Computational and experimental methods to decipher the epigenetic code

Frontiers in Genetics

Volumn 5, Issue SEP, 2014, Pages

  de Pretis, Stefano ^a   Pelizzola, Mattia ^a  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

Author keywords

Chromatin regulators; Chromatin state; Epigenetic code; Epigenome editing; Histone code; Histone mark

Indexed keywords

8 QUINOLINOL INDIUM IN 111; BESILESOMAB; DIGLYCINE TECHNETIUM TC 99M; ETIDRONIC ACID TC 99M; FANOLESOMAB TC 99M; FLUORODEOXYGLUCOSE F 18; GALLIUM CITRATE GA 67; HEXAMETHYLPROPYLENE AMINE OXIME TECHNETIUM TC 99M; SULESOMAB TC 99M;

ARTICLE; BACKACHE; BONE INFECTION; BONE SCINTISCANNING; CARDIAC IMPLANT; CARDIAC IMPLANTABLE ELECTRONIC DEVICE; CARDIOVASCULAR INFECTION; CLINICAL ASSESSMENT; DIAGNOSTIC ACCURACY; ECHOGRAPHY; ENDOCARDITIS; FOLLOW UP; GRAFT INFECTION; HUMAN; INFECTION; INFLAMMATION; INFLAMMATORY BOWEL DISEASE; NUCLEAR MAGNETIC RESONANCE IMAGING; OSTEOARTHRITIS; OSTEOMYELITIS; PANORAMIC RADIOGRAPHY; PREDICTIVE VALUE; PROSTHESIS INFECTION; RELIABILITY; SENSITIVITY AND SPECIFICITY; SINGLE PHOTON EMISSION COMPUTER TOMOGRAPHY; SOFT TISSUE INFECTION; SPONDYLODESIS;

EID: 84919500041     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2014.00335     Document Type: Article

References (51)

1. Akhtar, W., de Jong, J., Pindyurin, A. V., Pagie, L., Meuleman, W., de Ridder, J.,et al. (2013). Chromatin position effects assayed by thousands of reporters integrated in parallel. Cell 154, 914-927. doi: 10.1016/j.cell.2013.07.018
2. Akhtar, W., Pindyurin, A. V., de Jong, J., Pagie, L., Hoeve ten, J., Berns, A.,et al. (2014). Using TRIP for genome-wide position effect analysis in cultured cells. Nat. Protoc. 9, 1255-1281. doi: 10.1038/nprot.2014.072
3. Barratt, M. J., Hazzalin, C. A., Cano, E., and Mahadevan, L. C. (1994). Mitogen-stimulated phosphorylation of histone H3 is targeted to a small hyperacetylation-sensitive fraction. Proc. Natl. Acad. Sci. U.S.A. 91, 4781-4785. doi: 10.1073/pnas.91.11.4781
4. Baubec, T., and Schübeler, D. (2014). Genomic patterns and context specific interpretation of DNA methylation. Curr. Opin. Genet. Dev. 25, 85-92. doi: 10.1016/j.gde.2013.11.015
5. Blancafort, P., Jin, J., and Frye, S. (2013). Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol. Pharmacol. 83, 563-576. doi: 10.1124/mol.112.080697
6. Braunstein, M., Sobel, R. E., Allis, C. D., Turner, B. M., and Broach, J. R. (1996). Efficient transcriptional silencing in Saccharomyces cerevisiae requires a heterochromatin histone acetylation pattern. Mol. Cell. Biol. 16, 4349-4356.
7. Chen, C., Zhang, S., and Zhang, X. S. (2013). Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. Nucleic Acids Res. 41, 9230-9242. doi: 10.1093/nar/gkt712
8. De Rubertis, F., Kadosh, D., Henchoz, S., Pauli, D., Reuter, G., Struhl, K.,et al. (1996). The histone deacetylase RPD3 counteracts genomic silencing in Drosophila and yeast. Nature 384, 589-591. doi: 10.1038/384589a0
9. Dion, M. F., Altschuler, S. J., Wu, L. F., and Rando, O. J. (2005). Genomic characterization reveals a simple histone H4 acetylation code. Proc. Natl. Acad. Sci. U.S.A. 102, 5501-5506. doi: 10.1073/pnas.0500136102
10. Elsässer, S. J., Allis, C. D., and Lewis, P. W. (2011). Cancer. New epigenetic drivers of cancers. Science 331, 1145-1146. doi: 10.1126/science.1203280
11. Ernst, J., and Kellis, M. (2010). Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat. Biotechnol. 28, 817-825. doi: 10.1038/nbt.1662
12. Ernst, J., and Kellis, M. (2012). ChromHMM: automating chromatin-state discovery and characterization. Nat. Methods 9, 215-216. doi: 10.1038/nmeth.1906
13. Ernst, J., and Kellis, M. (2013). Interplay between chromatin state, regulator binding, and regulatory motifs in six human cell types. Genome Res. 23, 1142-1154. doi: 10.1101/gr.144840.112
14. Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B.,et al. (2011). Mapping and analysis of chromatin state dynamics in nine human cell types. Nature 473, 43-49. doi: 10.1038/nature09906
15. Fatica, A., and Bozzoni, I. (2013). Long non-coding RNAs: new players in cell differentiation and development. Nat. Rev. Genet. 15, 7-21. doi: 10.1038/nrg3606
16. Guttman, M., Amit, I., Garber, M., French, C., Lin, M. F., Feldser, D.,et al. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 457, 223-227. doi: 10.1038/nature07672
17. Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D.,et al. (2007). Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet. 39, 311-318. doi: 10.1038/ng1966
18. Hendzel, M. J., Wei, Y., Mancini, M. A., Van Hooser, A., Ranalli, T., Brinkley, B. R.,et al. (1997). Mitosis-specific phosphorylation of histone H3 initiates primarily within pericentromeric heterochromatin during G2 and spreads in an ordered fashion coincident with mitotic chromosome condensation. Chromosoma 106, 348-360. doi: 10.1007/s004120050256
19. Ho, L., and Crabtree, G. R. (2010). Chromatin remodelling during development. Nature 463, 474-484. doi: 10.1038/nature08911
20. Ho, L., Ronan, J. L., Wu, J., Staahl, B. T., Chen, L., Kuo, A.,et al. (2009). An embryonic stem cell chromatin remodeling complex, esBAF, is essential for embryonic stem cell self-renewal and pluripotency. Proc. Natl. Acad. Sci. U.S.A. 106, 5181-5186. doi: 10.1073/pnas.0812889106
21. Hon, G., Ren, B., and Wang, W. (2008). ChromaSig: a probabilistic approach to finding common chromatin signatures in the human genome. PLoS Comput. Biol. 4:e1000201. doi: 10.1371/journal.pcbi.1000201
22. Huff, J. T., Plocik, A. M., Guthrie, C., and Yamamoto, K. R. (2010). Reciprocal intronic and exonic histone modification regions in humans. Nat. Struct. Mol. Biol. 17, 1495-1499. doi: 10.1038/nsmb.1924
23. Keung, A. J., Bashor, C. J., Kiriakov, S., Collins, J. J., and Khalil, A. S. (2014). Using targeted chromatin regulators to engineer combinatorialand spatial transcriptional regulation. Cell 158, 110-120. doi: 10.1016/j.cell.2014.04.047
24. Kouzarides, T. (2007). Chromatin modifications and their function. Cell 128, 693-705. doi: 10.1016/j.cell.2007.02.005
25. Lasserre, J., Chung, H.-R., and Vingron, M. (2013). Finding associations among histone modifications using sparse partial correlation networks. PLoS Comput. Biol. 9:e1003168. doi: 10.1371/journal.pcbi.1003168
26. Lessard, J., Wu, J. I., Ranish, J. A., Wan, M., Winslow, M. M., Staahl, B. T.,et al. (2007). An essential switch in subunit composition of a chromatin remodeling complex during neural development. Neuron 55, 201-215. doi: 10.1016/j.neuron.2007.06.019
27. Lindroth, A. M., Shultis, D., Jasencakova, Z., Fuchs, J., Johnson, L., Schubert, D.,et al. (2004). Dual histone H3 methylation marks at lysines 9 and 27 required for interaction with CHROMOMETHYLASE3. EMBO J. 23, 4286-4296. doi: 10.1038/sj.emboj.7600430
28. Maeder, M. L., Angstman, J. F., Richardson, M. E., Linder, S. J., Cascio, V. M., Tsai, S. Q.,et al. (2013). Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat. Biotechnol. 31, 1137-1142. doi: 10.1038/nbt.2726
29. Martin, A. M., Pouchnik, D. J., Walker, J. L., and Wyrick, J. J. (2004). Redundant roles for histone H3 N-terminal lysine residues in subtelomeric gene repression in Saccharomyces cerevisiae. Genetics 167, 1123-1132. doi: 10.1534/genetics.104.026674
30. Mendenhall, E. M., Williamson, K. E., Reyon, D., Zou, J. Y., Ram, O., Joung, J. K.,et al. (2013). Locus-specific editing of histone modifications at endogenous enhancers. Nat. Biotechnol. 31, 1133-1136. doi: 10.1038/nbt.2701
31. Morinière, J., Rousseaux, S., Steuerwald, U., Soler-López, M., Curtet, S., Vitte, A.-L.,et al. (2009). Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461, 664-668. doi: 10.1038/nature08397
32. Nguyen, U. T. T., Bittova, L., Muller, M. M., Fierz, B., David, Y., Houck-Loomis, B.,et al. (2014). Accelerated chromatin biochemistry using DNA- barcoded nucleosome libraries. Nat. Methods 11, 834-840. doi: 10.1038/nmeth.3022
33. Pelizzola, M., and Ecker, J. R. (2011). The DNA methylome. FEBS Lett. 585, 1994-2000. doi: 10.1016/j.febslet.2010.10.061
34. Ram, O., Goren, A., Amit, I., Shoresh, N., Yosef, N., Ernst, J.,et al. (2011). Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell 147, 1628-1639. doi: 10.1016/j.cell.2011.09.057
35. Rando, O. J. (2012). Combinatorial complexity in chromatin structure and function: revisiting the histone code. Curr. Opin. Genet. Dev. 22, 148-155. doi: 10.1016/j.gde.2012.02.013
36. Rivenbark, A. G., Stolzenburg, S., Beltran, A. S., Yuan, X., Rots, M. G., Strahl, B. D.,et al. (2012). Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 7, 350-360. doi: 10.4161/epi.19507
37. Rivera, C. M., and Ren, B. (2013). Mapping human epigenomes. Cell 155, 39-55. doi: 10.1016/j.cell.2013.09.011
38. Rothbart, S. B., and Strahl, B. D. (2014). Interpreting the language of histone and DNA modifications. Biochim. Biophys. Acta 1839, 627-643. doi: 10.1016/j.bbagrm.2014.03.001
39. Ruthenburg, A. J., Li, H., Milne, T. A., Dewell, S., McGinty, R. K., Yuen, M.,et al. (2011). Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 145, 692-706. doi: 10.1016/j.cell.2011.03.053
40. Ruthenburg, A. J., Li, H., Patel, D. J., and Allis, C. D. (2007). Multivalent engagement of chromatin modifications by linked binding modules. Nat. Rev. Mol. Cell Biol. 8, 983-994. doi: 10.1038/nrm2298
41. Schreiber, S. L., and Bernstein, B. E. (2002). Signaling network model of chromatin. Cell 111, 771-778. doi: 10.1016/S0092-8674(02)01196-0
42. Strahl, B. D., and Allis, C. D. (2000). The language of covalent histone modifications. Nature 403, 41-45. doi: 10.1038/47412
43. Turner, B. M. (2007). Defining an epigenetic code. Nat. Cell Biol. 9, 2-6. doi: 10.1038/ncb0107-2
44. Voigt, P., Leroy, G., Drury, W. J. III., Zee, B. M., Son, J., Beck, D. B.,et al. (2012). Asymmetrically modified nucleosomes. Cell 151, 181-193. doi: 10.1016/j.cell.2012.09.002
45. Wang, C., Zhang, M. Q., and Zhang, Z. (2013). Computational identification of active enhancers in model organisms. Genomics Proteomics Bioinformatics 11, 142-150. doi: 10.1016/j.gpb.2013.04.002
46. Wei, Y., Yu, L., Bowen, J., Gorovsky, M. A., and Allis, C. D. (1999). Phosphorylation of histone H3 is required for proper chromosome condensation and segregation. Cell 97, 99-109. doi: 10.1016/S0092-8674(00)80718-7
47. Wu, W., Cheng, Y., Keller, C. A., Ernst, J., Kumar, S. A., Mishra, T.,et al. (2011). Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res. 21, 1659-1671. doi: 10.1101/gr.125088.111
48. Yan, Z., Wang, Z., Sharova, L., Sharov, A. A., Ling, C., Piao, Y.,et al. (2008). BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. Stem Cells 26, 1155-1165. doi: 10.1634/stemcells.2007-0846
49. Yu, H., Zhu, S., Zhou, B., Xue, H., and Han, J.-D. J. (2008). Inferring causal relationships among different histone modifications and gene expression. Genome Res. 18, 1314-1324. doi: 10.1101/gr.073080.107
50. Yuan, G.-C., Ma, P., Zhong, W., and Liu, J. S. (2006). Statistical assessment of the global regulatory role of histone acetylation in Saccharomyces cerevisiae. Genome Biol. 7, R70. doi: 10.1186/gb-2006-7-8-r70
51. Zhou, J., and Troyanskaya, O. G. (2014). Global quantitative modeling of chromatin factor interactions. PLoS Comput. Biol. 10:e1003525. doi: 10.1371/journal.pcbi.1003525