Regulation of histone deacetylase activities

Journal of Cellular Biochemistry

Volumn 93, Issue 1, 2004, Pages 57-67

  Sengupta, Nilanjan ^a   Seto, Edward ^a  

^a H LEE MOFFITT CANCER CENTER AND RESEARCH INSTITUTE   (United States)

Author keywords

Chromatin; Gene regulation; HDAC; Histone deacetylation; Post translational modification; Protein protein interaction; Subcellular localization

Indexed keywords

HISTONE DEACETYLASE; HISTONE DEACETYLASE INHIBITOR; PEPTIDE HYDROLASE;

ARTICLE; CARCINOGENESIS; CELL CYCLE REGULATION; CELL DIFFERENTIATION; CELL PROLIFERATION; CELLULAR DISTRIBUTION; CHROMATIN STRUCTURE; ENZYME ACTIVITY; ENZYME REGULATION; GENE CONTROL; HUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN EXPRESSION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; TRANSCRIPTION REGULATION; ANIMAL; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; PROTEIN TRANSPORT; REVIEW;

ANIMALS; GENE EXPRESSION REGULATION, ENZYMOLOGIC; HISTONE DEACETYLASES; HUMANS; PEPTIDE HYDROLASES; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN TRANSPORT;

EID: 13844252820     PISSN: 07302312     EISSN: 10974644     Source Type: Journal    
DOI: 10.1002/jcb.20179     Document Type: Article

References (103)

1. Ajuh PM, Browne GJ, Hawkes NA, Cohen PT, Roberts SG, Lamond AI. 2000. Association of a protein phosphatase 1 activity with the human factor C1 (HCF) complex. Nucleic Acids Res 28:678-686.
2. Alland L, Muhle R, Hou H, Jr., Potes J, Chin L, Schreiber-Agus N, DePinho RA. 1997. Role for N-CoR and histone deacetylase in Sin3-mediated transcriptional repression. Nature 387:49-55.
3. Alland L, David G, Shen-Li H, Potes J, Muhle R, Lee HC, Hou H, Jr., Chen K, DePinho RA. 2002. Identification of mammalian Sds3 as an integral component of the Sin3/histone deacetylase corepressor complex. Mol Cell Biol 22:2743-2750.
4. Anderson RM, Bitterman KJ, Wood JG, Medvedik O, Sinclair DA. 2003. Nicotinamide and PNC1 govern Iifespan extension by calorie restriction in Saccharomyces cerevisiae. Nature 423:181-185.
5. Ayer DE. 1999. Histone deacetylases: Transcriptional repression with SINers and NuRDs. Trends Cell Biol 9:193-198.
6. Baek SH, Ohgi KA, Rose DW, Koo EH, Glass CK, Rosenfeld MG. 2002. Exchange of N-CoR corepressor and Tip60 coactivator complexes links gene expression by NF-kappaB and beta-amyloid precursor protein. Cell 110:55-67.
7. Bartl S, Taplick J, Lagger G, Khier H, Kuchler K, Seiser C. 1997. Identification of mouse histone deacetylase 1 as a growth factor-inducible gene. Mol Cell Biol 17:5033-5043.
8. Becker PB, Horz W. 2002. ATP-dependent nucleosome remodeling. Annu Rev Biochem 71:247-273.
9. Berger SL. 2002. Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12:142-148.
10. Bitterman KJ, Anderson RM, Cohen HY, Latorre-Esteves M, Sinclair DA. 2002. Inhibition of silencing and accelerated aging by nicotinamide, a putative negative regulator of yeast sir2 and human SIRT1. J Biol Chem 277:45099-45107.
11. Brosch G, Georgieva EI, Lopez-Rodas G, Lindner H, Loidl P. 1992. Specificity of Zea mays histone deacetylase is regulated by phosphorylation. J Biol Chem 267:20561-20564.
12. Brush MH, Guardiola A, Connor JH, Yao TP, Shenolikar S. 2004. Deactylase inhibitors disrupt cellular complexes containing protein phosphatases and deacetylases. J Biol Chem 279:7685-7691.
13. Cai R, Kwon P, Yan-Neale Y, Sambuccetti L, Fischer D, Cohen D. 2001. Mammalian histone deacetylase 1 protein is posttranslationally modified by phosphorylation. Biochem Biophys Res Commun 283:445-453.
14. Canettieri G, Morantte I, Guzman E, Asahara H, Herzig S, Anderson SD, Yates JR, Montminy M. 2003. Attenuation of a phosphorylation-dependent activator by an HDAC-PP1 complex. Nat Struct Biol 10:175-181.
15. Carmen AA, Griffin PR, Calaycay JR, Rundlett SE, Suka Y, Grunstein M. 1999. Yeast HOS3 forms a novel trichostatin A-insensitive homodimer with intrinsic histone deacetylase activity. Proc Natl Acad Sci USA 96:12356-12361.
16. Colombo R, Boggio R, Seiser C, Draetta GF, Chiocca S. 2002. The adenovirus protein Gam1 interferes with sumoylation of histone deacetylase 1. EMBO Rep 3:1062-1068.
17. Cress WD, Seto E. 2000. Histone deacetylases, transcriptional control, and cancer. J Cell Physiol 184:1-16.
18. Dangond F, Hafler DA, Tong JK, Randall J, Kojima R, Utku N, Gullans SR. 1998. Differential display cloning of a novel human histone deacetylase (HDAC3) cDNA from PHA-activated immune cells. Biochem Biophys Res Commun 242:648-652.
19. Darkin-Rattray SJ, Gurnett AM, Myers RW, Dulski PM, Crumley TM, Allocco JJ, Cannova C, Meinke PT, Colletti SL, Bednarek MA, Singh SB, Goetz MA, Dombrowski AW, Polishook JD, Schmatz DM. 1996. Apicidin: A novel antiprotozoal agent that inhibits parasite histone deacetylase. Proc Natl Acad Sci USA 93:13143-13147.
20. David G, Neptune MA, DePinho RA. 2002. SUMO-1 modification of histone deacetylase 1 (HDAC1) modulates its biological activities. J Biol Chem 277:23658-23663.
21. Fischer DD, Cai R, Bhatia U, Asselbergs FA, Song C, Terry R, Trogani N, Widmer R, Atadja P, Cohen D. 2001. Isolation and characterization of a novel class II histone deacetylase, HDAC10. J Biol Chem 277:6656-6666.
22. Fischle W, Dequiedt F, Fillion M, Hendzel MJ, Voelter W, Verdin E. 2001. Human HDAC7 histone deacetylase activity is associated with HDAC3 in vivo. J Biol Chem 276:35826-35835.
23. Fischle W, Dequiedt F, Hendzel MJ, Guenther MG, Lazar MA, Voelter W, Verdin E. 2002. Enzymatic activity associated with class II HDACs is dependent on a multiprotein complex containing HDAC3 and SMRT/N-CoR. Mol Cell 9:45-57.
24. Galasinski SC, Resing KA, Goodrich JA, Ahn NG. 2002. Phosphatase inhibition leads to histone deacetylases 1 and 2 phosphorylation and disruption of corepressor interactions. J Biol Chem 277:19618-19626.
25. Girdwood D, Bumpass D, Vaughan OA, Thain A, Anderson LA, Snowden AW, Garcia-Wilson E, Perkins ND, Hay RT. 2003. p300 transcriptional repression is mediated by SUMO modification. Mol Cell 11:1043-1054.
26. Gray SG, Iglesias AH, Teh BT, Dangond F. 2003. Modulation of splicing events in histone deacetylase 3 by various extracellular and signal transduction pathways. Gene Expr 11:13-21.
27. Grozinger CM, Schreiber SL. 2000. Regulation of histone deacetylase 4 and 5 and transcriptional activity by 14-3-3-dependent cellular localization. Proc Natl Acad Sci USA 97:7835-7840.
28. Grozinger CM, Schreiber SL. 2002. Deacetylase enzymes: Biological functions and the use of small-molecule inhibitors. Chem Biol 9:3-16.
29. Guardiola AR, Yao TP. 2001. Molecular cloning and characterization of a novel histone deacetylase HDAC10. J Biol Chem 277:3350-3356.
30. Guenther MG, Barak O, Lazar MA. 2001. The SMRT and N-CoR corepressors are activating cofactors for histone deacetylase 3. Mol Cell Biol 21:6091-6101.
31. Guenther MG, Yu J, Kao GD, Yen TJ, Lazar MA. 2002. Assembly of the SMRT-histone deacetylase 3 repression complex requires the TCP-1 ring complex. Genes Dev 16:3130-3135.
32. Hassig CA, Fleischer TC, Billin AN, Schreiber SL, Ayer DE. 1997. Histone deacetylase activity is required for full transcriptional repression by mSin3A. Cell 89:341-347.
33. Hauser C, Schuettengruber B, Bartl S, Lagger G, Seiser C. 2002. Activation of the mouse histone deacetylase 1 gene by cooperative histone phosphorylation and acetylation. Mol Cell Biol 22:7820-7830.
34. Heinzel T, Lavinsky RM, Mullen TM, Soderstrom M, Laherty CD, Torchia J, Yang WM, Brard G, Ngo SD, Davie JR, Seto E, Eisenman RN, Rose DW, Glass CK, Rosenfeld MG. 1997. A complex containing N-CoR, mSin3, and histone deacetylase mediates transcriptional repression. Nature 387:43-48.
35. Hu E, Chen Z, Fredrickson T, Zhu Y, Kirkpatrick R, Zhang GF, Johanson K, Sung CM, Liu R, Winkler J. 2000. Cloning and characterization of a novel human class I histone deacetylase that functions as a transcription repressor. J Biol Chem 275:15254-15264.
36. Hubbert C, Guardiola A, Shao R, Kawaguchi Y, Ito A, Nixon A, Yoshida M, Wang XF, Yao TP. 2002. HDAC6 is a microtubule-associated deacetylase. Nature 417:455-458.
37. Humphrey GW, Wang Y, Russanova VR, Hirai T, Qin J, Nakatani Y, Howard BH. 2001. Stable histone deacetylase complexes distinguished by the presence of SANT domain proteins CoREST/kiaa0071 and Mta-L1. J Biol Chem 276:6817-6824.
38. Johnson CA, White DA, Lavender JS, O'Neill LP, Turner BM. 2002. Human class I histone deacetylase complexes show enhanced catalytic activity in the presence of ATP and co-immunoprecipitate with the ATP-dependent chaperone protein Hsp70. J Biol Chem 277:9590-9597.
39. Johnstone RW. 2002. Histone-deacetylase inhibitors: Novel drugs for the treatment of cancer. Nat Rev Drug Discov 1:287-299.
40. Johnstone RW, Licht JD. 2003. Histone deacetylase inhibitors in cancer therapy: Is transcription the primary target? Cancer Cell 4:13-18.
41. Kao HY, Verdel A, Tsai CC, Simon C, Juguilon H, Khochbin S. 2001. Mechanism for nucleocytoplasmic shuttling of histone deacetylase 7. J Biol Chem 276:47496-47507.
42. Kao HY, Lee CH, Komarov A, Han CC, Evans RM. 2002. Isolation and characterization of mammalian HDAC10, a novel histone deacetylase. J Biol Chem 277:187-193.
43. Kirsh O, Seeler JS, Pichler A, Gast A, Muller S, Miska E, Mathieu M, Harel-Bellan A, Kouzarides T, Melchior F, Dejean A. 2002. The SUMO E3 ligase RanBP2 promotes modification of the HDAC4 deacetylase. EMBO J 21:2682-2691.
44. Lagger G, O'Carroll D, Rembold M, Khier H, Tischler J, Weitzer G, Schuettengruber B, Hauser C, Brunmeir R, Jenuwein T, Seiser C. 2002. Essential function of histone deacetylase 1 in proliferation control and CDK inhibitor repression. EMBO J 21:2672-2681.
45. Laherty CD, Yang WM, Sun JM, Davie JR, Seto E, Eisenman RN. 1997. Histone deacetylases associated with the mSin3 corepressor mediate mad transcriptional repression. Cell 89:349-356.
46. Lechner T, Carrozza MJ, Yu Y, Grant PA, Eberharter A, Vannier D, Brosch G, Stillman DJ, Shore D, Workman JL. 2000. Sds3 (suppressor of defective silencing 3) is an integral component of the yeast Sin3-Rpd3 histone deacetylase complex and is required for histone deacetylase activity. J Biol Chem 275:40961-40966.
47. Lee H, Rezai-Zadeh N, Seto E. 2004. Negative regulation of histone deacetylase 8 activity by cyclic AMP-dependent protein kinase A. Mol Cell Biol 24:765-773.
48. Lin SJ, Ford E, Haigis M, Liszt G, Guarente L. 2004. Calorie restriction extends yeast life span by lowering the level of NADH. Genes Dev 18:12-16.
49. Ling Y, Sankpal UT, Robertson AK, McNally JG, Karpova T1 Robertson KD. 2004. Modification of de novo DNA methyltransferase 3a (Dnmt3a) by SUMO-1 modulates its interaction with histone deacetylases (HDACs) and its capacity to repress transcription. Nucleic Acids Res 32:598-610.
50. Lu J, McKinsey TA, Nicol RL, Olson EN. 2000a. Signal-dependent activation of the MEF2 transcription factor by dissociation from histone deacetylases. Proc Natl Acad Sci USA 97:4070-4075.
51. Lu J, McKinsey TA, Zhang CL, Olson EN. 2000b. Regulation of skeletal myogenesis by association of the MEF2 transcription factor with class II histone deacetylases. Mol Cell 6:233-244.
52. Lusser A, Kadonaga JT. 2003. Chromatin remodeling by ATP-dependent molecular machines. Bioessays 25:1192-1200.
53. Lusser A, Brosch G, Loidl A, Haas H, Loidl P. 1997. Identification of maize histone deacetylase HD2 as an acidic nucleolar phosphoprotein. Science 277:88-91.
54. Marks PA, Richon VM, Breslow R, Rifkind RA. 2001a. Histone deacetylase inhibitors as new cancer drugs. Curr Opin Oncol 13:477-483.
55. Marks PA, Rifkind RA, Richon VM, Breslow R. 2001b. Inhibitors of histone deacetylase are potentially effective anticancer agents. Clin Cancer Res 7:759-760.
56. Marks PA, Rifkind RA, Richon VM, Breslow R, Miller T, Kelly WK. 2001c. Histone deacetylases and cancer: Causes and therapies. Nat Rev Cancer 1:194-202.
57. Marks PA, Miller T, Richon VM. 2003. Histone deacetylases. Curr Opin Pharmacol 3:344-351.
58. Matsuyama A, Shimazu T, Sumida Y, Saito A, Yoshimatsu Y, Seigneurin-Berny D, Osada H, Komatsu Y, Nishino N, Khochbin S, Horinouchi S, Yoshida M. 2002. In vivo destabilization of dynamic microtubules by HDAC6-mediated deacetylation. EMBO J 21:6820-6831.
59. McKinsey TA, Zhang CL, Lu J, Olson EN. 2000a. Signal-dependent nuclear export of a histone deacetylase regulates muscle differentiation. Nature 408:106-111.
60. McKinsey TA, Zhang CL, Olson EN. 2000b. Activation of the myocyte enhancer factor-2 transcription factor by calcium/calmodulin-dependent protein kinase-stimulated binding of 14-3-3 to histone deacetylase 5. Proc Natl Acad Sci USA 97:14400-14405.
61. McKinsey TA, Zhang CL, Olson EN. 2001. Identification of a signal-responsive nuclear export sequence in class II histone deacetylases. Mol Cell Biol 21:6312-6321.
62. McLaughlin F, Finn P, La Thangue NB. 2003. The cell cycle, chromatin and cancer: Mechanism-based therapeutics come of age. Drug Discov Today 8:793-802.
63. Melnick A, Licht JD. 2002. Histone deacetylases as therapeutic targets in hematologic malignancies. Curr Opin Hematol 9:322-332.
64. Miska EA, Karlsson C, Langley E, Nielsen SJ, Pines J, Kouzarides T. 1999. HDAC4 deacetylase associates with and represses the MEF2 transcription factor. EMBO J 18:5099-5107.
65. Ng HH, Bird A. 2000. Histone deacetylases: Silencers for hire. Trends Biochem Sci 25:121-126.
66. North BJ, Marshall BL, Borra MT, Denu JM, Verdin E. 2003. The human Sir2 ortholog, SIRT2, is an NAD+-dependent tubulin deacetylase. Mol Cell 11:437-444.
67. Petrie K, Guidez F, Howell L, Healy L, Waxman S, Greaves M, Zelent A. 2003. The histone deacetylase 9 gene encodes multiple protein isoforms. J Biol Chem 278:16059-16072.
68. Pflum MK, Tong JK, Lane WS, Schreiber SL. 2001. Histone deacetylase 1 phosphorylation promotes enzymatic activity and complex formation. J Biol Chem 276:47733-47741.
69. Pipal A, Goralik-Schramel M, Lusser A, Lanzanova C, Sarg B, Loidl A, Lindner H, Rossi V, Loidl P. 2003. Regulation and processing of maize histone deacetylase Hda1 by limited proteolysis. Plant Cell 15:1904-1917.
70. Roth SY, Denu JM, Allis CD. 2001. Histone acetyltransferases. Annu Rev Biochem 70:81-120.
71. Schuettengruber B, Simboeck E, Khier H, Seiser C. 2003. Autoregulation of mouse histone deacetylase 1 expression. Mol Cell Biol 23:6993-7004.
72. Schwer B, North BJ, Frye RA, Ott M, Verdin E. 2002. The human silent information regulator (Sir)2 homologue hSIRT3 is a mitochondrial nicotinamide adenine dinucleotide-dependent deacetylase. J Cell Biol 158:647-657.
73. Secrist JP, Zhou X, Richon VM. 2003. HDAC inhibitors for the treatment of cancer. Curr Opin Investig Drugs 4:1422-1427.
74. Steffan JS, Bodai L, Pallos J, Poelman M, McCampbell A, Apostol BL, Kazantsev A, Schmidt E, Zhu YZ, Greenwald M, Kurokawa R, Housman DE, Jackson GR, Marsh JL, Thompson LM. 2001. Histone deacetylase inhibitors arrest polyglutamine-dependent neurodegeneration in Drosophila. Nature 413:739-743.
75. Strahl BD, Allis CD. 2000. The language of covalent histone modifications. Nature 403:41-45.
76. Sun JM, Chen HY, Moniwa M, Litchfield DW, Seto E, Davie JR. 2002. The transcriptional repressor Sp3 is associated with CK2-phosphorylated histone deacetylase 2. J Biol Chem 277:35783-35786.
77. Thiagalingam S, Cheng KH, Lee HJ, Mineva N, Thiagalingam A, Ponte JF. 2003. Histone deacetylases: Unique players in shaping the epigenetic histone code. Ann NY Acad Sci 983:84-100.
78. Tong JK, Hassig CA, Schnitzler GR, Kingston RE, Schreiber SL. 1998. Chromatin deacetylation by an ATP-dependent nucleosome remodelling complex. Nature 395:917-921.
79. Tong JJ, Liu J, Bertos NR, Yang XJ. 2002. Identification of HDAC10, a novel class II human histone deacetylase containing a leucine-rich domain. Nucleic Acids Res 30:1114-1123.
80. Tsai SC, Seto E. 2002. Regulation of histone deacetylase 2 by protein kinase CK2. J Biol Chem 277:31826-31833.
81. Verdel A, Curtet S, Brocard MP, Rousseaux S, Lemercier C, Yoshida M, Khochbin S. 2000. Active maintenance of mHDA2/mHDAC6 histone-deacetylase in the cytoplasm. Curr Biol 10:747-749.
82. Verdin E, Dequiedt F, Kasler HG. 2003. Class II histone deacetylases: Versatile regulators. Trends Genet 19:286-293.
83. Wang AH, Yang XJ. 2001. Histone deacetylase 4 possesses intrinsic nuclear import and export signals. Mol Cell Biol 21:5992-6005.
84. Wang AH, Kruhlak MJ, Wu J, Bertos NR, Vezmar M, Posner BI, Bazett-Jones DP, Yang XJ. 2000. Regulation of histone deacetylase 4 by binding of 14-3-3 proteins. Mol Cell Biol 20:6904-6912.
85. Wen YD, Perissi V, Staszewski LM, Yang WM, Krones A, Glass CK, Rosenfeld MG, Seto E. 2000. The histone deacetylase-3 complex contains nuclear receptor corepressors. Proc Natl Acad Sci USA 97:7202-7207.
86. Wiper-Bergeron N, Wu D, Pope L, Schild-Poulter C, Hache RJ. 2003. Stimulation of preadipocyte differentiation by steroid through targeting of an HDAC1 complex. EMBO J 22:2135-2145.
87. Yang XJ, Seto E. 2003. Collaborative spirit of histone deacetylases in regulating chromatin structure and gene expression. Curr Opin Genet Dev 13:143-153.
88. Yang SH, Sharrocks AD. 2004. SUMO promotes HDAC-mediated transcriptional repression. Mol Cell 13:611-617.
89. Yang WM, Yao YL, Sun JM, Davie JR, Seto E. 1997. Isolation and characterization of cDNAs corresponding to an additional member of the human histone deacetylase gene family. J Biol Chem 272:28001-28007.
90. Yoshida M, Shimazu T, Matsuyama A. 2003. Protein deacetylases: Enzymes with functional diversity as novel therapeutic targets. Prog Cell Cycle Res 5:269-278.
91. You A, Tong JK, Grozinger CM, Schreiber SL. 2001. CoREST is an integral component of the CoREST-human histone deacetylase complex. Proc Natl Acad Sci USA 98:1454-1458.
92. Yu J, Li Y, Ishizuka T, Guenther MG, Lazar MA. 2003. A SANT motif in the SMRT corepressor interprets the histone code and promotes histone deacetylation. EMBO J 22:3403-3410.
93. Zhang Y, Reinberg D. 2001. Transcription regulation by histone methylation: Interplay between different covalent modifications of the core histone tails. Genes Dev 15:2343-2360.
94. Zhang Y, Iratni R, Erdjument-Bromage H, Tempst P, Reinberg D. 1997. Histone deacetylases and SAP18, a novel polypeptide, are components of a human sin3 complex. Cell 89:357-364.
95. Zhang J, Guenther MG, Carthew RW, Lazar MA. 1998a. Proteasomal regulation of nuclear receptor corepressor-mediated repression. Genes Dev 12:1775-1780.
96. Zhang Y, LeRoy G, Seelig HP, Lane WS, Reinberg D. 1998b. The dermatomyositis-specific autoantigen Mi2 is a component of a complex containing histone deacetylase and nucleosome remodeling activities. Cell 95:279-289.
97. Zhang Y, Ng HH, Erdjument-Bromage H, Tempst P, Bird A, Reinberg D. 1999. Analysis of the NuRD subunits reveals a histone deacetylase core complex and a connection with DNA methylation. Genes Dev 13:1924-1935.
98. Zhang CL, McKinsey TA, Olson EN. 2001. The transcriptional corepressor MITR is a signal-responsive inhibitor of myogenesis. Proc Natl Acad Sci USA 98:7354-7359.
99. Zhang J, Kalkum M, Chait BT, Roeder RG. 2002. The N-Cor-HDAC3 nuclear receptor corepressor complex inhibits the JNK pathway through the integral subunit GPS2. Mol Cell 9:611-623.
100. Zhang CL, McKinsey TA, Chang S, Antos CL, Hill JA, Olson EN. 2002. Class II histone deacetylases act as signal-responsive repressors of cardiac hypertrophy. Cell 110:479-488.
101. Zhang Y, Li N, Caron C, Matthias G, Hess D, Khochbin S, Matthias P. 2003. HDAC-6 interacts with and deacetylates tubulin and microtubules in vivo. EMBO J 22:1168-1179.
102. Zhou X, Richon VM, Wang AH, Yang XJ, Rifkind RA, Marks PA. 2000. Histone deacetylase 4 associates with extracellular signal-regulated kinases 1 and 2, and its cellular localization is regulated by oncogenic Ras. Proc Natl Acad Sci USA 97:14329-14333.
103. Zhou X, Marks PA, Rifkind RA, Richon VM. 2001. Cloning and characterization of a histone deacetylase, HDAC9. Proc Natl Acad Sci USA 98:10572-10577.