HMGA1 directly interacts with TAR to modulate basal and Tat-dependent HIV transcription

References

• Kao SY, Calman AF, Luciw PA, Peterlin BM. Anti-termination of transcription within the long terminal repeat of HIV-1 by tat gene product. Nature 1987; 330:489 - 93; http://dx.doi.org/10.1038/330489a0; PMID: 2825027
   PubMed Web of Science ®Google Scholar
• Herrmann CH, Gold MO, Rice AP. Viral transactivators specifically target distinct cellular protein kinases that phosphorylate the RNA polymerase II C-terminal domain. Nucleic Acids Res 1996; 24:501 - 8; http://dx.doi.org/10.1093/nar/24.3.501; PMID: 8602364
   PubMed Web of Science ®Google Scholar
• Herrmann CH, Rice AP. Lentivirus Tat proteins specifically associate with a cellular protein kinase, TAK, that hyperphosphorylates the carboxyl-terminal domain of the large subunit of RNA polymerase II: candidate for a Tat cofactor. J Virol 1995; 69:1612 - 20; PMID: 7853496
   PubMed Web of Science ®Google Scholar
• Marshall NF, Peng J, Xie Z, Price DH. Control of RNA polymerase II elongation potential by a novel carboxyl-terminal domain kinase. J Biol Chem 1996; 271:27176 - 83; http://dx.doi.org/10.1074/jbc.271.43.27176; PMID: 8900211
   PubMed Web of Science ®Google Scholar
• Marshall NF, Price DH. Purification of P-TEFb, a transcription factor required for the transition into productive elongation. J Biol Chem 1995; 270:12335 - 8; http://dx.doi.org/10.1074/jbc.270.21.12335; PMID: 7759473
   PubMed Web of Science ®Google Scholar
• Zhu Y, Pe’ery T, Peng J, Ramanathan Y, Marshall N, Marshall T, et al. Transcription elongation factor P-TEFb is required for HIV-1 tat transactivation in vitro. Genes Dev 1997; 11:2622 - 32; http://dx.doi.org/10.1101/gad.11.20.2622; PMID: 9334325
   PubMed Web of Science ®Google Scholar
• Peterlin BM, Price DH. Controlling the elongation phase of transcription with P-TEFb. Mol Cell 2006; 23:297 - 305; http://dx.doi.org/10.1016/j.molcel.2006.06.014; PMID: 16885020
   PubMed Web of Science ®Google Scholar
• Wei P, Garber ME, Fang SM, Fischer WH, Jones KA. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 1998; 92:451 - 62; http://dx.doi.org/10.1016/S0092-8674(00)80939-3; PMID: 9491887
   PubMed Web of Science ®Google Scholar
• Zhou Q, Yik JH. The Yin and Yang of P-TEFb regulation: implications for human immunodeficiency virus gene expression and global control of cell growth and differentiation. Microbiol Mol Biol Rev 2006; 70:646 - 59; http://dx.doi.org/10.1128/MMBR.00011-06; PMID: 16959964
   PubMed Web of Science ®Google Scholar
• Chao SH, Price DH. Flavopiridol inactivates P-TEFb and blocks most RNA polymerase II transcription in vivo. J Biol Chem 2001; 276:31793 - 9; http://dx.doi.org/10.1074/jbc.M102306200; PMID: 11431468
   PubMed Web of Science ®Google Scholar
• Rahl PB, Lin CY, Seila AC, Flynn RA, McCuine S, Burge CB, et al. c-Myc regulates transcriptional pause release. Cell 2010; 141:432 - 45; http://dx.doi.org/10.1016/j.cell.2010.03.030; PMID: 20434984
   PubMed Web of Science ®Google Scholar
• Eilebrecht S, Benecke BJ, Benecke A. 7SK snRNA-mediated, gene-specific cooperativity of HMGA1 and P-TEFb. RNA Biol 2011; 8:1084 - 93; http://dx.doi.org/10.4161/rna.8.6.17015; PMID: 21957495
   PubMed Web of Science ®Google Scholar
• Nguyen VT, Kiss T, Michels AA, Bensaude O. 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes. Nature 2001; 414:322 - 5; http://dx.doi.org/10.1038/35104581; PMID: 11713533
   PubMed Web of Science ®Google Scholar
• Yang Z, Zhu Q, Luo K, Zhou Q. The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription. Nature 2001; 414:317 - 22; http://dx.doi.org/10.1038/35104575; PMID: 11713532
   PubMed Web of Science ®Google Scholar
• Jang MK, Mochizuki K, Zhou M, Jeong HS, Brady JN, Ozato K. The bromodomain protein Brd4 is a positive regulatory component of P-TEFb and stimulates RNA polymerase II-dependent transcription. Mol Cell 2005; 19:523 - 34; http://dx.doi.org/10.1016/j.molcel.2005.06.027; PMID: 16109376
   PubMed Web of Science ®Google Scholar
• Yang Z, Yik JH, Chen R, He N, Jang MK, Ozato K, et al. Recruitment of P-TEFb for stimulation of transcriptional elongation by the bromodomain protein Brd4. Mol Cell 2005; 19:535 - 45; http://dx.doi.org/10.1016/j.molcel.2005.06.029; PMID: 16109377
   PubMed Web of Science ®Google Scholar
• D’Orso I, Frankel AD. RNA-mediated displacement of an inhibitory snRNP complex activates transcription elongation. Nat Struct Mol Biol 2010; 17:815 - 21; http://dx.doi.org/10.1038/nsmb.1827; PMID: 20562857
   PubMed Web of Science ®Google Scholar
• He N, Liu M, Hsu J, Xue Y, Chou S, Burlingame A, et al. HIV-1 Tat and host AFF4 recruit two transcription elongation factors into a bifunctional complex for coordinated activation of HIV-1 transcription. Mol Cell 2010; 38:428 - 38; http://dx.doi.org/10.1016/j.molcel.2010.04.013; PMID: 20471948
   PubMed Web of Science ®Google Scholar
• Sobhian B, Laguette N, Yatim A, Nakamura M, Levy Y, Kiernan R, et al. HIV-1 Tat assembles a multifunctional transcription elongation complex and stably associates with the 7SK snRNP. Mol Cell 2010; 38:439 - 51; http://dx.doi.org/10.1016/j.molcel.2010.04.012; PMID: 20471949
   PubMed Web of Science ®Google Scholar
• Pereira LA, Bentley K, Peeters A, Churchill MJ, Deacon NJ. A compilation of cellular transcription factor interactions with the HIV-1 LTR promoter. Nucleic Acids Res 2000; 28:663 - 8; http://dx.doi.org/10.1093/nar/28.3.663; PMID: 10637316
   PubMed Web of Science ®Google Scholar
• Gaynor R. Cellular transcription factors involved in the regulation of HIV-1 gene expression. AIDS 1992; 6:347 - 63; http://dx.doi.org/10.1097/00002030-199204000-00001; PMID: 1616633
   PubMed Web of Science ®Google Scholar
• Gatignol A, Buckler-White A, Berkhout B, Jeang KT. Characterization of a human TAR RNA-binding protein that activates the HIV-1 LTR. Science 1991; 251:1597 - 600; http://dx.doi.org/10.1126/science.2011739; PMID: 2011739
   PubMed Web of Science ®Google Scholar
• Gatignol A, Duarte M, Daviet L, Chang YN, Jeang KT. Sequential steps in Tat trans-activation of HIV-1 mediated through cellular DNA, RNA, and protein binding factors. Gene Expr 1996; 5:217 - 28; PMID: 8723388
   PubMed Web of Science ®Google Scholar
• Ansari SA, Safak M, Gallia GL, Sawaya BE, Amini S, Khalili K. Interaction of YB-1 with human immunodeficiency virus type 1 Tat and TAR RNA modulates viral promoter activity. J Gen Virol 1999; 80:2629 - 38; PMID: 10573156
   PubMed Web of Science ®Google Scholar
• Chepenik LG, Tretiakova AP, Krachmarov CP, Johnson EM, Khalili K. The single-stranded DNA binding protein, Pur-alpha, binds HIV-1 TAR RNA and activates HIV-1 transcription. Gene 1998; 210:37 - 44; http://dx.doi.org/10.1016/S0378-1119(98)00033-X; PMID: 9524214
   PubMed Web of Science ®Google Scholar
• Fujii R, Okamoto M, Aratani S, Oishi T, Ohshima T, Taira K, et al. A Role of RNA Helicase A in cis-Acting Transactivation Response Element-mediated Transcriptional Regulation of Human Immunodeficiency Virus Type 1. J Biol Chem 2001; 276:5445 - 51; http://dx.doi.org/10.1074/jbc.M006892200; PMID: 11096080
   PubMed Web of Science ®Google Scholar
• Eilebrecht S, Brysbaert G, Wegert T, Urlaub H, Benecke BJ, Benecke A. 7SK small nuclear RNA directly affects HMGA1 function in transcription regulation. Nucleic Acids Res 2011; 39:2057 - 72; http://dx.doi.org/10.1093/nar/gkq1153; PMID: 21087998
   PubMed Web of Science ®Google Scholar
• Reeves R, Nissen MS. The A.T-DNA-binding domain of mammalian high mobility group I chromosomal proteins. A novel peptide motif for recognizing DNA structure. J Biol Chem 1990; 265:8573 - 82; PMID: 1692833
   PubMed Web of Science ®Google Scholar
• Farnet CM, Bushman FD. HIV-1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro. Cell 1997; 88:483 - 92; http://dx.doi.org/10.1016/S0092-8674(00)81888-7; PMID: 9038339
   PubMed Web of Science ®Google Scholar
• Gao K, Gorelick RJ, Johnson DG, Bushman F. Cofactors for human immunodeficiency virus type 1 cDNA integration in vitro. J Virol 2003; 77:1598 - 603; http://dx.doi.org/10.1128/JVI.77.2.1598-1603.2003; PMID: 12502875
   PubMed Web of Science ®Google Scholar
• Van Maele B, Busschots K, Vandekerckhove L, Christ F, Debyser Z. Cellular co-factors of HIV-1 integration. Trends Biochem Sci 2006; 31:98 - 105; http://dx.doi.org/10.1016/j.tibs.2005.12.002; PMID: 16403635
   PubMed Web of Science ®Google Scholar
• Tsuruno C, Ohe K, Kuramitsu M, Kohma T, Takahama Y, Hamaguchi Y, et al. HMGA1a is involved in specific splice site regulation of human immunodeficiency virus type 1. Biochem Biophys Res Commun 2011; 406:512 - 7; http://dx.doi.org/10.1016/j.bbrc.2011.02.059; PMID: 21329653
   PubMed Web of Science ®Google Scholar
• Henderson A, Holloway A, Reeves R, Tremethick DJ. Recruitment of SWI/SNF to the human immunodeficiency virus type 1 promoter. Mol Cell Biol 2004; 24:389 - 97; http://dx.doi.org/10.1128/MCB.24.1.389-397.2004; PMID: 14673171
   PubMed Web of Science ®Google Scholar
• Henderson A, Bunce M, Siddon N, Reeves R, Tremethick DJ. High-mobility-group protein I can modulate binding of transcription factors to the U5 region of the human immunodeficiency virus type 1 proviral promoter. J Virol 2000; 74:10523 - 34; http://dx.doi.org/10.1128/JVI.74.22.10523-10534.2000; PMID: 11044097
   PubMed Web of Science ®Google Scholar
• Chi YH, Semmes OJ, Jeang KT. A proteomic study of TAR-RNA binding protein (TRBP)-associated factors. Cell Biosci 2011; 1:9; http://dx.doi.org/10.1186/2045-3701-1-9; PMID: 21711701
   PubMed Web of Science ®Google Scholar
• Foti D, Iuliano R, Chiefari E, Brunetti A. A nucleoprotein complex containing Sp1, C/EBP beta, and HMGI-Y controls human insulin receptor gene transcription. Mol Cell Biol 2003; 23:2720 - 32; http://dx.doi.org/10.1128/MCB.23.8.2720-2732.2003; PMID: 12665574
   PubMed Web of Science ®Google Scholar
• Harrer M, Lührs H, Bustin M, Scheer U, Hock R. Dynamic interaction of HMGA1a proteins with chromatin. J Cell Sci 2004; 117:3459 - 71; http://dx.doi.org/10.1242/jcs.01160; PMID: 15213251
   PubMed Web of Science ®Google Scholar
• Wei P, Garber ME, Fang SM, Fischer WH, Jones KA. A novel CDK9-associated C-type cyclin interacts directly with HIV-1 Tat and mediates its high-affinity, loop-specific binding to TAR RNA. Cell 1998; 92:451 - 62; http://dx.doi.org/10.1016/S0092-8674(00)80939-3; PMID: 9491887
   PubMed Web of Science ®Google Scholar
• Berkhout B, Jeang KT. trans activation of human immunodeficiency virus type 1 is sequence specific for both the single-stranded bulge and loop of the trans-acting-responsive hairpin: a quantitative analysis. J Virol 1989; 63:5501 - 4; PMID: 2479775
   PubMed Web of Science ®Google Scholar
• Huthoff H, Girard F, Wijmenga SS, Berkhout B. Evidence for a base triple in the free HIV-1 TAR RNA. RNA 2004; 10:412 - 23; http://dx.doi.org/10.1261/rna.5161304; PMID: 14970387
   PubMed Web of Science ®Google Scholar
• Jossinet F, Ludwig TE, Westhof E. Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 2010; 26:2057 - 9; http://dx.doi.org/10.1093/bioinformatics/btq321; PMID: 20562414
   PubMed Web of Science ®Google Scholar
• Desfosses Y, Solis M, Sun Q, Grandvaux N, Van Lint C, Burny A, et al. Regulation of human immunodeficiency virus type 1 gene expression by clade-specific Tat proteins. J Virol 2005; 79:9180 - 91; http://dx.doi.org/10.1128/JVI.79.14.9180-9191.2005; PMID: 15994812
   PubMed Web of Science ®Google Scholar
• Muniz L, Egloff S, Ughy B, Jády BE, Kiss T. Controlling cellular P-TEFb activity by the HIV-1 transcriptional transactivator Tat. PLoS Pathog 2010; 6:e1001152; http://dx.doi.org/10.1371/journal.ppat.1001152; PMID: 20976203
   PubMedGoogle Scholar
• Eilebrecht S, Pellay FX, Odenwälder P, Brysbaert G, Benecke BJ, Benecke A. EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection. BMC Res Notes 2008; 1:100; http://dx.doi.org/10.1186/1756-0500-1-100; PMID: 18957101
   PubMedGoogle Scholar
• Reeves R, Leonard WJ, Nissen MS. Binding of HMG-I(Y) imparts architectural specificity to a positioned nucleosome on the promoter of the human interleukin-2 receptor alpha gene. Mol Cell Biol 2000; 20:4666 - 79; http://dx.doi.org/10.1128/MCB.20.13.4666-4679.2000; PMID: 10848593
   PubMed Web of Science ®Google Scholar
• John S, Reeves RB, Lin JX, Child R, Leiden JM, Thompson CB, et al. Regulation of cell-type-specific interleukin-2 receptor alpha-chain gene expression: potential role of physical interactions between Elf-1, HMG-I(Y), and NF-kappa B family proteins. Mol Cell Biol 1995; 15:1786 - 96; PMID: 7862168
   PubMed Web of Science ®Google Scholar
• Zhang XM, Verdine GL. A small region in HMG I(Y) is critical for cooperation with NF-kappaB on DNA. J Biol Chem 1999; 274:20235 - 43; http://dx.doi.org/10.1074/jbc.274.29.20235; PMID: 10400641
   PubMed Web of Science ®Google Scholar
• Kretzschmar M, Meisterernst M, Scheidereit C, Li G, Roeder RG. Transcriptional regulation of the HIV-1 promoter by NF-kappa B in vitro. Genes Dev 1992; 6:761 - 74; http://dx.doi.org/10.1101/gad.6.5.761; PMID: 1577271
   PubMed Web of Science ®Google Scholar
• Harrich D, Garcia J, Wu F, Mitsuyasu R, Gonazalez J, Gaynor R. Role of SP1-binding domains in in vivo transcriptional regulation of the human immunodeficiency virus type 1 long terminal repeat. J Virol 1989; 63:2585 - 91; PMID: 2657100
   PubMed Web of Science ®Google Scholar
• Sedore SC, Byers SA, Biglione S, Price JP, Maury WJ, Price DH. Manipulation of P-TEFb control machinery by HIV: recruitment of P-TEFb from the large form by Tat and binding of HEXIM1 to TAR. Nucleic Acids Res 2007; 35:4347 - 58; http://dx.doi.org/10.1093/nar/gkm443; PMID: 17576689
   PubMed Web of Science ®Google Scholar
• Mashima T, Udagawa S, Tsuruo T. Involvement of transcriptional repressor ATF3 in acceleration of caspase protease activation during DNA damaging agent-induced apoptosis. J Cell Physiol 2001; 188:352 - 8; http://dx.doi.org/10.1002/jcp.1130; PMID: 11473362
   PubMed Web of Science ®Google Scholar
• Mancebo HS, Lee G, Flygare J, Tomassini J, Luu P, Zhu Y, et al. P-TEFb kinase is required for HIV Tat transcriptional activation in vivo and in vitro. Genes Dev 1997; 11:2633 - 44; http://dx.doi.org/10.1101/gad.11.20.2633; PMID: 9334326
   PubMed Web of Science ®Google Scholar
• Sanghvi VR, Steel LF. The cellular TAR RNA binding protein, TRBP, promotes HIV-1 replication primarily by inhibiting the activation of double-stranded RNA-dependent kinase PKR. J Virol 2011; 85:12614 - 21; http://dx.doi.org/10.1128/JVI.05240-11; PMID: 21937648
   PubMed Web of Science ®Google Scholar
• Dorin D, Bonnet MC, Bannwarth S, Gatignol A, Meurs EF, Vaquero C. The TAR RNA-binding protein, TRBP, stimulates the expression of TAR-containing RNAs in vitro and in vivo independently of its ability to inhibit the dsRNA-dependent kinase PKR. J Biol Chem 2003; 278:4440 - 8; http://dx.doi.org/10.1074/jbc.M208954200; PMID: 12475984
   PubMed Web of Science ®Google Scholar
• Wagschal A, Rousset E, Basavarajaiah P, Contreras X, Harwig A, Laurent-Chabalier S, et al. Microprocessor, Setx, Xrn2, and Rrp6 co-operate to induce premature termination of transcription by RNAPII. Cell 2012; 150:1147 - 57; http://dx.doi.org/10.1016/j.cell.2012.08.004; PMID: 22980978
   PubMed Web of Science ®Google Scholar
• Laemmli UK. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 1970; 227:680 - 5; http://dx.doi.org/10.1038/227680a0; PMID: 5432063
   PubMed Web of Science ®Google Scholar
• Wienken CJ, Baaske P, Rothbauer U, Braun D, Duhr S. Protein-binding assays in biological liquids using microscale thermophoresis. Nat Commun 2010; 1:100; http://dx.doi.org/10.1038/ncomms1093; PMID: 20981028
   PubMed Web of Science ®Google Scholar
• Wienken CJ, Baaske P, Duhr S, Braun D. Thermophoretic melting curves quantify the conformation and stability of RNA and DNA. Nucleic Acids Res 2011; 39:e52; http://dx.doi.org/10.1093/nar/gkr035; PMID: 21297115
   PubMed Web of Science ®Google Scholar
• Zuker M. Computer prediction of RNA structure. Methods Enzymol 1989; 180:262 - 88; http://dx.doi.org/10.1016/0076-6879(89)80106-5; PMID: 2482418
   PubMed Web of Science ®Google Scholar
• Wilhelm E, Doyle MC, Nzaramba I, Magdzinski A, Dumais N, Bell B. CTGC motifs within the HIV core promoter specify Tat-responsive pre-initiation complexes. Retrovirology 2012; 9:62; http://dx.doi.org/10.1186/1742-4690-9-62; PMID: 22834489
   PubMed Web of Science ®Google Scholar