51. Lu, X., T. M. Welsh, and B. M. Peterlin. 1993. The human immunodeficiency virus type 1 long terminal repeat specifies two different transcription complexes, only one of which is regulated by Tat. J. Virol. 67:1752-1760.  
52.  Luo, Y., S. J. Madore, T. G. Parslow, B. R. Cullen, and B. M. Peterlin. 1993. Functional analysis of interactions between Tat and the trans- activation response element of human immunodeficiency virus type 1 in cells. J. Virol. 67:5617-5622.  
53. Luo, Y., and B. M. Peterlin. 1993. Juxtaposition between activation and basic domains of human immunodeficiency virus type 1 Tat is required for optimal interactions between Tat and TAR. J. Virol. 67:3441-3445.  
54. Peterlin, B. M. 1993. Introduction:  Transcriptional regulation of viruses. Sem. Virol.  4:1.
55. Peterlin, B. M. 1993. Transcriptional regulation of viruses. Sem. Virol.  4:2-80.
56. Tong-Starksen, S. E., A. Baur, X. B. Lu, E. Peck, and B. M. Peterlin. 1993. Second exon of Tat of HIV-2 is required for optimal trans-activation of HIV-1 and HIV-2 LTRs.Virology 195:826-830.  
57. Voliva, C. F., S. Tsang, and B. M. Peterlin. 1993. Mapping cis-acting defects in promoters of transcriptionally silent DQA2, DQB2, and DOB genes. Proc. Natl. Acad. Sci. USA90:3408-3412. 
58. Zhang, X. Y., N. Jabrane-Ferrat, C. K. Asiedu, S. Samac, B. M. Peterlin, and M. Ehrlich. 1993. The major histocompatibility complex class II promoter-binding protein RFX (NF-X) is a methylated DNA-binding protein. Mol. Cell. Biol.  13:6810-6818. 
59. Adams, M., L. Sharmeen, J. Kimpton, J. M. Romeo, J. V. Garcia, B. M. Peterlin, M. Groudine, and M. Emerman. 1994. Cellular latency in human immunodeficiency virus-infected individuals with high CD4 levels can be detected by the presence of promoter- proximal transcripts. Proc. Natl. Acad. Sci. USA 91:3862-3866.  
60. Alonso, A., T. P. Cujec, and B. M. Peterlin. 1994. Effects of human chromosome 12 on interactions between Tat and TAR of human immunodeficiency virus type 1. J. Virol. 68:6505-6513.  
61. Baur, A., S. Garber, and B. M. Peterlin. 1994. Effects of CD45 on NF-kappa B. Implications for replication of HIV-1. J. Immunol. 152:976-983.
62. Baur, A. S., E. T. Sawai, P. Dazin, W. J. Fantl, C. Cheng-Mayer, and B. M. Peterlin. 1994. HIV-1 Nef leads to inhibition or activation of T cells depending on its intracellular localization. Immunity 1:373-384.
63. Chang, C. H., J. D. Fontes, B.M. Peterlin, and R. A. Flavell. 1994. Class II transactivator (CIITA) is sufficient for the inducible expression of major histocompatibility complex class II genes. J. Exp. Med. 180:1367-1374.  
64. Jabrane-Ferrat, N., and B. M. Peterlin. 1994. Ets-1 activates the DRA promoter in B cells. Mol. Cell. Biol. 14:7314-7321.  
65. Jones, K. A., and B. M. Peterlin. 1994. Control of RNA initiation and elongation at the HIV-1 promoter. Annu. Rev. Biochem. 63:717-743. 
66. Luo, Y., H. Yu, and B. M. Peterlin. 1994. Cellular protein modulates effects of human immunodeficiency virus type 1 Rev. J. Virol. 68:3850-3856. 
67. Mujeeb, A., K. Bishop, B. M. Peterlin, C. Turck, T. G. Parslow, and T. L. James. 1994. NMR structure of a biologically active peptide containing the RNA- binding domain of human immunodeficiency virus type 1 Tat. Proc. Natl. Acad. Sci. USA 91:8248-8252. 
68. Sawai, E. T., A. Baur, H. Struble, B. M. Peterlin, J. A. Levy, and C. Cheng-Mayer. 1994. Human immunodeficiency virus type 1 Nef associates with a cellular serine kinase in T lymphocytes. Proc. Natl. Acad. Sci. USA 91:1539-1543. 
69. Wright, S., X. Lu, and B. M. Peterlin. 1994. Human immunodeficiency virus type 1 Tat directs transcription through attenuation sites within the mouse c-myc gene. J. Mol. Biol.243:568-573. 
70. Itoh-Lindstrom, Y., B. M. Peterlin, and J. P. Ting. 1995. Affinity enrichment and functional characterization of TRAX1, a novel transcription activator and X1-sequence-binding protein of HLA-DRA. Mol. Cell. Biol.  15:282-289.  
71. Sawai, E. T., A. S. Baur, B. M. Peterlin, J. A. Levy, and C. Cheng-Mayer. 1995. A conserved domain and membrane targeting of Nef from HIV and SIV are required for association with a cellular serine kinase activity. J. Biol. Chem. 270:15307-15314.  
72. Fontes, J. D., N. Jabrane-Ferrat, C. R. Toth, and B. M. Peterlin. 1996. Binding and cooperative interactions between two B cell-specific transcriptional coactivators. J. Exp. Med. 183:2517-2521.  
73. Ghosh, S., C. Toth, B. M. Peterlin, and E. Seto. 1996. Synergistic activation of transcription by the mutant and wild-type minimal transcriptional activation domain of VP16. J. Biol. Chem. 271:9911-9918.  
74. Jabrane-Ferrat, N., J. D. Fontes, J. M. Boss, and B. M. Peterlin. 1996. Complex architecture of major histocompatibility complex class II promoters: reiterated motifs and conserved protein-protein interactions. Mol. Cell. Biol.  16:4683-4690.  
75. Lu, X., X. Wu, A. Plemenitas, H. Yu, E. T. Sawai, A. Abo, and B. M. Peterlin. 1996. CDC42 and Rac1 are implicated in the activation of the Nef-associated kinase and replication of HIV-1. Curr. Biol. 6:1677-1684.
76. Okamoto, H., C. T. Sheline, J. L. Corden, K. A. Jones, and B. M. Peterlin. 1996. Trans-activation by human immunodeficiency virus Tat protein requires the C-terminal domain of RNA polymerase II. Proc. Natl. Acad. Sci. USA 93:11575-11579.  
77. Sawai, E. T., I. H. Khan, P. M. Montbriand, B. M. Peterlin, C. Cheng-Mayer, and P. A. Luciw. 1996. Activation of PAK by HIV and SIV Nef: importance for AIDS in rhesus macaques. Curr. Biol. 6:1519-1527.
78. Voliva, C. F., N. Jabrane-Ferrat, and B. M. Peterlin. 1996. The function of the octamer-binding site in the DRA promoter. Immunogenetics 43:20-26.
79. Baur, A. S., G. Sass, B. Laffert, D. Willbold, C. Cheng-Mayer, and B. M. Peterlin. 1997. The N-terminus of Nef from HIV-1/SIV associates with a protein complex containing Lck and a serine kinase. Immunity 6:283-291.  
80. Cujec, T. P., H. Cho, E. Maldonado, J. Meyer, D. Reinberg, and B. M. Peterlin. 1997. The human immunodeficiency virus transactivator Tat interacts with the RNA polymerase II holoenzyme. Mol. Cell. Biol.     17:1817-1823
81. Cujec, T. P., H. Okamoto, K. Fujinaga, J. Meyer, H. Chamberlin, D. O. Morgan, and B. M. Peterlin. 1997. The HIV transactivator Tat binds to the CDK-activating kinase and activates the phosphorylation of the carboxy-terminal domain of RNA polymerase II. Genes Dev. 11:2645-2657.  
82. Fontes, J. D., N. Jabrane-Ferrat, and B. M. Peterlin. 1997. Assembly of functional regulatory complexes on MHC class II promoters in vivo. J. Mol. Biol. 270:336-345.
83. Fontes, J. D., B. Jiang, and B. M. Peterlin. 1997. The class II trans-activator CIITA interacts with the TBP-associated factor TAFII32. Nucleic Acids Res. 25:2522-2528.
84. Lim, C. S., N. Jabrane-Ferrat, J. D. Fontes, H. Okamoto, M. R. Garovoy, B. M. Peterlin, and C. A. Hunt. 1997. Sequence-independent inhibition of RNA transcription by DNA dumbbells and other decoys. Nucleic Acids Res. 25:575-581. 
85. Luo, W., and B. M. Peterlin. 1997. Activation of the T-cell receptor signaling pathway by Nef from an aggressive strain of simian immunodeficiency virus. J. Virol.  71:9531-9537.  
86. Setterblad, N., B. M. Peterlin, and G. Andersson. 1997. Role of the X2 box in activated transcription from the DRA promoter in B cells. Immunogenetics 46:318-25.
87. Fujinaga, K., T. P. Cujec, J. Peng, J. Garriga, D. H. Price, X. Grana, and B. M. Peterlin. 1998. The ability of positive transcription elongation factor B to transactivate human immunodeficiency virus transcription depends on a functional kinase domain, cyclin T1, and Tat. J. Virol.  72:7154-7159.  
88. Lu, X., H. Yu, S. H. Liu, F. M. Brodsky, and B. M. Peterlin. 1998. Interactions between HIV1 Nef and vacuolar ATPase facilitate the internalization of CD4. Immunity 8:647-656. 
89. Fackler, O. T., W. Luo, M. Geyer, A. S. Alberts, and B. M. Peterlin. 1999. Activation of Vav by Nef induces cytoskeletal rearrangements and downstream effector functions.Mol. Cell 3:729-739.
90. Fontes, J. D., S. Kanazawa, D. Jean, and B. M. Peterlin. 1999. Interactions between the class II transactivator and CREB binding protein increase transcription of major histocompatibility complex class II genes. Mol. Cell. Biol.  19:941-947.  
91. Fontes, J. D., S. Kanazawa, N. Nekrep, and B. M. Peterlin. 1999. The class II transactivator CIITA is a transcriptional integrator. Microbes Infect. 1:863-869.
92. Fujinaga, K., R. Taube, J. Wimmer, T. P. Cujec, and B. M. Peterlin. 1999. Interactions between human cyclin T, Tat, and the transactivation response element (TAR) are disrupted by a cysteine to tyrosine substitution found in mouse cyclin T. Proc. Natl. Acad. Sci. USA 96:1285-1290.  
93. Plemenitas, A., X. Lu, M. Geyer, P. Veranic, M. N. Simon, and B. M. Peterlin. 1999. Activation of Ste20 by Nef from human immunodeficiency virus induces cytoskeletal rearrangements and downstream effector functions in Saccharomyces cerevisiaeVirology 258:271-281.  
94. Taube, R., K. Fujinaga, J. Wimmer, M. Barboric, and B. M. Peterlin. 1999. Tat transactivation: a model for the regulation of eukaryotic transcriptional elongation. Virology264:245-253.  
95. Wimmer, J., K. Fujinaga, R. Taube, T. P. Cujec, Y. Zhu, J. Peng, D. H. Price, and B. M. Peterlin. 1999. Interactions between Tat and TAR and human immunodeficiency virus replication are facilitated by human cyclin T1 but not cyclins T2a or T2b. Virology 255:182-189.    
96. Barboric, M., R. Taube, N. Nekrep, K. Fujinaga, and B. M. Peterlin. 2000. The binding of Tat to TAR and the recruitment of P-TEFb occur independently in BIV. J. Virol.74:6039-44. 
97. Chao, S. H., K. Fujinaga, J. E. Marion, R. Taube, E. A. Sausville, A. M. Senderowicz, B. M. Peterlin, and D. H. Price. 2000. Flavopiridol inhibits P-TEFb and blocks HIV-1 replication, J. Biol. Chem. 275:28345-28352.  
98. Fackler, O. T., X. Lu, J. A. Frost, M. Geyer, B. Jiang, W. Luo, A. Abo, A. S. Alberts, and B. M. Peterlin. 2000. p21-activated kinase 1 plays a critical role in cellular activation by Nef. Mol. Cell. Biol.  20:2619-2627. 
99. Fackler, O.T., and B.M. Peterlin.  2000.  Endocytic entry of HIV.  Curr. Biol10:1005-1008.  
100. Kanazawa, S., T. Okamoto, and B. M. Peterlin. 2000. Tat competes with CIITA for the binding to P-TEFb and blocks the expression of MHC class II genes in HIV infection.Immunity 12:61-70.
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