The "histone mimicry" by pathogens

Cold Spring Harbor Symposia on Quantitative Biology

Volumn 78, Issue 1, 2013, Pages 81-90

  Schaefer, Uwe ^a   Ho, Jessica S Y ^a,b   Prinjha, Rab K ^c   Tarakhovsky, Alexander ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^c GLAXOSMITHKLINE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOKINE; HISTONE; HISTONE H3; INTERFERON; NONSTRUCTURAL PROTEIN 1; NUCLEIC ACID; PATTERN RECOGNITION RECEPTOR; ANTIVIRUS AGENT; INS1 PROTEIN, INFLUENZA VIRUS; VIRUS PROTEIN;

ARTICLE; CYTOKINE PRODUCTION; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENE REPRESSION; HISTONE MIMICRY; HOST PATHOGEN INTERACTION; HUMAN; INFLUENZA VIRUS A; INFLUENZA VIRUS A H1N1; INFLUENZA VIRUS A H3N2; INFLUENZA VIRUS A H5N1; MOLECULAR MIMICRY; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; TRANSCRIPTION ELONGATION; VIRUS INFECTION; VIRUS REPLICATION; AMINO ACID SEQUENCE; ANIMAL; GENE EXPRESSION PROFILING; GENETIC TRANSCRIPTION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN TERTIARY STRUCTURE; VIRUS;

AMINO ACID SEQUENCE; ANIMALS; ANTIVIRAL AGENTS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE EXPRESSION REGULATION, VIRAL; HISTONES; HOST-PATHOGEN INTERACTIONS; HUMANS; INFLUENZA A VIRUS; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, TERTIARY; TRANSCRIPTION, GENETIC; VIRAL NONSTRUCTURAL PROTEINS; VIRAL PROTEINS; VIRUS DISEASES; VIRUSES;

EID: 84904906237     PISSN: 00917451     EISSN: None     Source Type: Book Series    
DOI: 10.1101/sqb.2013.78.020339     Document Type: Article

References (88)

1. Ashour J, Laurent-Rolle M, Shi PY, Garcia-Sastre A. 2009. NS5 of dengue virus mediates STAT2 binding and degradation. J Virol 83: 5408-5418.
2. Badeaux AI, Shi Y. 2013. Emerging roles for chromatin as a signal integration and storage platform. Nat Rev Mol Cell Biol 14: 211-224.
3. Ballestas ME, Chatis PA, Kaye KM. 1999. Efficient persistence of extrachromosomal KSHV DNA mediated by latency-associated nuclear antigen. Science 284: 641-644.
4. Banerjee P, DeJesus R, Gjoerup O, Schaffhausen BS. 2013. Viral interference with DNA repair by targeting of the single-stranded DNA binding protein RPA. PLoS Pathog 9: e1003725.
5. Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Zaslavsky L, Tatusova T, Ostell J, Lipman D. 2008. The influenza virus resource at the National Center for Biotechnology Information. J Virol 82: 596-601.
6. Belkina AC, Nikolajczyk BS, Denis GV. 2013. BET protein function is required for inflammation: Brd2 genetic disruption and BET inhibitor JQ1 impair mouse macrophage inflammatory responses. J Immunol 190: 3670-3678.
7. Chapuy B, McKeown MR, Lin CY, Monti S, Roemer MG, Qi J, Rahl PB, Sun HH, Yeda KT, Doench JG, et al. 2013. Discovery and characterization of super-enhancer-associated dependencies in diffuse large B cell lymphoma. Cancer Cell 24: 777-790.
8. Chua MA, Schmid S, Perez JT, Langlois RA, Tenoever BR. 2013. Influenza A virus utilizes suboptimal splicing to coordinate the timing of infection. Cell Rep 3: 23-29.
9. Collins RE, Northrop JP, Horton JR, Lee DY, Zhang X, Stallcup MR, 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.
10. Colpitts TM, Barthel S, Wang P, Fikrig E. 2011. Dengue virus capsid protein binds core histones and inhibits nucleosome formation in human liver cells. PLoS One 6: e24365.
11. Davey NE, Trave G, Gibson TJ. 2011. How viruses hijack cell regulation. Trends Biochem Sci 36: 159-169.
12. Davey NE, Van Roey K,Weatheritt RJ, Toedt G, Uyar B, Altenberg B, Budd A, Diella F, Dinkel H, Gibson TJ. 2012. Attributes of short linear motifs. Mol Biosyst 8: 268-281.
13. Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM, et al. 2011. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478: 529-533.
14. Delmore JE, Issa GC, Lemieux ME, Rahl PB, Shi J, Jacobs HM, Kastritis E, Gilpatrick T, Paranal RM, Qi J, et al. 2011. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146: 904-917.
15. Dey A, Ellenberg J, Farina A, Coleman AE, Maruyama T, Sciortino S, Lippincott-Schwartz J, Ozato K. 2000. A bromodomain protein, MCAP, associates with mitotic chromosomes and affects G(2)-to-M transition. Mol Cell Biol 20: 6537-6549.
16. Dey A, Chitsaz F, Abbasi A, Misteli T, Ozato K. 2003. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc Natl Acad Sci 100: 8758-8763.
17. Diella F, Haslam N, Chica C, Budd A, Michael S, Brown NP, Trave G, Gibson TJ. 2008. Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front Biosci 13: 6580-6603.
18. Dinkel H, Van Roey K, Michael S, Davey NE, Weatheritt RJ, Born D, Speck T, Kruger D, Grebnev G, Kuban M, et al. 2014. The eukaryotic linear motif resource ELM: 10 years and counting. Nucleic Acids Res 42: D259-D266.
19. Donlin LT, Andresen C, Just S, Rudensky E, Pappas CT, Kruger M, Jacobs EY, Unger A, Zieseniss A, Dobenecker MW, et al. 2012. Smyd2 controls cytoplasmic lysine methylation of Hsp90 and myofilament organization. Genes Dev 26: 114-119.
20. Dover J, Schneider J, Tawiah-Boateng MA, Wood A, Dean K, Johnston M, Shilatifard A. 2002. Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem 277: 28368-28371.
21. Edwards RJ, Davey NE, O'Brien K, Shields DC. 2012. Interactome-wide prediction of short, disordered protein interaction motifs in humans. Mol Biosyst 8: 282-295.
22. Elde NC, Malik HS. 2009. The evolutionary conundrum of pathogen mimicry. Nat Rev Microbiol 7: 787-797.
23. Filippakopoulos P, Qi J, Picaud S, Shen Y, Smith WB, Fedorov O, Morse EM, Keates T, Hickman TT, Felletar I, et al. 2010. Selective inhibition of BET bromodomains. Nature 468: 1067-1073.
24. Fischle W, Wang Y, Allis CD. 2003. Histone and chromatin cross-talk. Curr Opin Cell Biol 15: 172-183.
25. Fonseca GJ, Thillainadesan G,Yousef AF, Ablack JN, Mossman KL, Torchia J, Mymryk JS. 2012. Adenovirus evasion of interferon-mediated innate immunity by direct antagonism of a cellular histone posttranslational modification. Cell Host Microbe 11: 597-606.
26. Fonseca GJ, Cohen MJ, Nichols AC, Barrett JW, Mymryk JS. 2013. Viral retasking of hBre1/RNF20 to recruit hPaf1 for transcriptional activation. PLoS Pathog 9: e1003411.
27. Friborg J Jr, Kong W, Hottiger MO, Nabel GJ. 1999. p53 inhibition by the LANA protein of KSHV protects against cell death. Nature 402: 889-894.
28. Fujimuro M, Wu FY, ApRhys C, Kajumbula H, Young DB, Hayward GS, Hayward SD. 2003. A novel viral mechanism for dysregulation of beta-catenin in Kaposi's sarcoma-associated herpesvirus latency. Nat Med 9: 300-306.
29. Garcia-Sastre A, Biron CA. 2006. Type 1 interferons and the virus-host relationship: A lesson in detente. Science 312: 879-882.
30. Garcia-Sastre A, Egorov A, Matassov D, Brandt S, Levy DE, Durbin JE, Palese P, Muster T. 1998. Influenza A virus lacking the NS1 gene replicates in interferon-deficient systems. Virology 252: 324-330.
31. Golebiewski L, Liu H, Javier RT, Rice AP. 2011. The avian influenza virus NS1 ESEV PDZ binding motif associates with Dlg1 and Scribble to disrupt cellular tight junctions. J Virol 85: 10639-10648.
32. Greenspan D, Palese P, Krystal M. 1988. Two nuclear location signals in the influenza virus NS1 nonstructural protein. J Virol 62: 3020-3026.
33. Hahn MA, Dickson KA, Jackson S, Clarkson A, Gill AJ, Marsh DJ. 2012. The tumor suppressor CDC73 interacts with the ring finger proteins RNF20 and RNF40 and is required for the maintenance of histone 2B monoubiquitination. Hum Mol Genet 21: 559-568.
34. Hargreaves DC, Horng T, Medzhitov R. 2009. Control of inducible gene expression by signal-dependent transcriptional elongation. Cell 138: 129-145.
35. Hopfield JJ. 1974. Kinetic proofreading: A new mechanism for reducing errors in biosynthetic processes requiring high specificity. Proc Natl Acad Sci 71: 4135-4139.
36. Huang H, Zhang J, Shen W, Wang X, Wu J, Shi Y. 2007. Solution structure of the second bromodomain of Brd2 and its specific interaction with acetylated histone tails. BMC Struct Biol 7: 57.
37. Jackson D, Hossain MJ, Hickman D, Perez DR, Lamb RA. 2008. A new influenza virus virulence determinant: The NS1 protein four C-terminal residues modulate pathogenicity. Proc Natl Acad Sci 105: 4381-4386.
38. Jang MK, Mochizuki K, Zhou M, Jeong HS, Brady JN, Ozato K. 2005. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase IIdependent transcription. Mol Cell 19: 523-534.
39. Kanno T, Kanno Y, Siegel RM, Jang MK, Lenardo MJ, Ozato K. 2004. Selective recognition of acetylated histones by bromodomain proteins visualized in living cells. MolCell 13: 33-43.
40. Katze MG, He Y, Gale M Jr. 2002. Viruses and interferon: A fight for supremacy. Nat Rev Immunol 2: 675-687.
41. Kawai T, Akira S. 2006. Innate immune recognition of viral infection. Nat Immunol 7: 131-137.
42. Kim J, Roeder RG. 2009. Direct Bre1-Paf1 complex interactions and RING finger-independent Bre1-Rad6 interactions mediate histone H2B ubiquitylation in yeast. J Biol Chem 284: 20582-20592.
43. Kim J, Guermah M, Roeder RG. 2010. The human PAF1 complex acts in chromatin transcription elongation both independently and cooperatively with SII/TFIIS. Cell 140: 491-503.
44. Krug RM, Yuan W, Noah DL, Latham AG. 2003. Intracellular warfare between human influenza viruses and human cells:The roles of the viral NS1 protein. Virology 309: 181-189.
45. Lee JS, Kim Y, Kim IS, Kim B, Choi HJ, Lee JM, Shin HJ, Kim JH, Kim JY, Seo SB, et al. 2010. Negative regulation of hypoxic responses via induced Reptin methylation. Mol Cell 39: 71-85.
46. Lee JM, Lee JS, Kim H, Kim K, Park H, Kim JY, Lee SH, Kim IS, Kim J, Lee M, et al. 2012. EZH2 generates a methyl degron that is recognized by the DCAF1/DDB1/CUL4 E3 ubiquitin ligase complex. Mol Cell 48: 572-586.
47. Liu L, Oliveira NM, Cheney KM, Pade C, Dreja H, Bergin AM, Borgdorff V, Beach DH, Bishop CL, Dittmar MT, et al. 2011. A whole genome screen for HIV restriction factors. Retrovirology 8: 94.
48. Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang J, Aggarwal AK, Rosenfeld MG. 2013. Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. Cell 155: 1581-1595.
49. Loven J, Hoke HA, Lin CY, Lau A, Orlando DA, Vakoc CR, Bradner JE, Lee TI, Young RA. 2013. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153: 320-334.
50. Marazzi I, Ho JS, Kim J, Manicassamy B, Dewell S, Albrecht RA, Seibert CW, Schaefer U, Jeffrey KL, Prinjha RK, et al. 2012. Suppression of the antiviral response by an influenza histone mimic. Nature 483: 428-433.
51. Mueller CL, Porter SE, Hoffman MG, Jaehning JA. 2004. The Paf1 complex has functions independent of actively transcribing RNA polymerase II. Mol Cell 14: 447-456.
52. Nagaike T, Logan C, Hotta I, Rozenblatt-Rosen O, Meyerson M, Manley JL. 2011. Transcriptional activators enhance polyadenylation of mRNA precursors. Mol Cell 41: 409-418.
53. Nakanishi S, Lee JS, Gardner KE, Gardner JM, Takahashi YH, Chandrasekharan MB, Sun ZW, Osley MA, Strahl BD, Jaspersen SL, et al. 2009. Histone H2BK123 monoubiquitination is the critical determinant for H3K4 and H3K79 trimethylation by COMPASS and Dot1. J Cell Biol 186: 371-377.
54. Nemeroff ME, Barabino SM, Li Y, Keller W, Krug RM. 1998. Influenza virus NS1 protein interacts with the cellular 30 kDa subunit of CPSF and inhibits 30end formation of cellular premRNAs. Mol Cell 1: 991-1000.
55. Nicodeme E, Jeffrey KL, Schaefer U, Beinke S, Dewell S, Chung CW, Chandwani R, Marazzi I, Wilson P, Coste H, et al. 2010. Suppression of inflammation by a synthetic histone mimic. Nature 468: 1119-1123.
56. Ninio J. 1975. Kinetic amplification of enzyme discrimination. Biochimie 57: 587-595.
57. Nordick K, Hoffman MG, Betz JL, Jaehning JA. 2008. Direct interactions between the Paf1 complex and a cleavage and polyadenylation factor are revealed by dissociation of Paf1 from RNA polymerase II. Eukaryot Cell 7: 1158-1167.
58. Obenauer JC, Denson J, Mehta PK, Su X, Mukatira S, Finkelstein DB, Xu X,Wang J, Ma J, Fan Y, et al. 2006. Large-scale sequence analysis of avian influenza isolates. Science 311: 1576-1580.
59. Penheiter KL, Washburn TM, Porter SE, Hoffman MG, Jaehning JA. 2005. A posttranscriptional role for the yeast Paf1-RNA polymerase II complex is revealed by identification of primary targets. Mol Cell 20: 213-223.
60. Rahman S, Sowa ME, Ottinger M, Smith JA, Shi Y, Harper JW, Howley PM. 2011. The Brd4 extraterminal domain confers transcription activation independent of pTEFb by recruiting multiple proteins, including NSD3. Mol Cell Biol 31: 2641-2652.
61. Rozenblatt-Rosen O, Nagaike T, Francis JM, Kaneko S, Glatt KA, Hughes CM, LaFramboise T, Manley JL, Meyerson M. 2009. The tumor suppressor Cdc73 functionally associates with CPSF and CstF 30 mRNA processing factors. Proc Natl Acad Sci 106: 755-760.
62. Ruthenburg AJ, Li H, Patel DJ, Allis CD. 2007. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol 8: 983-994.
63. Sampath SC, Marazzi I, Yap KL, Krutchinsky AN, Mecklenbrauker I, Viale A, Rudensky E, Zhou MM, Chait BT, Tarakhovsky A. 2007. Methylation of a histone mimic within the histone methyltransferase G9a regulates protein complex assembly. Mol Cell 27: 596-608.
64. Santos A, Pal S, Chacon J, Meraz K, Gonzalez J, Prieto K, Rosas-Acosta G. 2013. SUMOylation affects the interferon blocking activity of the influenza A nonstructural protein NS1 without affecting its stability or cellular localization. J Virol 87: 5602-5620.
65. Satterly N, Tsai PL, van Deursen J, Nussenzveig DR, Wang Y, Faria PA, Levay A, Levy DE, Fontoura BM. 2007. Influenza virus targets the mRNA export machinery and the nuclear pore complex. Proc Natl Acad Sci 104: 1853-1858.
66. Schoggins JW, Wilson SJ, Panis M, Murphy MY, Jones CT, Bieniasz P, Rice CM. 2011. A diverse range of gene products are effectors of the type I interferon antiviral response. Nature 472: 481-485.
67. Shi J,WangY, Zeng L,WuY, Deng J, Zhang Q, LinY, Li J, Kang T, Tao M, et al. 2014. Disrupting the Interaction of BRD4 with diacetylated twist suppresses tumorigenesis in basal-like breast cancer. Cancer Cell 25: 210-225.
68. Simic R, Lindstrom DL, Tran HG, Roinick KL, Costa PJ, Johnson AD, Hartzog GA, Arndt KM. 2003. Chromatin remodeling protein Chd1 interacts with transcription elongation factors and localizes to transcribed genes. EMBO J 22: 1846-1856.
69. Sims RJ III, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, Tempst P, Manley JL, Reinberg D. 2007. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and premRNA splicing. Mol Cell 28: 665-676.
70. Smock RG, Gierasch LM. 2009. Sending signals dynamically. Science 324: 198-203.
71. Sobhian B, Laguette N, Yatim A, Nakamura M, Levy Y, Kiernan R, Benkirane M. 2010. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol Cell 38: 439-451.
72. Stein A, Pache RA, Bernado P, Pons M, Aloy P. 2009. Dynamic interactions of proteins in complex networks: A more structured view. FEBS J 276: 5390-5405.
73. Sun ZW, Allis CD. 2002. Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast. Nature 418: 104-108.
74. Tachibana M, Ueda J, Fukuda M, Takeda N, Ohta T, Iwanari H, Sakihama T, Kodama T, Hamakubo T, Shinkai Y. 2005. Histone methyltransferases G9a and GLP form heteromeric complexes and are both crucial for methylation of euchromatin at H3-K9. Genes Dev 19: 815-826.
75. Tarakhovsky A. 2013. Logic of the inflammation-associated transcriptional response. Adv Immunol 119: 107-133.
76. Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. 2007. How chromatin-binding modules interpret histone modifications:Lessons from professional pocket pickers. Nat Struct Mol Biol 14: 1025-1040.
77. Thomas M, Kranjec C, Nagasaka K, Matlashewski G, Banks L. 2011. Analysis of the PDZ binding specificities of Influenza A virus NS1 proteins. Virol J 8: 25.
78. Van Roey K, Gibson TJ, Davey NE. 2012. Motif switches: Decision-making in cell regulation. Curr Opin Struct Biol 22: 378-385.
79. Van Roey K, Dinkel H, Weatheritt RJ, Gibson TJ, Davey NE. 2013. The switches.ELM resource: A compendium of conditional regulatory interaction interfaces. Sci Signal 6: rs7.
80. Wang X, Li M, Zheng H, Muster T, Palese P, Beg AA, Garcia-Sastre A. 2000. Influenza A virus NS1 protein prevents activation of NF-kappaB and induction of alpha/beta interferon. J Virol 74: 11566-11573.
81. Weatheritt RJ, Davey NE, Gibson TJ. 2012a. Linear motifs confer functional diversity onto splice variants. Nucleic Acids Res 40: 7123-7131.
82. Weatheritt RJ, Luck K, Petsalaki E, Davey NE, Gibson TJ. 2012b. The identification of short linear motif-mediated interfaces within the human interactome. Bioinformatics 28: 976-982.
83. Wood A, Schneider J, Dover J, Johnston M, Shilatifard A. 2003. The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem 278: 34739-34742.
84. Yang Z, Yik JH, Chen R, He N, Jang MK, Ozato K, Zhou Q. 2005. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 19: 535-545.
85. You J, Croyle JL, Nishimura A, Ozato K, Howley PM. 2004. Interaction of the bovine papillomavirus E2 protein with Brd4 tethers the viral DNA to host mitotic chromosomes. Cell 117: 349-360.
86. Zhao RY, Elder RT. 2005. Viral infections and cell cycle G2/M regulation. Cell Res 15: 143-149.
87. Zhou Q, Li T, Price DH. 2012. RNA polymerase II elongation control. Annu Rev Biochem 81: 119-143.
88. Zuber J, Shi J,Wang E, Rappaport AR, Herrmann H, Sison EA, Magoon D, Qi J, Blatt K, Wunderlich M, et al. 2011. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478: 524-528.