Recognition of non-methyl histone marks

Current Opinion in Structural Biology

Volumn 21, Issue 6, 2011, Pages 761-766

  Bycroft, Mark ^a  

^a MRC LABORATORY OF MOLECULAR BIOLOGY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; HISTONE;

ADENOSINE DIPHOSPHATE RIBOSYLATION; CHROMATIN; COMPLEX FORMATION; DNA REPAIR; DNA REPLICATION; HISTONE ACETYLATION; HISTONE MODIFICATION; HISTONE UBIQUITINATION; NONHUMAN; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROCESSING; REVIEW; TRANSCRIPTION REGULATION;

ACETYLATION; ANIMALS; DNA REPLICATION; HISTONES; HUMANS; MODELS, MOLECULAR; PHOSPHORYLATION; PROTEIN CONFORMATION; PROTEIN PROCESSING, POST-TRANSLATIONAL; UBIQUITINATION;

EUKARYOTA;

EID: 82955195929     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2011.09.006     Document Type: Review

References (47)

1. Bannister A.J., Kouzarides T. Regulation of chromatin by histone modifications. Cell Res 2011, 21:381-395.
2. Campos E.I., Reinberg D. Histones: annotating chromatin. Annu Rev Genet 2009, 43:559-599.
3. Chi P., Allis C.D., Wang G.G. Covalent histone modifications-miswritten, misinterpreted and mis-erased in human cancers. Nat Rev Cancer 2010, 10:457-469.
4. Yun M., Wu J., Workman J.L., Li B. Readers of histone modifications. Cell Res 2011, 21:564-578.
5. Mujtaba S., Zeng L., Zhou M.M. Structure and acetyl-lysine recognition of the bromodomain. Oncogene 2007, 26:5521-5527.
6. Varela I., Tarpey P., Raine K., Huang D., Ong C.K., Stephens P., Davies H., Jones D., Lin M.L., Teague J., et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011, 469:539-542.
7. Charles G.M., Chen C., Shih S.C., Collins S.R., Beltrao P., Zhang X., Sharma T., Tan S., Burlingame A.L., Krogan N.J., et al. Site-specific acetylation mark on an essential chromatin-remodeling complex promotes resistance to replication stress. Proc Natl Acad Sci U S A 2011.
8. Moriniere J., Rousseaux S., Steuerwald U., Soler-Lopez M., Curtet S., Vitte A.L., Govin J., Gaucher J., Sadoul K., Hart D.J., et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 2009, 461:664-668.
9. Lamonica J.M., Deng W., Kadauke S., Campbell A.E., Gamsjaeger R., Wang H., Cheng Y., Billin A.N., Hardison R.C., Mackay J.P., et al. Bromodomain protein Brd3 associates with acetylated GATA1 to promote its chromatin occupancy at erythroid target genes. Proc Natl Acad Sci U S A 2011, 108:E159-E168.
10. Nicodeme E., Jeffrey K.L., Schaefer U., Beinke S., Dewell S., Chung C.W., Chandwani R., Marazzi I., Wilson P., Coste H., et al. Suppression of inflammation by a synthetic histone mimic. Nature 2010, 468:1119-1123.
11. Filippakopoulos P., Qi J., Picaud S., Shen Y., Smith W.B., Fedorov O., Morse E.M., Keates T., Hickman T.T., Felletar I., et al. Selective inhibition of BET bromodomains. Nature 2010, 468:1067-1073.
12. Chung C.W., Coste H., White J.H., Mirguet O., Wilde J., Gosmini R.L., Delves C., Magny S.M., Woodward R., Hughes S.A., et al. Discovery and characterization of small molecule inhibitors of the BET family bromodomains. J Med Chem 2011, 54:3827-3838.
13. Wang Z., Patel D.J. Combinatorial readout of dual histone modifications by paired chromatin-associated modules. J Biol Chem 2011, 286:18363-18368.
14. Li H., Ilin S., Wang W., Duncan E.M., Wysocka J., Allis C.D., Patel D.J. Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF. Nature 2006, 442:91-95.
15. Wang Z., Song J., Milne T.A., Wang G.G., Li H., Allis C.D., Patel D.J. Pro isomerization in MLL1 PHD3-bromo cassette connects H3K4me readout to CyP33 and HDAC-mediated repression. Cell 2010, 141:1183-1194.
16. Tsai W.W., Wang Z., Yiu T.T., Akdemir K.C., Xia W., Winter S., Tsai C.Y., Shi X., Schwarzer D., Plunkett W., et al. TRIM24 links a non-canonical histone signature to breast cancer. Nature 2010, 468:927-932.
17. Ruthenburg A.J., Li H., Milne T.A., Dewell S., McGinty R.K., Yuen M., Ueberheide B., Dou Y., Muir T.W., Patel D.J., et al. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 2011, 145:692-706.
18. Zeng L., Zhang Q., Li S., Plotnikov A.N., Walsh M.J., Zhou M.M. Mechanism and regulation of acetylated histone binding by the tandem PHD finger of DPF3b. Nature 2010, 466:258-262.
19. Baek S.H. When signaling kinases meet histones and histone modifiers in the nucleus. Mol Cell 2011, 42:274-284.
20. Drobic B., Perez-Cadahia B., Yu J., Kung S.K., Davie J.R. Promoter chromatin remodeling of immediate-early genes is mediated through H3 phosphorylation at either serine 28 or 10 by the MSK1 multi-protein complex. Nucleic Acids Res 2010, 38:3196-3208.
21. Macdonald N., Welburn J.P., Noble M.E., Nguyen A., Yaffe M.B., Clynes D., Moggs J.G., Orphanides G., Thomson S., Edmunds J.W., et al. Molecular basis for the recognition of phosphorylated and phosphoacetylated histone h3 by 14-3-3. Mol Cell 2005, 20:199-211.
22. Zippo A., Serafini R., Rocchigiani M., Pennacchini S., Krepelova A., Oliviero S. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 2009, 138:1122-1136.
23. Wang F., Dai J., Daum J.R., Niedzialkowska E., Banerjee B., Stukenberg P.T., Gorbsky G.J., Higgins J.M. Histone H3 Thr-3 phosphorylation by Haspin positions Aurora B at centromeres in mitosis. Science 2010, 330:231-235.
24. Kelly A.E., Ghenoiu C., Xue J.Z., Zierhut C., Kimura H., Funabiki H. Survivin reads phosphorylated histone H3 threonine 3 to activate the mitotic kinase Aurora B. Science 2010, 330:235-239.
25. Yamagishi Y., Honda T., Tanno Y., Watanabe Y. Two histone marks establish the inner centromere and chromosome bi-orientation. Science 2010, 330:239-243.
26. Eckelman B.P., Drag M., Snipas S.J., Salvesen G.S. The mechanism of peptide-binding specificity of IAP BIR domains. Cell Death Differ 2008, 15:920-928.
27. Polo S.E., Jackson S.P. Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications. Genes Dev 2011, 25:409-433.
28. Stucki M., Clapperton J.A., Mohammad D., Yaffe M.B., Smerdon S.J., Jackson S.P. MDC1 directly binds phosphorylated histone H2AX to regulate cellular responses to DNA double-strand breaks. Cell 2005, 123:1213-1226.
29. Cook P.J., Ju B.G., Telese F., Wang X., Glass C.K., Rosenfeld M.G. Tyrosine dephosphorylation of H2AX modulates apoptosis and survival decisions. Nature 2009, 458:591-596.
30. Xiao A., Li H., Shechter D., Ahn S.H., Fabrizio L.A., Erdjument-Bromage H., Ishibe-Murakami S., Wang B., Tempst P., Hofmann K., et al. WSTF regulates the H2A.X. DNA damage response via a novel tyrosine kinase activity. Nature 2009, 457:57-62.
31. Stante M., Minopoli G., Passaro F., Raia M., Vecchio L.D., Russo T. Fe65 is required for Tip60-directed histone H4 acetylation at DNA strand breaks. Proc Natl Acad Sci U S A 2009, 106:5093-5098.
32. Campbell S.J., Edwards R.A., Glover J.N. Comparison of the structures and peptide binding specificities of the BRCT domains of MDC1 and BRCA1. Structure 2010, 18:167-176.
33. Weake V.M., Workman J.L. Histone ubiquitination: triggering gene activity. Mol Cell 2008, 29:653-663.
34. Chatterjee C., McGinty R.K., Fierz B., Muir T.W. Disulfide-directed histone ubiquitylation reveals plasticity in hDot1L activation. Nat Chem Biol 2010, 6:267-269.
35. Richly H., Rocha-Viegas L., Ribeiro J.D., Demajo S., Gundem G., Lopez-Bigas N., Nakagawa T., Rospert S., Ito T., Di Croce L. Transcriptional activation of polycomb-repressed genes by ZRF1. Nature 2010, 468:1124-1128.
36. Al-Hakim A., Escribano-Diaz C., Landry M.C., O'Donnell L., Panier S., Szilard R.K., Durocher D. The ubiquitous role of ubiquitin in the DNA damage response. DNA Repair (Amst) 2010, 9:1229-1240.
37. Sato Y., Yoshikawa A., Mimura H., Yamashita M., Yamagata A., Fukai S. Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80. EMBO J 2009, 28:2461-2468.
38. Ji Y., Tulin A.V. The roles of PARP1 in gene control and cell differentiation. Curr Opin Genet Dev 2010, 20:512-518.
39. Hottiger M.O. ADP-ribosylation of histones by ARTD1: An additional module of the histone code?. FEBS Lett 2010, 585:1595-1599.
40. Eustermann S., Brockmann C., Mehrotra P.V., Yang J.C., Loakes D., West S.C., Ahel I., Neuhaus D. Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Nat Struct Mol Biol 2010, 17:241-243.
41. Karras G.I., Kustatscher G., Buhecha H.R., Allen M.D., Pugieux C., Sait F., Bycroft M., Ladurner A.G. The macro domain is an ADP-ribose binding module. EMBO J 2005, 24:1911-1920.
42. Timinszky G., Till S., Hassa P.O., Hothorn M., Kustatscher G., Nijmeijer B., Colombelli J., Altmeyer M., Stelzer E.H., Scheffzek K., et al. A macrodomain-containing histone rearranges chromatin upon sensing PARP1 activation. Nat Struct Mol Biol 2009, 16:923-929.
43. Ahel D., Horejsi Z., Wiechens N., Polo S.E., Garcia-Wilson E., Ahel I., Flynn H., Skehel M., West S.C., Jackson S.P., et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme ALC1. Science 2009, 325:1240-1243.
44. Gottschalk A.J., Timinszky G., Kong S.E., Jin J., Cai Y., Swanson S.K., Washburn M.P., Florens L., Ladurner A.G., Conaway J.W., et al. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci U S A 2009, 106:13770-13774.
45. Sakabe K., Wang Z., Hart G.W. Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc Natl Acad Sci U S A 2010, 107:19915-19920.
46. Chatterjee C., Muir T.W. Chemical approaches for studying histone modifications. J Biol Chem 2010, 285:11045-11050.
47. Neumann H., Hancock S.M., Buning R., Routh A., Chapman L., Somers J., Owen-Hughes T., van Noort J., Rhodes D., Chin J.W. A method for genetically installing site-specific acetylation in recombinant histones defines the effects of H3 K56 acetylation. Mol Cell 2009, 36:153-163.