A Global Genome Segmentation Method for Exploration of Epigenetic Patterns

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Steiner, Lydia ^a   Hopp, Lydia ^a   Wirth, Henry ^a   Galle, Jörg ^a   Binder, Hans ^a   Prohaska, Sonja J ^a   Rohlf, Thimo ^a,b  

^a UNIVERSITY OF LEIPZIG   (Germany)

^b MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3;

ANIMAL CELL; ARTICLE; CELL TYPE; CONTROLLED STUDY; EPIGENETICS; FIBROBLAST; GENE EXPRESSION; GENE MAPPING; GENETIC ALGORITHM; GENETIC PROCEDURES; GENETIC REGULATION; GENOME SEGMENTATION; HISTONE METHYLATION; HISTONE MODIFICATION; HOUSEKEEPING GENE; MOUSE; NONHUMAN; X CHROMOSOME;

ALGORITHMS; ANIMALS; CELL DIFFERENTIATION; CELL LINEAGE; DNA METHYLATION; EPIGENESIS, GENETIC; EPIGENOMICS; GENES, ESSENTIAL; GENOME; HISTONES; MICE;

EID: 84867412914     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046811     Document Type: Article

References (42)

1. ENCODE Project Consortium (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447: 799-816.
2. ENCODE Project Consortium (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol 9: e1001046.
3. Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-80.
4. Metzker ML, (2010) Sequencing technologies- the next generation. Nat Rev Genet 11: 31-46.
5. Schübeler D, MacAlpine DM, Scalzo D, Wirbelauer C, Kooperberg C, et al. (2004) The histone modification pattern of active genes revealed through genome-wide chromatin analysis of a higher eukaryote. Genes Dev 18: 1263-71.
6. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, et al. (2005) Genomic maps and comparative analysis of histone modifications in human and mouse. Cell 120: 169-81.
7. 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: 876-80.
8. Hashimoto H, Vertino PM, Cheng X, (2010) Molecular coupling of DNA methylation and histone methylation. Epigenomics 2: 657-669.
9. 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: 15782-7.
10. Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, et al. (2006) A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell 125: 315-26.
11. Mikkelsen TS, KuM, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-60.
12. Collas P, (2009) Epigenetic states in stem cells. Biochim Biophys Acta 1790: 900-5.
13. Cheng X, Blumenthal RM, (2010) Coordinated chromatin control: structural and functional linkage of DNA and histone methylation. Biochemistry 49: 2999-3008.
14. Mohn F, Schbeler D, (2009) Genetics and epigenetics: stability and plasticity during cellular differentiation. Trends Genet 25: 129-36.
15. 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: 823-37.
16. Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, et al. (2008) Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet 40: 897-903.
17. Latham JA, Dent SY, (2007) Cross-regulation of histone modifications. Nat Struct Mol Biol 14: 1017-24.
18. Mardis ER, (2007) ChIP-seq: welcome to the new frontier. Nat Methods 4: 613-4.
19. Asp P, Blum R, Vethantham V, Parisi F, Micsinai M, et al. (2011) Genome-wide remodeling of the epigenetic landscape during myogenic differentiation. Proc Natl Acad Sci U S A 108: E149-58.
20. Park SJ, Nakai K, (2011) A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. BMC Bioinformatics 12 (Suppl 1):: S50.
21. Hebenstreit D, Gu M, Haider S, Turner DJ, Liò P, et al. (2011) EpiChIP: gene-by-gene quantification of epigenetic modification levels. Nucleic Acids Res 39: e27.
22. Statham AL, Strbenac D, Coolen MW, Stirzaker C, Clark SJ, et al. (2010) Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26: 1662-3.
23. Karlić R, Chung HR, Lasserre J, Vlahovicek K, Vingron M, (2010) Histone modification levels are predictive for gene expression. Proc Natl Acad Sci U S A 107: 2926-31.
24. Eichler GS, Huang S, Ingber DE, (2003) Gene expression dynamics inspector (gedi): for integrative analysis of expression profiles. Bioinformatics 19: 2321-2.
25. Wirth H, Lffler M, von Bergen M, Binder H, (2011) Expression cartography of human tissues using self organizing maps. BMC Bioinformatics 12: 306.
26. Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, et al. (2009) Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 5: e1000502.
27. Kohonen T, (1990) The self-organizing map. Proceedings of the IEEE 78: 1464-1480.
28. Vesanto J, Alhoniemi E, (2000) Clustering of the self-organizing map. IEEE Trans Neural Netw 11: 586-600.
29. Vesanto J, (1999) SOM-Based Data Visualization Methods. Intelligent Data Analysis 3: 111-126.
30. Dodd IB, Micheelsen MA, Sneppen K, Thon G, (2007) Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell 129: 813-22.
31. Rohlf T, Steiner L, Przybilla J, Prohaska S, Binder H, et al. (2012) Modeling the dynamic epigenome: from histone modifications towards self-organizing chromatin. Epigenomics 4: 205-19.
32. Allen MD, Grummitt CG, Hilcenko C, Min SY, Tonkin LM, et al. (2006) Solution structure of the nonmethyl-cpg-binding cxxc domain of the leukaemia-associated mll histone methyltransferase. EMBO J 25: 4503-12.
33. Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, et al. (2008) Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet 4: e1000242.
34. De Ferrari L, Aitken S, (2006) Mining housekeeping genes with a Naive Bayes classifier. BMC Genomics 7: 277.
35. Ernst J, Kellis M, (2010) Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol 28: 817-25.
36. Ernst J, Kellis M, (2012) Chromhmm: automating chromatin-state discovery and characterization. Nat Methods 9: 215-6.
37. Hon G, Ren B, Wang W, (2008) Chromasig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput Biol 4: e1000201.
38. Gehlenborg N, O'Donoghue SI, Baliga NS, Goesmann A, Hibbs MA, et al. (2010) Visualization of omics data for systems biology. Nat Methods 7: S56-68.
39. NIH Roadmap Epigenomics Mapping Consortium (2009) Roadmap Epigenomics Project Website. Available: http://www.roadmapepigenomics.org. Accessed 2012 Sep 11.
40. International Human Epigenome Consortium (2010) Human Epigenome Project Website. Available: http://www.epigenome.org. Accessed 2012 Sep 11.
41. Erwin E, Obermayer K, Schulten K, (1992) Self-organizing maps: stationary states, metastability and convergence rate. Biol Cybern 67: 35-45.
42. Fasold M, Stadler PF, Binder H, (2010) G-stack modulated probe intensities on expression arrays- sequence corrections and signal calibration. BMC Bioinformatics 11: 207.