A homogeneous method for investigation of methylation-dependent protein-protein interactions in epigenetics

Nucleic Acids Research

Volumn 38, Issue 2, 2009, Pages

  Quinn, Amy M ^a   Bedford, Mark T ^b   Espejo, Alexsandra ^b   Spannhoff, Astrid ^b   Austin, Christopher P ^a   Oppermann, Udo ^c,d   Simeonov, Anton ^a  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d NIHR OXFORD BIOMEDICAL RESEARCH CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

HETEROCHROMATIN PROTEIN 1; HISTONE; LYSINE; RAG2 PROTEIN; HETEROCHROMATIN SPECIFIC NONHISTONE CHROMOSOMAL PROTEIN HP 1; HETEROCHROMATIN-SPECIFIC NONHISTONE CHROMOSOMAL PROTEIN HP-1; MPP8 PROTEIN, HUMAN; NONHISTONE PROTEIN; PEPTIDE; PHOSPHOPROTEIN;

ARTICLE; BINDING AFFINITY; CHEMOLUMINESCENCE; CONTROLLED STUDY; ELECTRONICS; EPIGENETICS; GENE EXPRESSION PROFILING; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN METHYLATION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; SENSITIVITY ANALYSIS; BINDING COMPETITION; CHEMISTRY; GENETIC EPIGENESIS; METABOLISM; METHODOLOGY; METHYLATION; PROTEIN ANALYSIS;

BINDING, COMPETITIVE; CHEMILUMINESCENT MEASUREMENTS; CHROMOSOMAL PROTEINS, NON-HISTONE; EPIGENESIS, GENETIC; HISTONES; LYSINE; METHYLATION; PEPTIDES; PHOSPHOPROTEINS; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPPING;

EID: 77951161223     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp899     Document Type: Article

References (37)

1. Kouzarides, T. (2007) Chromatin modifications and their function. Cell, 128, 693-705.
2. Jenuwein, T. and Allis, C.D. (2001) Translating the histone code. Science, 293, 1074-1080.
3. Bannister, A.J., Zegerman, P., Partridge, J.F., Miska, E.A., Thomas, J.O., Allshire, R.C. and Kouzarides, T. (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature, 410, 120-124.
4. Schneider, R., Bannister, A.J. and Kouzarides, T. (2002) Unsafe SETs: histone lysine methyltransferases and cancer. Trends Biochem. Sci., 27, 396-402.
5. Noma, K., Allis, C.D. and Grewal, S.I. (2001) Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science, 293, 1150-1155.
6. Liang, G., Lin, J.C., Wei, V., Yoo, C., Cheng, J.C., Nguyen, C.T., Weisenberger, D.J., Egger, G., Takai, D., Gonzales, F.A. et al. (2004) Distinct localization of histone H3 acetylation and H3-K4 methylation to the transcription start sites in the human genome. Proc. Natl Acad. Sci. USA, 101, 7357-7362.
7. Pavri, R., Zhu, B., Li, G., Trojer, P., Mandal, S., Shilatifard, A. and Reinberg, D. (2006) Histone H2B monoubiquitination functions cooperatively with FACT to regulate elongation by RNA polymerase II. Cell, 125, 703-717.
8. Collins, R.E., Northrop, J.P., Horton, J.R., Lee, D.Y., Zhang, X., Stallcup, M.R. and Cheng, X. (2008) The ankyrin repeats of G9a and GLP histone methyltransferases are mono-and dimethyllysine binding modules. Nat. Struct. Mol. Biol., 15, 245-250.
9. Huyen, Y., Zgheib, O., Ditullio, R.A. Jr, Gorgoulis, V.G., Zacharatos, P., Petty, T.J., Sheston, E.A., Mellert, H.S., Stavridi, E.S. and Halazonetis, T.D. (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature, 432, 406-411
10. Pray-Grant, M.G., Daniel, J.A., Schieltz, D., Yates, J.R. III and Grant, P.A. (2005) Chd1 chromodomain links histone H3 methylation with SAGA-and SLIK-dependent acetylation. Nature, 433, 434-438.
11. Shi, X., Hong, T., Walter, K.L., Ewalt, M., Michishita, E., Hung, T., Carney, D., Pena, P., Lan, F., Kaadige, M.R. et al. (2006) ING2 PHD domain links histone H3 lysine 4 methylation to active gene repression. Nature, 442, 96-99.
12. Wysocka, J., Swigut, T., Xiao, H., Milne, T.A., Kwon, S.Y., Landry, J., Kauer, M., Tackett, A.J., Chait, B.T., Badenhorst, P. et al. (2006) A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling. Nature, 442, 86-90.
13. Kim, J., Daniel, J., Espejo, A., Lake, A., Krishna, M., Xia, L., Zhang, Y. and Bedford, M.T. (2006) Tudor, MBT and chromo domains gauge the degree of lysine methylation. EMBO Rep., 7, 397-403.
14. Ng, S.S., Yue, W.W., Oppermann, U. and Klose, R.J. (2009) Dynamic protein methylation in chromatin biology. Cell Mol. Life Sci., 66, 407-422.
15. Eftink, M.R. (1997) Fluorescence methods for studying equilibrium macromolecule-ligand interactions. Methods Enzymol., 278, 221-257.
16. Flanagan, J.F., Mi, L.Z., Chruszcz, M., Cymborowski, M., Clines, K.L., Kim, Y., Minor, W., Rastinejad, F. and Khorasanizadeh, S. (2005) Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature, 438, 1181-1185
17. Lin, C.W., Jao, C.Y. and Ting, A.Y. (2004) Genetically encoded fluorescent reporters of histone methylation in living cells. J. Am. Chem. Soc., 126, 5982-5983.
18. Fischle, W., Franz, H., Jacobs, S.A., Allis, C.D. and Khorasanizadeh, S. (2008) Specificity of the chromodomain Y chromosome family of chromodomains for lysine-methylated ARK(S/T) motifs. J. Biol. Chem., 283, 19626-19635.
19. Jacobs, S.A. and Khorasanizadeh, S. (2002) Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science, 295, 2080-2083.
20. Jacobs, S.A., Fischle, W. and Khorasanizadeh, S. (2004) Assays for the determination of structure and dynamics of the interaction of the chromodomain with histone peptides. Methods Enzymol., 376, 131-148.
21. Sun, B., Hong, J., Zhang, P., Dong, X., Shen, X., Lin, D. and Ding, J. (2008) Molecular basis of the interaction of Saccharomyces cerevisiae Eaf3 chromo domain with methylated H3K36. J. Biol. Chem., 283, 36504-36512.
22. Ullman, E.F., Kirakossian, H., Switchenko, A.C., Ishkanian, J., Ericson, M., Wartchow, C.A., Pirio, M., Pease, J., Irvin, B.R., Singh, S. et al. (1996) Luminescent oxygen channeling assay (LOCI): sensitive, broadly applicable homogeneous immunoassay method. Clin. Chem., 42, 1518-1526.
23. Cauchon, E., Liu, S., Percival, M.D., Rowland, S.E., Xu, D., Binkert, C., Strickner, P. and Falgueyret, J.P. (2009) Development of a homogeneous immunoassay for the detection of angiotensin I in plasma using AlphaLISA acceptor beads technology. Anal. Biochem., 388, 134-139.
24. Jacobs, S.A., Taverna, S.D., Zhang, Y., Briggs, S.D., Li, J., Eissenberg, J.C., Allis, C.D. and Khorasanizadeh, S. (2001) Specificity of the HP1 chromo domain for the methylated N-terminus of histone H3. EMBO J., 20, 5232-5241.
25. Huang, Y., Fang, J., Bedford, M.T., Zhang, Y. and Xu, R.M. (2006) Recognition of histone H3 lysine-4 methylation by the double tudor domain of JMJD2A. Science, 312, 748-751.
26. Lee, J., Thompson, J.R., Botuyan, M.V. and Mer, G. (2008) Distinct binding modes specify the recognition of methylated histones H3K4 and H4K20 by JMJD2A-tudor. Nat. Struct. Mol. Biol., 15, 109-111.
27. Simeonov, A., Jadhav, A., Thomas, C.J., Wang, Y., Huang, R., Southall, N.T., Shinn, P., Smith, J., Austin, C.P., Auld, D.S. et al. (2008) Fluorescence spectroscopic profiling of compound libraries. J. Med. Chem., 51, 2363-2371.
28. Feinberg, A.P. and Tycko, B. (2004) The history of cancer epigenetics. Nat. Rev. Cancer, 4, 143-153.
29. Klose, R.J. and Bird, A.P. (2006) Genomic DNA methylation: the mark and its mediators. Trends Biochem. Sci., 31, 89-97.
30. Suzuki, M.M. and Bird, A. (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat. Rev. Genet., 9, 465-476.
31. Seckl, J.R. and Holmes, M.C. (2007) Mechanisms of disease: glucocorticoids, their placental metabolism and fetal 'programming' of adult pathophysiology. Nat. Clin. Pract. Endocrinol. Metab., 3, 479-488.
32. Weaver, I.C. (2007) Epigenetic programming by maternal behavior and pharmacological intervention. Nature versus nurture: let's call the whole thing off. Epigenetics, 2, 22-28.
33. Cortez, C.C. and Jones, P.A. (2008) Chromatin, cancer and drug therapies. Mutat. Res., 647, 44-51.
34. Okada, Y., Feng, Q., Lin, Y., Jiang, Q., Li, Y., Coffield, V.M., Su, L., Xu, G. and Zhang, Y. (2005) hDOT1L links histone methylation to leukemogenesis. Cell, 121, 167-178.
35. Varambally, S., Dhanasekaran, S.M., Zhou, M., Barrette, T.R., Kumar-Sinha, C., Sanda, M.G., Ghosh, D., Pienta, K.J., Sewalt, R.G., Otte, A.P. et al. (2002) The polycomb group protein EZH2 is involved in progression of prostate cancer. Nature, 419, 624-629
36. Metzger, E., Wissmann, M., Yin, N., Muller, J.M., Schneider, R., Peters, A.H., Gunther, T., Buettner, R. and Schule, R. (2005) LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription. Nature, 437, 436-439
37. Baker, L.A., Allis, C.D. and Wang, G.G. (2008) PHD fingers in human diseases: disorders arising from misinterpreting epigenetic marks. Mutat. Res., 647, 3-12.