Structure and function of protein modules in chromatin biology

Results and Problems in Cell Differentiation

Volumn 41, Issue , 2006, Pages 1-23

  Yap, Kyoko L ^a   Zhou, Ming Ming ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE; NONHISTONE PROTEIN;

ACETYLATION; ANIMAL; CHEMISTRY; CHROMATIN; HUMAN; METABOLISM; METHYLATION; PROTEIN BINDING; REVIEW;

ACETYLATION; ANIMALS; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; HISTONES; HUMANS; METHYLATION; PROTEIN BINDING;

EID: 33845189663     PISSN: 00801844     EISSN: 18610412     Source Type: Book Series    
DOI: 10.1007/400_010     Document Type: Review

References (121)

1. Aapola U, Liiv I, Peterson P (2002) Imprinting regulator DNMT3L is a transcriptional repressor associated with histone deacetylase activity. Nucleic Acids Res 30(16):3602-3608
2. Aasland R, Gibson TJ, Stewart AF (1995) The PHD finger: Implications for chromatinmediated transcriptional regulation. Trends Biochem Sci 20(2):56-59
3. Aasland R, Stewart AF (1995) The chromo shadow domain, a second chromo domain in heterochromatin-binding protein 1, HP1. Nucleic Acids Res 23(16):3168-3173
4. Akhtar A, Zink D, Becker PB (2000) Chromodomains are protein-RNA interaction modules. Nature 407(6802):405-409
5. Aravind L, Iyer LM (2002) The SWIRM domain: A conserved module found in chromosomal proteins points to novel chromatin-modifying activities. Genome Biol 3(8):RESEARCH0039
6. Aravind L, Koonin EV (1998) The HORMA domain: A common structural denominator in mitotic checkpoints, chromosome synapsis and DNA repair. Trends Biochem Sci 23(8):284-286
7. Arnan C et al. (2003) Interaction of nucleoplasmin with core histones. J Biol Chem 278(33):31319-31324
8. Aviv T, et al. (2006) Sequence-specific recognition of RNA hairpins by the SAM domain of Vts1p. Nat Struct Mol Biol 13(2):168-176.
9. Ball LJ et al. (1997) Structure of the chromatin binding (chromo) domain from mouse modifier protein 1. Embo J 16(9):2473-2481
10. Banerjee-Basu S et al. (1999) The Homeodomain Resource: Sequences, structures and genomic information. Nucleic Acids Res 27(1):336-337
11. Bannister AJ et al. (2001) Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410(6824):120-124
12. Bennett-Lovsey R et al. (2002) The SWIB and the MDM2 domains are homologous and share a common fold. Bioinformatics 18(4):626-630
13. Bordoli L et al. (2001) Functional analysis of the p300 acetyltransferase domain: The PHD finger of p300 but not of CBP is dispensable for enzymatic activity. Nucleic Acids Res 29(21):4462-4471
14. Bottomley MJ et al. (2001) The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation. Nat Struct Biol 8(7):626-633
15. Bottomley MJ (2004) Structures of protein domains that create or recognize histone modifications. EMBORep 5(5):464-469
16. Boyer LA et al. (2002) Essential role for the SANT domain in the functioning of multiple chromatin remodeling enzymes. Mol Cell 10(4):935-942
17. Boyer LA, Latek RR, Peterson CL (2004) The SANT domain: A unique histone-tail-binding module? Nat Rev Mol Cell Biol 5(2):158-163
18. Brahms H et al. (2001) Symmetrical dimethylation of arginine residues in spliceosomal Sm protein B/B′ and the Sm-like protein LSm4, and their interaction with the SMN protein. RNA 7(11):1531-1542
19. Brasher SV et al. (2000) The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer. Embo J 19(7):1587-1597
20. Callebaut I, Courvalin JC, Mornon JP (1999) The BAH (bromo-adjacent homology) domain: A link between DNA methylation, replication and transcriptional regulation. FEBS Lett 446(1):189-193
21. Cao R et al. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science 298(5595):1039-1043
22. Capili AD et al. (2001) Solution structure of the PHD domain from the KAP-1 corepressor: Structural determinants for PHD, RING and LIM zinc-binding domains. Embo J 20(1-2):165-177
23. Chavali GB et al. (2005) Crystal structure of the ENT domain of human EMSY. J Mol Biol 350(5):964-973
24. Col E et al. (2001) The histone acetyltransferase, hGCN5, interacts with and acetylates the HIV transactivator, Tat. J Biol Chem 276(30):28179-28184
25. Cote J, Richard S (2005) Tudor domains bind symmetrical dimethylated arginines. J Biol Chem 280(31):28476-28483
26. Dhalluin C et al. (1999) Structure and ligand of a histone acetyltransferase bromodomain. Nature 399(6735):491-496
27. Dorr A et al. (2002) Transcriptional synergy between Tat and PCAF is dependent on the binding of acetylated Tat to the PCAF bromodomain. Embo J 21(11):2715-2723
28. Dutta S et al. (2001) The crystal structure of nucleoplasmin-core: implications for histone binding and nucleosome assembly. Mol Cell 8(4):841-853
29. Eberharter A et al. (2001) Acf1, the largest subunit of CHRAC, regulates ISWI-induced nucleosome remodelling. Embo J 20(14):3781-3788
30. Eberharter A et al. (2004) ACF1 improves the effectiveness of nucleosome mobilization by ISWI through PHD-histone contacts. Embo J 23(20):4029-4039
31. Edwards TA et al. (2005) Solution Structure of the Vts1 SAM Domain in the Presence of RNA. J Mol Biol (in press)
32. Ekblad CM et al. (2005) Binding of EMSY to HP1beta: Implications for recruitment of HP1beta and BS69. EMBO Rep 6(7):675-680
33. Ekman D et al. (2005) Multi-domain proteins in the three kingdoms of life: Orphan domains and other unassigned regions. J Mol Biol 348(1):231-243
34. Fischle W, Wang Y, Jacobs SA, Kim Y, Allis CD, Khorasanizadeh S (2003) Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev 17(15):1870-1881
35. Friesen WJ et al. (2001) SMN, the product of the spinal muscular atrophy gene, binds preferentially to dimethylarginine-containing protein targets. Mol Cell 7(5):1111-1117
36. Ge YZ et al. (2004) Chromatin targeting of de novo DNA methyltransferases by the PWWP domain. J Biol Chem 279(24):25447-25454
37. Gibson TJ et al. (1998) The APECED polyglandular autoimmune syndrome protein, AIRE-1, contains the SAND domain and is probably a transcription factor. Trends Biochem Sci 23(7):242-244
38. Goodwin GH, Nicolas RH (2001) The BAH domain, polybromo and the RSC chromatin remodelling complex. Gene 268(1-2):1-7
39. Gozani O et al. (2003) The PHD finger of the chromatin-associated protein ING2 functions as a nuclear phosphoinositide receptor. Cell 114(1):99-111
40. Green JB et al. (2003) RNA recognition via the SAM domain of Smaug. Mol Cell 11(6):1537-1548
41. Grune T et al. (2003) Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cell 12(2):449-460
42. Halbach T, Scheer N, Werr W (2000) Transcriptional activation by the PHD finger is inhibited through an adjacent leucine zipper that binds 14-3-3 proteins. Nucleic Acids Res 28(18):3542-3550
43. Haynes SR et al. (1992) The bromodomain: A conserved sequence found in human, Drosophila and yeast proteins. Nucleic Acids Res 20(10):2603
44. Hennig L, Bouveret R, Gruissem W (2005) MSI1-like proteins: An escort service for chromatin assembly and remodeling complexes. Trends Cell Biol 15(6):295-302
45. Hou Z et al. (2005) Structural basis of the Sir1-origin recognition complex interaction in transcriptional silencing. Proc Natl Acad Sci USA 102(24):8489-8494
46. Hsu HC, Stillman B, Xu RM (2005) Structural basis for origin recognition complex 1 protein-silence information regulator 1 protein interaction in epigenetic silencing. Proc Natl Acad Sci USA 102(24):8519-8524
47. Hudson BP et al. (2000) Solution structure and acetyl-lysine binding activity of the GCN5 bromodomain. J Mol Biol 304:355-370
48. Huyen Y et al. (2004) Methylated lysine 79 of histone H3 targets 53BP1 to DNA double-strand breaks. Nature 432(7015):406-411
49. Ito T et al. (1996) ATP-facilitated chromatin assembly with a nucleoplasmin-like protein from Drosophila melanogaster. J Biol Chem 271(40):25041-25048
50. Ito T et al. (1999) ACF consists of two subunits, Acf1 and ISWI, that function cooperatively in the ATP-dependent catalysis of chromatin assembly. Genes Dev 13(12):1529-1539
51. Iwahara J et al. (2002) The structure of the Dead ringer-DNA complex reveals how AT-rich interaction domains (ARIDs) recognize DNA. Embo J 21(5):1197-1209
52. Jacobs SA, Khorasanizadeh S (2002) Structure of HP1 chromodomain bound to a lysine 9-methylated histone H3 tail. Science 295(5562):2080-2083
53. Jacobson RH et al. (2000) Structure and function of a human TAFII250 double bromo-domain module. Science 288:1422-1425
54. Jeanmougin F et al. (1997) The bromodomain revisited. Trends Biochem Sci 22(5):151-153
55. Johnson PE, Donaldson LW (2006) RNA recognition by the Vts1p SAM domain. Nat Struct Mol Biol 13(2):177-178.
56. Kalkhoven E et al. (2002) The PHD type zinc finger is an integral part of the CBP acetyltransferase domain. Mol Cell Biol 22(7):1961-1970
57. Kalkhoven E et al. (2003) Loss of CBP acetyltransferase activity by PHD finger mutations in Rubinstein-Taybi syndrome. Hum Mol Genet 12(4):441-450
58. Kanno T et al. (2004) Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. Mol Cell 13(1):33-43
59. Kasten M et al. (2004) Tandem bromodomains in the chromatin remodeler RSC recognize acetylated histone H3 Lys14. Embo J 23(6):1348-1359
60. Kim CA et al. (2002) The SAM domain of polyhomeotic forms a helical polymer. Nat Struct Biol 9(6):453-457
61. Kim CA et al. (2005) Structural organization of a Sex-comb-on-midleg/ polyhomeotic copolymer. J Biol Chem 280(30):27769-27775
62. Kim S et al. (2004) Structure and DNA-binding sites of the SWI1 AT-rich interaction domain (ARID) suggest determinants for sequence-specific DNA recognition. J Biol Chem 279(16):16670-16676
63. Kodandapani R et al. (1996) A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature 380(6573):456-460
64. Kortschak RD, Tucker PW, Saint R (2000) ARID proteins come in from the desert. Trends Biochem Sci 25(6):294-299
65. Kwan AH et al. (2003) Engineering a protein scaffold from a PHD finger. Structure (Camb) 11(7):803-813
66. Lachner M et al. (2001) Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins. Nature 410(6824):116-120
67. Ladurner AG et al. (2003) Bromodomains mediate an acetyl-histone encoded antisilencing function at heterochromatin boundaries. Mol Cell 11(2):365-376
68. Lu Z et al. (2002) The PHD domain of MEKK1 acts as an E3 ubiquitin ligase and mediates ubiquitination and degradation of ERK1/2. Mol Cell 9(5):945-956
69. Martinez-Campa C et al. (2004) Precise nucleosome positioning and the TATA box dictate requirements for the histone H4 tail and the bromodomain factor Bdf1. Mol Cell 15(1):69-81
70. Matangkasombut O, Buratowski S (2003) Different sensitivities of bromodomain factors 1 and 2 to histone H4 acetylation. Mol Cell 11(2):353-363
71. Maurer-Stroh S et al. (2003) The Tudor domain Royal Family: Tudor, plant Agenet, Chromo, PWWP and MBT domains. Trends Biochem Sci 28(2):69-74
72. Min J, Zhang Y, Xu RM (2003) Structural basis for specific binding of Polycomb chromodomain to histone H3 methylated at Lys 27. Genes Dev 17(15):1823-1828
73. Mujtaba S et al. (2002) Structural basis of lysine-acetylated HIV-1 Tat recognition by PCAF bromodomain. Mol Cell 9(3):575-586
74. Mujtaba S et al. (2004) Structural mechanism of the bromodomain of the coactivator CBP in p53 transcriptional activation. Mol Cell 13(2):251-263
75. Nakayama J et al. (2001) Role of histone H3 lysine 9 methylation in epigenetic control of heterochromatin assembly. Science 292(5514):110-113
76. Namboodiri VM et al. (2003) The crystal structure of Drosophila NLP-core provides insight into pentamer formation and histone binding. Structure (Camb) 11(2):175-186
77. Nameki N et al. (2005) Solution structure of the PWWP domain of the hepatoma-derived growth factor family. Protein Sci 14(3):756-764
78. Nielsen PR et al. (2002) Structure of the HP1 chromodomain bound to histone H3 methylated at lysine 9. Nature 416(6876):103-107
79. Nielsen PR et al. (2005) Structure of the chromo barrel domain from the MOF acetyltransferase. J Biol Chem 280(37):32326-32331
80. Noguchi E et al. (2003) Swi1 prevents replication fork collapse and controls checkpoint kinase Cds1. Mol Cell Biol 23(21):7861-7874
81. Oberstrass FC et al. (2006) Shape-specific recognition in the structure of the Vts1p SAM domain with RNA. Nat Struct Mol Biol 13(2):160-167.
82. Oliver AW et al. (2005) Crystal structure of the proximal BAH domain of the polybromo protein. Biochem J 389(Pt 3):657-664
83. Ornaghi P et al. (1999) The bromodomain of Gcn5p interacts in vitro with specific residues in the N terminus of histone H4. J Mol Biol 287(1):1-7
84. Owen DJ et al. (2000) The structural basis for the recognition of acetylated histone H4 by the bromodomain of histone acetyltransferase gcn5p. Embo J 19(22):6141-6149
85. Pak DT et al. (1997) Association of the origin recognition complex with heterochromatin and HP1 in higher eukaryotes. Cell 91(3):311-323
86. Pascual J et al. (2000) Structure of the PHD zinc finger from human Williams-Beuren syndrome transcription factor. J Mol Biol 304(5):723-729
87. Patsialou A, Wilsker D, Moran E (2005) DNA-binding properties of ARID family proteins. Nucleic Acids Res 33(1):66-80
88. Polesskaya A et al. (2001) Interaction between acetylated MyoD and the bromodomain of CBP and/or p300. Mol Cell Biol 21(16):5312-5320
89. Poot RA et al. (2000) HuCHRAC, a human ISWI chromatin remodelling complex contains hACF1 and two novel histone-fold proteins. Embo J 19(13):3377-3387
90. Pray-Grant MG et al. (2005) Chd1 chromodomain links histone H3 methylation with SAGA- and SLIK-dependent acetylation. Nature 433(7024):434-438
91. Qian C et al. (2005) Structure and chromosomal DNA binding of the SWIRM domain. Nat Struct Mol Biol 12(12):1078-1085
92. Qiao F, Bowie JU (2005) The many faces of SAM. Sci STKE 2005(286):rE7
93. Qiu C et al. (2002) The PWWP domain of mammalian DNA methyltransferase Dnmt3b defines a new family of DNA-binding folds. Nat Struct Biol 9(3):217-224
94. Ragvin A et al. (2004) Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300. J Mol Biol 337(4):773-788
95. Ramakrishnan V et al. (1993) Crystal structure of globular domain of histone H5 and its implications for nucleosome binding. Nature 362(6417):219-223
96. Roth SY, Denu JM, Allis CD (2001) Histone acetyltransferases. Annu Rev Biochem 70:81-120
97. Sathyamurthy A et al. (2003) Crystal structure of the malignant brain tumor (MBT) repeats in Sex Comb on Midleg-like 2 (SCML2). J Biol Chem 278(47):46968-46973
98. Selenko P et al. (2001) SMN tudor domain structure and its interaction with the Sm proteins. Nat Struct Biol 8(1):27-31
99. Shamay M et al. (2002) Hepatitis B virus pX interacts with HBXAP, a PHD finger protein to coactivate transcription. J Biol Chem 277(12):9982-9988
100. Shi Y et al. (2004) Histone demethylation mediated by the nuclear amine oxidase homolog LSD1. Cell 119(7):941-953
101. Simic R et al. (2003) Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. Embo J 22(8):1846-1856
102. Slater LM, Allen MD, Bycroft M (2003) Structural variation in PWWP domains. J Mol Biol 330(3):571-576
103. Smith TF et al. (1999) The WD repeat: A common architecture for diverse functions. Trends Biochem Sci 24(5):181-185
104. Stec I et al. (2000) The PWWP domain: A potential protein-protein interaction domain in nuclear proteins influencing differentiation? FEBS Lett 473(1):1-5
105. Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403(6765):41-45
106. Surdo PL et al. (2003) Crystal structure and nuclear magnetic resonance analyses of the SAND domain from glucocorticoid modulatory element binding protein-1 reveals deoxyribonucleic acid and zinc binding regions. Mol Endocrinol 17(7):1283-1295
107. Thiru A et al. (2004) Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin. Embo J 23(3):489-499
108. Turner BM (2002) Cellular memory and the histone code. Cell 111(3):285-291
109. Vermaak D et al. (1999) Functional analysis of the SIN3-histone deacetylase RPD3-RbAp48-histone H4 connection in the Xenopus oocyte. Mol Cell Biol 19(9):5847-5860
110. Verreault A et al. (1998) Nucleosomal DNA regulates the core-histone-binding subunit of the human Hat1 acetyltransferase. Curr Biol 8(2):96-108
111. Wang WK et al. (2003) Malignant brain tumor repeats: A three-leaved propeller architecture with ligand/peptide binding pockets. Structure (Camb) 11(7):775-789
112. Wilsker D et al. (2004) The DNA-binding properties of the ARID-containing subunits of yeast and mammalian SWI/SNF complexes. Nucleic Acids Res 32(4):1345-1353
113. Wilsker D et al. (2005) Nomenclature of the ARID family of DNA-binding proteins. Genomics 86(2):242-251
114. Wood LD et al. (2003) Small ubiquitin-like modifier conjugation regulates nuclear export of TEL, a putative tumor suppressor. Proc Natl Acad Sci USA 100(6):3257-3262
115. Wysocka J et al. (2005) WDR5 associates with histone H3 methylated at K4 and is essential for H3 K4 methylation and vertebrate development. Cell 121(6):859-872
116. Yu J et al. (2003) A SANT motif in the SMRT corepressor interprets the histone code and promotes histone deacetylation. Embo J 22(13):3403-3410
117. Zeng L, Zhou MM (2002) Bromodomain: An acetyl-lysine binding domain. FEBS Lett 513(1):124-128
118. Zhang Z et al. (2002) Structure and function of the BAH-containing domain of Orc1p in epigenetic silencing. Embo J 21(17):4600-4611
119. Zheng N et al. (1999) Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev 13(6):666-674
120. Zhou Y, Grummt I (2005) The PHD finger/bromodomain of NoRC interacts with acetylated histone H4K16 and is sufficient for rDNA silencing. Curr Biol 15(15):1434-1438
121. Zhu L et al. (2001) Dynamics of the Mrf-2 DNA-binding domain free and in complex with DNA. Biochemistry 40(31):9142-9150