Abstract
Histone posttranslational modifications (PTMs) have a crucial role in chromatin regulation and dynamics. They are specifically bound by so-called reading domains, which mediate the biological effects of histone PTMs. On a similar note, antibodies are invaluable reagents in chromatin biology for the detection, characterization, and mapping of histone PTMs. Despite these central roles in chromatin research and biology, the specificity of many antibodies and reading domains has been insufficiently characterized and documented. Here we describe in detail the application of the MODified™ Histone Peptide Array for the investigation of the binding specificity of histone binding antibodies or domains. The array contains 384 histone tail peptides carrying 59 posttranslational modifications in different combinations which can be used to study the primary binding specificity, but at the same time also allow to determine the combinatorial effect of secondary marks on antibody or reading domain binding.
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References
Hubner MR, Spector DL (2010) Chromatin dynamics. Annu Rev Biophys 39:471–489
Luger K, Mader AW, Richmond RK et al (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251–260
Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693–705
Margueron R, Reinberg D (2010) Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet 11:285–296
Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395
Tan M, Luo H, Lee S et al (2011) Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification. Cell 146:1016–1028
Suva ML, Riggi N, Bernstein BE (2013) Epigenetic reprogramming in cancer. Science 339:1567–1570
Beck S, Rakyan VK (2008) The methylome: approaches for global DNA methylation profiling. Trends Genet 24:231–237
Huttenhofer A, Vogel J (2006) Experimental approaches to identify non-coding RNAs. Nucleic Acids Res 34:635–646
Bock I, Dhayalan A, Kudithipudi S et al (2011) Detailed specificity analysis of antibodies binding to modified histone tails with peptide arrays. Epigenetics 6:256–263
Egelhofer TA, Minoda A, Klugman S et al (2011) An assessment of histone-modification antibody quality. Nat Struct Mol Biol 18:91–93
Fuchs SM, Strahl BD (2011) Antibody recognition of histone post-translational modifications: emerging issues and future prospects. Epigenomics 3:247–249
Nishikori S, Hattori T, Fuchs SM et al (2012) Broad ranges of affinity and specificity of anti-histone antibodies revealed by a quantitative peptide immunoprecipitation assay. J Mol Biol 424:391–399
Peach SE, Rudomin EL, Udeshi ND et al (2012) Quantitative assessment of chromatin immunoprecipitation grade antibodies directed against histone modifications reveals patterns of co-occurring marks on histone protein molecules. Mol Cell Proteomics 11:128–137
Hattori T, Taft JM, Swist KM et al (2013) Recombinant antibodies to histone post-translational modifications. Nat Methods 10:992–995
Heubach Y, Planatscher H, Sommersdorf C et al (2013) From spots to beads-PTM-peptide bead arrays for the characterization of anti-histone antibodies. Proteomics 13:1010–1015
Taverna SD, Li H, Ruthenburg AJ et al (2007) How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol 14:1025–1040
Patel DJ, Wang Z (2013) Readout of epigenetic modifications. Annu Rev Biochem 82:81–118
Winkler DF, Hilpert K, Brandt O et al (2009) Synthesis of peptide arrays using SPOT-technology and the CelluSpots-method. Methods Mol Biol 570:157–174
Bock I, Kudithipudi S, Tamas R et al (2011) Application of Celluspots peptide arrays for the analysis of the binding specificity of epigenetic reading domains to modified histone tails. BMC Biochem 12:48
Dhayalan A, Tamas R, Bock I et al (2011) The ATRX-ADD domain binds to H3 tail peptides and reads the combined methylation state of K4 and K9. Hum Mol Genet 20:2195–2203
Kycia I, Kudithipudi S, Tamas R et al (2014) The Tudor domain of the PHD finger protein 1 is a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t. J Mol Biol 426:1651–1660
Pradeepa MM, Sutherland HG, Ule J et al (2012) Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet 8, e1002717
Du J, Zhong X, Bernatavichute YV et al (2012) Dual binding of chromomethylase domains to H3K9me2-containing nucleosomes directs DNA methylation in plants. Cell 151:167–180
Darvekar S, Johnsen SS, Eriksen AB et al (2012) Identification of two independent nucleosome-binding domains in the transcriptional co-activator SPBP. Biochem J 442:65–75
Kimura H (2013) Histone modifications for human epigenome analysis. J Hum Genet 58:439–445
Park S, Martinez-Yamout MA, Dyson HJ et al (2013) The CH2 domain of CBP/p300 is a novel zinc finger. FEBS Lett 587:2506–2511
Pestell RG, Yu Z (2014) Long and noncoding RNAs (lnc-RNAs) determine androgen receptor dependent gene expression in prostate cancer growth in vivo. Asian J Androl 16:268–269
Zucchelli C, Tamburri S, Quilici G et al (2014) Structure of human Sp140 PHD finger: an atypical fold interacting with Pin1. FEBS J 281:216–231
Alsarraj J, Faraji F, Geiger TR et al (2013) BRD4 short isoform interacts with RRP1B, SIPA1 and components of the LINC complex at the inner face of the nuclear membrane. PLoS One 8, e80746
Widiez T, Symeonidi A, Luo C et al (2014) The chromatin landscape of the moss Physcomitrella patens and its dynamics during development and drought stress. Plant J 79:67–81
Du J, Johnson LM, Groth M et al (2014) Mechanism of DNA methylation-directed histone methylation by KRYPTONITE. Mol Cell 55(3):495–504
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Work in the authors’ lab has been supported by the BMBF (0315886B).
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Kungulovski, G., Kycia, I., Mauser, R., Jeltsch, A. (2015). Specificity Analysis of Histone Modification-Specific Antibodies or Reading Domains on Histone Peptide Arrays. In: Houen, G. (eds) Peptide Antibodies. Methods in Molecular Biology, vol 1348. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-2999-3_24
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DOI: https://doi.org/10.1007/978-1-4939-2999-3_24
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-2998-6
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