V. Orlando (2007): "Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster," RNA, 13, 223-239.
37. Tsumagari, K., S. Chang, M. Lacey, C. Baribault, S. Chittur, J. Sowden, R. Tawil, G. Crawford and M. Ehrlich (2011): "Gene expression during normal and FSHD myogenesis," BMC Medical Genomics, 4, 67.
38. Tsumagari, K., C. Baribault, J. Terragni, K. Varley, J. Gertz, S. Pradhan, M. Badoo, C. Crain, L. Song, G. Crawford, R. Myers, M. Lacey and M. Ehrlich (2013): "Early de novo DNA methylation and prolonged demethylation in the muscle lineage," Epigenetics, 8, 317-332.
39. Varley, K., J. Gertz, K. Bowling, S. Parker, T. Reddy, F. Pauli-Behn, M. Cross, B. Williams, J. Stamatoyannopoulos, G. Crawford, D. Absher, B. Wold and R. Myers (2013): "Dynamic DNA methylation across diverse human cell lines and tissues," Genome Res., 23, 555-567.
40. von Maltzahn, J., N. Chang, C. Bentzinger and M. Rudnicki (2012a): "Wnt signaling in myogenesis," Trends Cell Biol., 22, 602-609.
41. von Maltzahn, J., J. Renaud, G. Parise and M. Rudnicki (2012b): "Wnt7a treatment ameliorates muscular dystrophy," Proc. Natl. Acad. Sci. USA, 109, 20614-20619.
42. Zaykin, D., L. Zhivotovsky, P. Westfall and B. Weir (2002): "Truncated product method for combining p-values," Genetic Epidemiol., 22, 170-185.
43. Zhang, Y., H. Liu, J. Lv, X. Xiao, J. Zhu, X. Liu, J. Su, X. Li, Q. Wu, F. Wang and Y. Cui (2011): "QDMR: a quantitative method for identification of differentially methylated regions by entropy," Nucleic Acids Res., 39, e58.