High resolution detection and analysis of CpG dinucleotides methylation using MBD-seq technology

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Lan, Xun ^a   Adams, Christopher ^b   Landers, Mark ^b   Dudas, Miroslav ^b   Krissinger, Daniel ^b   Marnellos, George ^b   Bonneville, Russell ^a   Xu, Maoxiong ^a   Wang, Junbai ^c   Huang, Tim H M ^a   Meredith, Gavin ^b   Jin, Victor X ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b Life Technologies   (United States)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; CPG DINUCLEOTIDE; DINUCLEOTIDE; GENOMIC DNA; METHYL CPG BINDING PROTEIN; UNCLASSIFIED DRUG; CYTIDYLYL 3' 5' GUANOSINE; CYTIDYLYL-3'-5'-GUANOSINE; DINUCLEOSIDE PHOSPHATE;

ARTICLE; BI ASSYMETRIC LAPLACE MODEL; CELL STRAIN MCF 7; CONTROLLED STUDY; CPG ISLAND; DATA ANALYSIS; DNA METHYLATION; EXPERIMENTAL DESIGN; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; IMAGE ANALYSIS; MATHEMATICAL MODEL; METHYL CPG BINDING DOMAIN PROTEIN SEQUENCE; MOLECULAR CLONING; PROCESS DEVELOPMENT; PROCESS OPTIMIZATION; SEQUENCE ANALYSIS; VALIDATION PROCESS; BIOLOGICAL MODEL; CELL LINE; GENETICS; METABOLISM; METHODOLOGY; MOLECULAR BIOLOGY;

CELL LINE; DINUCLEOSIDE PHOSPHATES; DNA METHYLATION; HUMANS; MODELS, BIOLOGICAL; MOLECULAR BIOLOGY;

EID: 79960115813     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022226     Document Type: Article

References (53)

1. Elnitski L, Jin VX, Farnham PJ, Jones SJ, (2006) Locating mammalian transcription factor binding sites: a survey of computational and experimental techniques. Genome Res 16: 1455-1464.
2. Kim TH, Barrera LO, Zheng M, Qu C, Singer MA, et al. (2005) A high-resolution map of active promoters in the human genome. Nature 436: 876-880.
3. Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ, (2002) Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev 16: 235-244.
4. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, et al. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409: 533-538.
5. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
6. Johnson DS, Mortazavi A, Myers RM, Wold B, (2007) Genome-wide mapping of in vivo protein-DNA interactions. Science 316: 1497-1502.
7. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 4: 651-657.
8. Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322.
9. Mikkelsen TS, Ku MC, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-U552.
10. Pan G, Tian S, Nie J, Yang C, Ruotti V, et al. (2007) Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell 1: 299-312.
11. Rauch T, Li H, Wu X, Pfeifer GP, (2006) MIRA-assisted microarray analysis, a new technology for the determination of DNA methylation patterns, identifies frequent methylation of homeodomain-containing genes in lung cancer cells. Cancer Res 66: 7939-7947.
12. Patra SK, Bettuzzi S, (2007) Epigenetic DNA-methylation regulation of genes coding for lipid raft-associated components: a role for raft proteins in cell transformation and cancer progression (review). Oncol Rep 17: 1279-1290.
13. Vaid M, Floros J, (2009) Surfactant protein DNA methylation: a new entrant in the field of lung cancer diagnostics? (Review). Oncol Rep 21: 3-11.
14. Jacinto FV, Ballestar E, Esteller M, (2008) Methyl-DNA immunoprecipitation (MeDIP): hunting down the DNA methylome. Biotechniques 44: 35, 37, 39 passim.
15. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, et al. (2008) A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol 26: 779-785.
16. Pomraning KR, Smith KM, Freitag M, (2009) Genome-wide high throughput analysis of DNA methylation in eukaryotes. Methods 47: 142-150.
17. Rauch TA, Pfeifer GP, (2010) DNA methylation profiling using the methylated-CpG island recovery assay (MIRA). Methods 52: 213-217.
18. 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 Res 38: 391-399.
19. Brinkman AB, Simmer F, Ma K, Kaan A, Zhu J, et al. (2010) Whole-genome DNA methylation profiling using MethylCap-seq. Methods 52: 232-236.
20. Lister R, O'Malley RC, Tonti-Filippini J, Gregory BD, Berry CC, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133: 523-536.
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.
22. Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215-219.
23. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
24. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 5: 829-834.
25. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K, (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36: 5221-5231.
26. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, et al. (2010) PICS: Probabilistic Inference for ChIP-seq. Biometrics.
27. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729-1730.
28. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, et al. (2008) An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 26: 1293-1300.
29. Zang C, Schones DE, Zeng C, Cui K, Zhao K, et al. (2009) A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 25: 1952-1958.
30. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M, (2008) Modeling ChIP sequencing in silico with applications. PLoS Comput Biol 4: e1000158.
31. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 27: 66-75.
32. Wilbanks EG, Facciotti MT, (2010) Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS One 5: e11471.
33. Choi JK, Bae JB, Lyu J, Kim TY, Kim YJ, (2009) Nucleosome deposition and DNA methylation at coding region boundaries. Genome Biol 10: R89.
34. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol 28: 1097-1105.
35. Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10 (3): R25.
36. Kharchenko PV, Tolstorukov MY, Park PJ, (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
37. Lan X, Bonneville R, Apostolos J, Wu W, Jin VX, (2011) W-ChIPeaks: a comprehensive web application tool for processing ChIP-chip and ChIP-seq data. Bioinformatics 27: 428-430.
38. Kotz S, Kozubowski TJ, Podgórski K, (2001) The Laplace distribution and generalizations: a revisit with applications to communications, economics, engineering, and finance Boston Birkhäuser pp. xviii 349.
39. Kotz S, Kozubowski TJ, Podgorski K, (2002) Maximum likelihood estimation of asymmetric Laplace parameters. Annals of the Institute of Statistical Mathematics 54: 816-826.
40. Fragiadakis K, Meintanis SG, (2008) Tests of Fit for Asymmetric Laplace Distributions with Applications on Financial Data. International Electronic Conference on Computer Science 1060: 121-124, 423.
41. Bruzzone L, Prieto DF, (2000) Automatic analysis of the difference image for unsupervised change detection. Ieee Transactions on Geoscience and Remote Sensing 38: 1171-1182.
42. Xuan GR, Zhang W, Chai PQ, (2001) EM algorithms of Gaussian Mixture Model and Hidden Markov Model. 2001 International Conference on Image Processing, Vol I, Proceedings pp. 145-148, 1133.
43. Schwarz G, (1978) Estimating the dimension of a model. The Annals of Statistics 6: 461-464.
44. Dai X, Erkkila T, Yli-Harja O, Lahdesmaki H, (2009) A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. BMC Bioinformatics 10: 165.
45. Dempster AP, Laird NM, Rubin DB, (1977) Maximum Likelihood from Incomplete Data Via Em Algorithm. Journal of the Royal Statistical Society Series B-Methodological 39: 1-38.
46. Redner RA, Walker HF, (1984) Mixture Densities, Maximum-Likelihood and the Em Algorithm. Siam Review 26: 195-237.
47. Jordan MI, Jacobs RA, (1994) Hierarchical Mixtures of Experts and the Em Algorithm. Neural Computation 6: 181-214.
48. Ball MP, Li JB, Gao Y, Lee JH, LeProust EM, et al. (2009) Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nat Biotechnol 27: 361-368.
49. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, et al. (2010) Dynamic changes in the human methylome during differentiation. Genome Res 20: 320-331.
50. Welboren WJ, van Driel MA, Janssen-Megens EM, van Heeringen SJ, Sweep FC, et al. (2009) ChIP-Seq of ERalpha and RNA polymerase II defines genes differentially responding to ligands. EMBO J 28: 1418-1428.
51. Volik S, Zhao S, Chin K, Brebner JH, Herndon DR, et al. (2003) End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A 100: 7696-7701.
52. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, et al. (2002) The human genome browser at UCSC. Genome Res 12: 996-1006.
53. Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE, (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730-2731.