Genome-wide localization of protein-DNA binding and histone modification by a bayesian change-point method with ChIP-seq data

PLoS Computational Biology

Volumn 8, Issue 7, 2012, Pages

  Xing, Haipeng ^a   Mo, Yifan ^a,b   Liao, Will ^a,b   Zhang, Michael Q ^b,c,d  

^a Stony Brook University   (United States)

^b Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^c TSINGHUA UNIVERSITY   (China)

^d UNIVERSITY OF TEXAS AT DALLAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BARIUM COMPOUNDS; GENE ENCODING; PROTEINS; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

BAYESIAN; CHANGE-POINTS; CHROMATIN IMMUNOPRECIPITATION; EXPLICIT FORMULA; HIDDEN-MARKOV MODELS; LOCALISATION; NEXT-GENERATION SEQUENCING; POINT METHODS; POSTERIOR MEANS; PROTEIN-DNA BINDING;

HIDDEN MARKOV MODELS;

HISTONE H3;

ACCURACY; ARTICLE; BAYESIAN CHANGE POINT METHOD; CHROMATIN IMMUNOPRECIPITATION; DATA ANALYSIS; HISTONE MODIFICATION; MATHEMATICAL MODEL; PROTEIN DNA BINDING; REPRODUCIBILITY; SEQUENCE ANALYSIS; STATISTICAL ANALYSIS;

EID: 84864587283     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002613     Document Type: Article

References (59)

1. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, et al. (2000) Genome-wide location and function of dna binding proteins. Science 290: 2306-2309.
2. Johnson DS, Mortazavi A, Myers RM, Wold B, (2007) Genome-wide mapping of in vivo protein-dna interactions. Science 316: 1497-1502.
3. Robertson, 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.
4. Barski, 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.
5. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
6. Chen X, Xu H, Yuan P, Fang F, Huss M, et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133: 1106-1117.
7. Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
8. Consortium TEP, (2011) A User's Guide to the Encyclopedia of DNA Elements (ENCODE). PLoS Biol 9: e1001046+.
9. Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, et al. (2010) The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol 28: 1045-1048.
10. Guttman M, Amit I, Garber M, French C, Lin MF, et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
11. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, et al. (2010) Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells. Cell Stem Cell 6: 479-491.
12. Kouzarides T, (2002) Histone methylation in transcriptional control. Curr Opin Genet Dev 12: 198-209.
13. Widschwendter M, Fiegl H, Egle D, Mueller-Holzner E, Spizzo G, et al. (2007) Epigenetic stem cell signature in cancer. Nat Genet 39: 157-158.
14. Zhang Z, Pugh BF, (2011) High-resolution genome-wide mapping of the primary structure of chromatin. Cell 144: 175-186.
15. Li B, Carey M, Workman JL, (2007) The Role of Chromatin during Transcription. Cell 128: 707-719.
16. Jenuwein T, Allis CD, (2001) Translating the histone code. Science 293: 1074-1080.
17. Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137+.
18. 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.
19. Qin Z, Yu J, Shen J, Maher C, Hu M, et al. (2010) HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinformatics 11: 369+.
20. Pepke S, Wold B, Mortazavi A, (2009) Computation for ChIP-seq and RNA-seq studies. Nat Methods 6: S22-S32.
21. Hawkins RD, Hon GC, Lee LK, Ngo Q, Lister R, et al. (2010) Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells. Cell Stem Cell 6: 479-491.
22. 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.
23. Song Q, Smith AD, (2011) Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics 27: 870-871.
24. Peng W, Zhao K, (2011) An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data. Genome Biol 12: 120+.
25. Lai TL, Xing H, (2011) A simple Bayesian approach to multiple change-points. Stat Sin 21: 539-569.
26. Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, et al. (2009) Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 41: 376-381.
27. Spyrou C, Stark R, Lynch AG, Tavaré S, (2009) BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics 10: 299+.
28. Martens JH, O'Sullivan RJ, Braunschweig U, Opravil S, Radolf M, et al. (2005) The profile of repeat-associated histone lysine methylation states in the mouse epigenome. EMBO J 24: 800-812.
29. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.
30. Ringrose L, (2007) Polycomb comes of age: genome-wide profiling of target sites. Curr Opin Cell Biol 19: 290-297.
31. Roh TY, Cuddapah S, Cui K, Zhao K, (2006) The genomic landscape of histone modifications in human T cells. Proc Natl Acad Sci U S A 103: 15782-15787.
32. Bernstein BE, Meissner A, Lander ES, (2007) The mammalian epigenome. Cell 128: 669-681.
33. Talbert PB, Henikoff S, (2006) Spreading of silent chromatin: inaction at a distance. Nat Rev Genet 7: 793-803.
34. Guenther MG, Young RA, (2010) Repressive transcription. Science 329: 150-151.
35. Hosey AM, Brand M, (2009) Chromodomain-mediated spreading on active genes. Nature Struct Mol Biol 16: 11-13.
36. Sural TH, Peng S, Li B, Workman JL, Park PJ, et al. (2008) The MSL3 chromodomain directs a key targeting step for dosage compensation of the Drosophila melanogaster X chromosome. Nature Struct Mol Biol 15: 1318-1325.
37. Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, et al. (2004) The UCSC Table Browser data retrieval tool. Nucleic Acids Res 32 Database issue: 493-496.
38. Pruitt KD, Tatusova T, Klimke W, Maglott DR, (2009) NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res 37: D32-D36.
39. Goecks J, Nekrutenko A, Taylor J, Team TG, (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 11: R86+.
40. Blankenberg D, Kuster GV, Coraor N, Ananda G, Lazarus R, et al. (2001) Galaxy: A Web-Based Genome Analysis Tool for Experimentalists. Curr Protoc Mol Biol Chapter 19: Unit 19.10.1-21.
41. Cui K, Zang C, Roh T, Schones D, Childs R, et al. (2009) Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation. Cell Stem Cell 4: 80-93.
42. Pauler FM, Sloane MA, Huang R, Regha K, Koerner MV, et al. (2009) H3K27me3 forms BLOCs over silent genes and intergenic regions and specifies a histone banding pattern on a mouse autosomal chromosome. Genome Res 19: 221-233.
43. Hon GC, Hawkins RD, Caballero OL, Lo C, Lister R, et al. (2011) Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer. Genome Res 22: 246-58.
44. Stitzel ML, Sethupathy P, Pearson DS, Chines PS, Song L, et al. (2010) Global epigenomic analysis of primary human pancreatic islets provides insights into type 2 diabetes susceptibility loci. Cell Metab 12: 443-455.
45. Wilbanks EG, Facciotti MT, (2010) Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE 5: e11471+.
46. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38: D105-D110.
47. Matys V, Fricke E, Geffers R, Gössling E, Haubrock M, et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31: 374-378.
48. Smith A, Sumazin P, Xuan Z, Zhang M, (2006) DNA motifs in human and mouse proximal promoters predict tissue-specific expression. Proc Natl Acad Sci U S A 103: 6275-6280.
49. Smith AD, Sumazin P, Das D, Zhang MQ, (2005) Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics 21 (Suppl 1): i403-12+.
50. Wilhelm BT, Marguerat S, Aligianni S, Codlin S, Watt S, et al. (2011) Differential patterns of intronic and exonic dna regions with respect to rna polymerase ii occupancy, nucleosome density and h3k36me3 marking in fission yeast. Genome Biol 12: R82.
51. Hansen KD, Wu Z, Irizarry RA, Leek JT, (2011) Sequencing technology does not eliminate biological variability. Nat Biotechol 29: 572-573.
52. Vega VB, Cheung E, Palanisamy N, Sung WKK, (2009) Inherent signals in sequencing-based Chromatin-ImmunoPrecipitation control libraries. PloS ONE 4: e5241+.
53. Dohm JC, Lottaz C, Borodina T, Himmelbauer H, (2008) Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 36: e105.
54. Meacham F, Boffelli D, Dhahbi J, Martin D, Singer M, et al. (2011) Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 12: 451+.
55. Hansen KD, Irizarry RA, Wu Z, (2012) Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics 13: 204-216.
56. Roberts A, Trapnell C, Donaghey J, Rinn J, Pachter L, et al. (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12: 1-14.
57. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
58. Cui K, Zang C, Roh T, Schones D, Childs R, et al. (2009) Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation. Cell Stem Cell 4: 80-93.
59. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifiations at human enhancers reect global cell-type-specific gene expression. Nature 459: 108-112.