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RNAa Induced by TATA Box-Targeting MicroRNAs

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RNA Activation

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 983))

Abstract

Recent studies reveal that some nuclear microRNAs (miRNA) and synthesized siRNAs target gene promoters to activate gene transcription (RNAa). Interestingly, our group identified a novel HIV-1-encoded miRNA, miR-H3, which targets specifically the core promoter TATA box of HIV-1 and activates viral gene expression. Depletion of miR-H3 significantly impaired the replication of HIV-1. miR-H3 mimics could activate viruses from CD4+ T cells isolated from patients receiving suppressive highly active antiretroviral therapy, which is very intriguing for reducing HIV-1 latent reservoir. Further study revealed that many cellular miRNAs also function like miR-H3. For instance, let-7i targets the TATA box of the interleukin-2 (IL-2) promoter and upregulates IL-2 expression in T-lymphocytes. In RNAa induced by TATA box-targeting miRNAs, Argonaute (AGO) proteins are needed, but there is no evidence for the involvement of promoter-associated transcripts or epigenetic modifications. We propose that the binding of small RNA-AGO complex to TATA box could facilitate the assembly of RNA Polymerase II transcription preinitiation complex. In addition, synthesized small RNAs targeting TATA box can also efficiently activate transcription of interested genes, such as insulin, IL-2, and c-Myc. The discovery of RNAa induced by TATA box-targeting miRNA provides an easy-to-use tool for activating gene expression.

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References

  1. Archin NM, Espeseth A, Parker D, Cheema M, Hazuda D, Margolis DM (2009) Expression of latent HIV induced by the potent HDAC inhibitor suberoylanilide hydroxamic acid. AIDS Res Hum Retrovir 25:207–212

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Badley AD, Dockrell D, Simpson M, Schut R, Lynch DH, Leibson P, Paya CV (1997) Macrophage-dependent apoptosis of CD4+ T lymphocytes from HIV-infected individuals is mediated by FasL and tumor necrosis factor. J Exp Med 185:55–64

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116:281–297

    Article  CAS  PubMed  Google Scholar 

  4. Bartel DP (2009) MicroRNAs: target recognition and regulatory functions. Cell 136:215–233

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Bennasser Y, Le SY, Yeung ML, Jeang KT (2004) HIV-1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1:43

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  6. Burley SK, Roeder RG (1996) Biochemistry and structural biology of transcription factor IID (TFIID). Annu Rev Biochem 65:769–799

    Article  CAS  PubMed  Google Scholar 

  7. Bushati N, Cohen SM (2007) microRNA functions. Annu Rev Cell Dev Biol 23:175–205

    Article  CAS  PubMed  Google Scholar 

  8. Cernilogar FM, Onorati MC, Kothe GO, Burroughs AM, Parsi KM, Breiling A, Lo Sardo F, Saxena A, Miyoshi K, Siomi H, Siomi MC, Carninci P, Gilmour DS, Corona DF, Orlando V (2011) Chromatin-associated RNA interference components contribute to transcriptional regulation in drosophila. Nature 480:391–395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  9. Chi T, Carey M (1993) The ZEBRA activation domain: modular organization and mechanism of action. Mol Cell Biol 13:7045–7055

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Chi T, Carey M (1996) Assembly of the isomerized TFIIA – TFIID – TATA ternary complex is necessary and sufficient for gene activation. Genes Dev 10:2540–2550

    Article  CAS  PubMed  Google Scholar 

  11. Choy EY, Siu KL, Kok KH, Lung RW, Tsang CM, To KF, Kwong DL, Tsao SW, Jin DY (2008) An Epstein-Barr virus-encoded microRNA targets PUMA to promote host cell survival. J Exp Med 205:2551–2560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Chu Y, Yue X, Younger ST, Janowski BA, Corey DR (2010) Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter. Nucleic Acids Res 38:7736–7748

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Chun TW, Engel D, Mizell SB, Hallahan CW, Fischette M, Park S, Davey RT Jr, Dybul M, Kovacs JA, Metcalf JA, Mican JM, Berrey MM, Corey L, Lane HC, Fauci AS (1999) Effect of interleukin-2 on the pool of latently infected, resting CD4+ T cells in HIV-1-infected patients receiving highly active anti-retroviral therapy. Nat Med 5:651–655

    Article  CAS  PubMed  Google Scholar 

  14. Coleman RA, Pugh BF (1995) Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA. J Biol Chem 270:13850–13859

    Article  CAS  PubMed  Google Scholar 

  15. Contreras X, Schweneker M, Chen CS, Mccune JM, Deeks SG, Martin J, Peterlin BM (2009) Suberoylanilide hydroxamic acid reactivates HIV from latently infected cells. J Biol Chem 284:6782–6789

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Cooper A, Garcia M, Petrovas C, Yamamoto T, Koup RA, Nabel GJ (2013) HIV-1 causes CD4 cell death through DNA-dependent protein kinase during viral integration. Nature 498:376–379

    Article  CAS  PubMed  Google Scholar 

  17. Cullen BR (2004) Transcription and processing of human microRNA precursors. Mol Cell 16:861–865

    Article  CAS  PubMed  Google Scholar 

  18. Delgadillo RF, Whittington JE, Parkhurst LK, Parkhurst LJ (2009) The TATA-binding protein core domain in solution variably bends TATA sequences via a three-step binding mechanism. Biochemistry 48:1801–1809

    Article  CAS  PubMed  Google Scholar 

  19. Doitsh G, Galloway NL, Geng X, Yang Z, Monroe KM, Zepeda O, Hunt PW, Hatano H, Sowinski S, Munoz-Arias I, Greene WC (2014) Cell death by pyroptosis drives CD4 T-cell depletion in HIV-1 infection. Nature 505:509–514

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Fan J, Bass HZ, Fahey JL (1993) Elevated IFN-gamma and decreased IL-2 gene expression are associated with HIV infection. J Immunol 151:5031–5040

    CAS  PubMed  Google Scholar 

  21. Fan M, Zhang Y, Huang Z, Liu J, Guo X, Zhang H, Luo H (2014) Optimizations of siRNA design for the activation of gene transcription by targeting the TATA-box motif. PLoS One 9:e108253

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  22. Gaffen SL, Liu KD (2004) Overview of interleukin-2 function, production and clinical applications. Cytokine 28:109–123

    Article  CAS  PubMed  Google Scholar 

  23. Gagnon KT, Li L, Chu Y, Janowski BA, Corey DR (2014) RNAi factors are present and active in human cell nuclei. Cell Rep 6:211–221

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ge H, Roeder RG (1994) Purification, cloning, and characterization of a human coactivator, PC4, that mediates transcriptional activation of class II genes. Cell 78:513–523

    Article  CAS  PubMed  Google Scholar 

  25. Gitlin L, Karelsky S, Andino R (2002) Short interfering RNA confers intracellular antiviral immunity in human cells. Nature 418:430–434

    Article  CAS  PubMed  Google Scholar 

  26. Gougeon ML (2003) Apoptosis as an HIV strategy to escape immune attack. Nat Rev Immunol 3:392–404

    Article  CAS  PubMed  Google Scholar 

  27. Gregory RI, Chendrimada TP, Cooch N, Shiekhattar R (2005) Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell 123:631–640

    Article  CAS  PubMed  Google Scholar 

  28. Group IES, Committee SS, Abrams D, Levy Y, Losso MH, Babiker A, Collins G, Cooper DA, Darbyshire J, Emery S, Fox L, Gordin F, Lane HC, Lundgren JD, Mitsuyasu R, Neaton JD, Phillips A, Routy JP, Tambussi G, Wentworth D (2009) Interleukin-2 therapy in patients with HIV infection. N Engl J Med 361:1548–1559

    Article  Google Scholar 

  29. Guang S, Bochner AF, Pavelec DM, Burkhart KB, Harding S, Lachowiec J, Kennedy S (2008) An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science 321:537–541

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  30. Guang S, Bochner AF, Burkhart KB, Burton N, Pavelec DM, Kennedy S (2010) Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature 465:1097–1101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Harwig A, Das AT, Berkhout B (2014) Retroviral microRNAs. Curr Opin Virol 7:47–54

    Article  PubMed  Google Scholar 

  32. Harwig A, Jongejan A, VAN Kampen AH, Berkhout B, DAS AT (2016) Tat-dependent production of an HIV-1 TAR-encoded miRNA-like small RNA. Nucleic Acids Res 44(9):4340–4353

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Herweijer H, Wolff JA (2003) Progress and prospects: naked DNA gene transfer and therapy. Gene Ther 10:453–458

    Article  CAS  PubMed  Google Scholar 

  34. Huang J, Wang F, Argyris E, Chen K, Liang Z, Tian H, Huang W, Squires K, Verlinghieri G, Zhang H (2007) Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med 13:1241–1247

    Article  CAS  PubMed  Google Scholar 

  35. Huang V, Place RF, Portnoy V, Wang J, Qi Z, Jia Z, Yu A, Shuman M, Yu J, Li LC (2012) Upregulation of Cyclin B1 by miRNA and its implications in cancer. Nucleic Acids Res 40:1695–1707

    Article  CAS  PubMed  Google Scholar 

  36. Huang XA, Yin H, Sweeney S, Raha D, Snyder M, Lin H (2013) A major epigenetic programming mechanism guided by piRNAs. Dev Cell 24:502–516

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Huisinga KL, Pugh BF (2004) A genome-wide housekeeping role for TFIID and a highly regulated stress-related role for SAGA in Saccharomyces cerevisiae. Mol Cell 13:573–585

    Article  CAS  PubMed  Google Scholar 

  38. Hussain M, Torres S, Schnettler E, Funk A, Grundhoff A, Pijlman GP, Khromykh AA, Asgari S (2012) West Nile virus encodes a microRNA-like small RNA in the 3′ untranslated region which up-regulates GATA4 mRNA and facilitates virus replication in mosquito cells. Nucleic Acids Res 40:2210–2223

    Article  CAS  PubMed  Google Scholar 

  39. Hutvagner G, Zamore PD (2002) A microRNA in a multiple-turnover RNAi enzyme complex. Science 297:2056–2060

    Article  CAS  PubMed  Google Scholar 

  40. Hutvagner G, Mclachlan J, Pasquinelli AE, Balint E, Tuschl T, Zamore PD (2001) A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293:834–838

    Article  CAS  PubMed  Google Scholar 

  41. Hwang HW, Wentzel EA, Mendell JT (2007) A hexanucleotide element directs microRNA nuclear import. Science 315:97–100

    Article  CAS  PubMed  Google Scholar 

  42. Jacotot E, Ravagnan L, Loeffler M, Ferri KF, Vieira HL, Zamzami N, Costantini P, Druillennec S, Hoebeke J, Briand JP, Irinopoulou T, Daugas E, Susin SA, Cointe D, Xie ZH, Reed JC, Roques BP, Kroemer G (2000) The HIV-1 viral protein R induces apoptosis via a direct effect on the mitochondrial permeability transition pore. J Exp Med 191:33–46

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Jacque JM, Triques K, Stevenson M (2002) Modulation of HIV-1 replication by RNA interference. Nature 418:435–438

    Article  CAS  PubMed  Google Scholar 

  44. Janowski BA, Younger ST, Hardy DB, Ram R, Huffman KE, Corey DR (2007) Activating gene expression in mammalian cells with promoter-targeted duplex RNAs. Nat Chem Biol 3:166–173

    Article  CAS  PubMed  Google Scholar 

  45. Jopling CL, Yi M, Lancaster AM, Lemon SM, Sarnow P (2005) Modulation of hepatitis C virus RNA abundance by a liver-specific MicroRNA. Science 309:1577–1581

    Article  CAS  PubMed  Google Scholar 

  46. Juven-Gershon T, Hsu JY, Theisen JW, Kadonaga JT (2008) The RNA polymerase II core promoter – the gateway to transcription. Curr Opin Cell Biol 20:253–259

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Kassu A, D’souza M, O’connor BP, Kelly-Mcknight E, Akkina R, Fontenot AP, Palmer BE (2009) Decreased 4-1BB expression on HIV-specific CD4+ T cells is associated with sustained viral replication and reduced IL-2 production. Clin Immunol 132:234–245

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Kawasaki H, Taira K (2004) Induction of DNA methylation and gene silencing by short interfering RNAs in human cells. Nature 431:211–217

    Article  CAS  PubMed  Google Scholar 

  49. Kincaid RP, Burke JM, Sullivan CS (2012) RNA virus microRNA that mimics a B-cell oncomiR. Proc Natl Acad Sci U S A 109:3077–3082

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Klase Z, Kale P, Winograd R, Gupta MV, Heydarian M, BERRO R, Mccaffrey T, Kashanchi F (2007) HIV-1 TAR element is processed by Dicer to yield a viral micro-RNA involved in chromatin remodeling of the viral LTR. BMC Mol Biol 8:63

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  51. Klase Z, Winograd R, Davis J, Carpio L, Hildreth R, Heydarian M, Fu S, Mccaffrey T, Meiri E, Ayash-Rashkovsky M, Gilad S, Bentwich Z, Kashanchi F (2009) HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology 6:18

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  52. Klase ZA, Sampey GC, Kashanchi F (2013) Retrovirus infected cells contain viral microRNAs. Retrovirology 10:15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Kovacs JA, Baseler M, Dewar RJ, Vogel S, Davey RT Jr, Falloon J, Polis MA, Walker RE, Stevens R, Salzman NP et al (1995) Increases in CD4 T lymphocytes with intermittent courses of interleukin-2 in patients with human immunodeficiency virus infection. A preliminary study. N Engl J Med 332:567–575

    Article  CAS  PubMed  Google Scholar 

  54. Kozomara A, Griffiths-Jones S (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res 39:D152–D157

    Article  CAS  PubMed  Google Scholar 

  55. Krol J, Loedige I, Filipowicz W (2010) The widespread regulation of microRNA biogenesis, function and decay. Nat Rev Genet 11:597–610

    CAS  PubMed  Google Scholar 

  56. Kruger J, Rehmsmeier M (2006) RNAhybrid: microRNA target prediction easy, fast and flexible. Nucleic Acids Res 34:W451–W454

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  57. Kulkosky J, Culnan DM, Roman J, Dornadula G, Schnell M, Boyd MR, Pomerantz RJ (2001) Prostratin: activation of latent HIV-1 expression suggests a potential inductive adjuvant therapy for HAART. Blood 98:3006–3015

    Article  CAS  PubMed  Google Scholar 

  58. Le Thomas A, Rogers AK, Webster A, Marinov GK, Liao SE, Perkins EM, Hur JK, Aravin AA, Toth KF (2013) Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state. Genes Dev 27:390–399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Lecellier CH, Dunoyer P, Arar K, Lehmann-Che J, Eyquem S, Himber C, Saib A, Voinnet O (2005) A cellular microRNA mediates antiviral defense in human cells. Science 308:557–560

    Article  CAS  PubMed  Google Scholar 

  60. Lee NS, Dohjima T, Bauer G, Li H, Li MJ, Ehsani A, Salvaterra P, Rossi J (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nat Biotechnol 20:500–505

    Article  CAS  PubMed  Google Scholar 

  61. Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN (2003) The nuclear RNase III Drosha initiates microRNA processing. Nature 425:415–419

    Article  CAS  PubMed  Google Scholar 

  62. Li S, Huang L (2000) Nonviral gene therapy: promises and challenges. Gene Ther 7:31–34

    Article  CAS  PubMed  Google Scholar 

  63. Li CJ, Friedman DJ, Wang C, Metelev V, Pardee AB (1995) Induction of apoptosis in uninfected lymphocytes by HIV-1 Tat protein. Science 268:429–431

    Article  CAS  PubMed  Google Scholar 

  64. Li LC, Okino ST, Zhao H, Pookot D, Place RF, Urakami S, Enokida H, Dahiya R (2006) Small dsRNAs induce transcriptional activation in human cells. Proc Natl Acad Sci U S A 103:17337–17342

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Liao JY, Ma LM, Guo YH, Zhang YC, Zhou H, Shao P, Chen YQ, Qu LH (2010) Deep sequencing of human nuclear and cytoplasmic small RNAs reveals an unexpectedly complex subcellular distribution of miRNAs and tRNA 3′ trailers. PLoS One 5:e10563

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  66. Liao W, Lin JX, Leonard WJ (2011) IL-2 family cytokines: new insights into the complex roles of IL-2 as a broad regulator of T helper cell differentiation. Curr Opin Immunol 23:598–604

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Lord JD, Mcintosh BC, Greenberg PD, Nelson BH (2000) The IL-2 receptor promotes lymphocyte proliferation and induction of the c-myc, bcl-2, and bcl-x genes through the trans-activation domain of Stat5. J Immunol 164:2533–2541

    Article  CAS  PubMed  Google Scholar 

  68. Lytle JR, Yario TA, Steitz JA (2007) Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5′ UTR as in the 3′ UTR. Proc Natl Acad Sci U S A 104:9667–9672

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  69. Manninen A, Renkema GH, Saksela K (2000) Synergistic activation of NFAT by HIV-1 nef and the Ras/MAPK pathway. J Biol Chem 275:16513–16517

    Article  CAS  PubMed  Google Scholar 

  70. Martinez J, Patkaniowska A, Urlaub H, Luhrmann R, Tuschl T (2002) Single-stranded antisense siRNAs guide target RNA cleavage in RNAi. Cell 110:563–574

    Article  CAS  PubMed  Google Scholar 

  71. Matsui M, Sakurai F, Elbashir S, Foster DJ, Manoharan M, Corey DR (2010) Activation of LDL receptor expression by small RNAs complementary to a noncoding transcript that overlaps the LDLR promoter. Chem Biol 17:1344–1355

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  72. Matzke M, Aufsatz W, Kanno T, Daxinger L, Papp I, Mette MF, Matzke AJ (2004) Genetic analysis of RNA-mediated transcriptional gene silencing. Biochim Biophys Acta 1677:129–141

    Article  CAS  PubMed  Google Scholar 

  73. Miyazaki T, Liu ZJ, Kawahara A, Minami Y, Yamada K, Tsujimoto Y, Barsoumian EL, Permutter RM, Taniguchi T (1995) Three distinct IL-2 signaling pathways mediated by bcl-2, c-myc, and lck cooperate in hematopoietic cell proliferation. Cell 81:223–231

    Article  CAS  PubMed  Google Scholar 

  74. Morris KV, Chan SW, Jacobsen SE, Looney DJ (2004) Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305:1289–1292

    Article  CAS  PubMed  Google Scholar 

  75. Motamedi MR, Verdel A, Colmenares SU, Gerber SA, Gygi SP, Moazed D (2004) Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119:789–802

    Article  CAS  PubMed  Google Scholar 

  76. Napoli S, Pastori C, Magistri M, Carbone GM, Catapano CV (2009) Promoter-specific transcriptional interference and c-myc gene silencing by siRNAs in human cells. EMBO J 28:1708–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  77. Nishi K, Nishi A, Nagasawa T, Ui-Tei K (2013) Human TNRC6A is an Argonaute-navigator protein for microRNA-mediated gene silencing in the nucleus. RNA 19:17–35

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Novina CD, Murray MF, Dykxhoorn DM, Beresford PJ, Riess J, Lee SK, Collman RG, Lieberman J, Shankar P, Sharp PA (2002) siRNA-directed inhibition of HIV-1 infection. Nat Med 8:681–686

    CAS  PubMed  Google Scholar 

  79. O’Donnell KA, Wentzel EA, Zeller KI, Dang CV, Mendell JT (2005) c-Myc-regulated microRNAs modulate E2F1 expression. Nature 435:839–843

    Article  PubMed  CAS  Google Scholar 

  80. Omoto S, Ito M, Tsutsumi Y, Ichikawa Y, Okuyama H, Brisibe EA, Saksena NK, Fujii YR (2004) HIV-1 nef suppression by virally encoded microRNA. Retrovirology 1:44

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  81. Orom UA, Nielsen FC, Lund AH (2008) MicroRNA-10a binds the 5′UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30:460–471

    Article  PubMed  CAS  Google Scholar 

  82. Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, Flamand L, Tremblay MJ, Provost P (2008) Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res 36:2353–2365

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Ouellet DL, Vigneault-Edwards J, Letourneau K, Gobeil LA, Plante I, Burnett JC, rossi JJ, Provost P (2013) Regulation of host gene expression by HIV-1 TAR microRNAs. Retrovirology 10:86

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  84. Pandolfi F, Pierdominici M, Marziali M, Livia Bernardi M, Antonelli G, Galati V, D’Offizi G, Aiuti F (2000) Low-dose IL-2 reduces lymphocyte apoptosis and increases naive CD4 cells in HIV-1 patients treated with HAART. Clin Immunol 94:153–159

    Article  CAS  PubMed  Google Scholar 

  85. Pelissier T, Thalmeir S, Kempe D, Sanger HL, Wassenegger M (1999) Heavy de novo methylation at symmetrical and non-symmetrical sites is a hallmark of RNA-directed DNA methylation. Nucleic Acids Res 27:1625–1634

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  86. Pfeffer S, Zavolan M, Grasser FA, Chien M, Russo JJ, Ju J, John B, Enright AJ, Marks D, Sander C, Tuschl T (2004) Identification of virus-encoded microRNAs. Science 304:734–736

    Article  CAS  PubMed  Google Scholar 

  87. Pfeffer S, Sewer A, Lagos-Quintana M, Sheridan R, Sander C, Grasser FA, van Dyk LF, Ho CK, Shuman S, Chien M, Russo JJ, Ju J, Randall G, Lindenbach BD, Rice CM, Simon V, Ho DD, Zavolan M, Tuschl T (2005) Identification of microRNAs of the herpesvirus family. Nat Methods 2:269–276

    Article  CAS  PubMed  Google Scholar 

  88. Place RF, Li LC, Pookot D, Noonan EJ, Dahiya R (2008) MicroRNA-373 induces expression of genes with complementary promoter sequences. Proc Natl Acad Sci U S A 105:1608–1613

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Place RF, Noonan EJ, Foldes-Papp Z, Li LC (2010) Defining features and exploring chemical modifications to manipulate RNAa activity. Curr Pharm Biotechnol 11:518–526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Porichis F, Kaufmann DE (2011) HIV-specific CD4 T cells and immune control of viral replication. Curr Opin HIV AIDS 6:174–180

    Article  PubMed  PubMed Central  Google Scholar 

  91. Portnoy V, Huang V, Place RF, Li LC (2011) Small RNA and transcriptional upregulation. Wiley Interdiscip Rev RNA 2:748–760

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Rajasethupathy P, Antonov I, Sheridan R, Frey S, Sander C, Tuschl T, Kandel ER (2012) A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell 149:693–707

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  93. Sandelin A, Carninci P, Lenhard B, Ponjavic J, Hayashizaki Y, Hume DA (2007) Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet 8:424–436

    Article  CAS  PubMed  Google Scholar 

  94. Schopman NC, Willemsen M, Liu YP, Bradley T, van Kampen A, Baas F, Berkhout B, Haasnoot J (2011) Deep sequencing of virus-infected cells reveals HIV-encoded small RNAs. Nucleic Acids Res 40:414–427

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  95. Schwartz JC, Younger ST, Nguyen NB, Hardy DB, Monia BP, Corey DR, Janowski BA (2008) Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol 15:842–848

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  96. Seddiki N, Phetsouphanh C, Swaminathan S, Xu Y, Rao S, Li J, Sutcliffe EL, Denyer G, Finlayson R, Gelgor L, Cooper DA, Zaunders J, Kelleher AD (2013) The microRNA-9/B-lymphocyte-induced maturation protein-1/IL-2 axis is differentially regulated in progressive HIV infection. Eur J Immunol 43:510–520

    Article  CAS  PubMed  Google Scholar 

  97. Shykind BM, Kim J, Sharp PA (1995) Activation of the TFIID-TFIIA complex with HMG-2. Genes Dev 9:1354–1365

    Article  CAS  PubMed  Google Scholar 

  98. Sieg SF, Bazdar DA, Harding CV, Lederman MM (2001) Differential expression of interleukin-2 and gamma interferon in human immunodeficiency virus disease. J Virol 75:9983–9985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Stern-Ginossar N, Elefant N, Zimmermann A, Wolf DG, Saleh N, Biton M, Horwitz E, Prokocimer Z, Prichard M, Hahn G, Goldman-Wohl D, Greenfield C, Yagel S, Hengel H, Altuvia Y, Margalit H, Mandelboim O (2007) Host immune system gene targeting by a viral miRNA. Science 317:376–381

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Sullivan CS, Grundhoff AT, Tevethia S, Pipas JM, Ganem D (2005) SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature 435:682–686

    Article  CAS  PubMed  Google Scholar 

  101. Swaminathan S, Suzuki K, Seddiki N, Kaplan W, Cowley MJ, Hood CL, Clancy JL, Murray DD, Mendez C, Gelgor L, Anderson B, Roth N, Cooper DA, Kelleher AD (2012) Differential regulation of the Let-7 family of microRNAs in CD4+ T cells alters IL-10 expression. J Immunol 188:6238–6246

    Article  CAS  PubMed  Google Scholar 

  102. Taft RJ, Simons C, Nahkuri S, Oey H, Korbie DJ, Mercer TR, Holst J, Ritchie W, Wong JJ, Rasko JE, Rokhsar DS, Degnan BM, Mattick JS (2010) Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. Nat Struct Mol Biol 17:1030–1034

    Article  CAS  PubMed  Google Scholar 

  103. Tan GS, Garchow BG, Liu X, Yeung J, Morris JPT, Cuellar TL, Mcmanus MT, Kiriakidou M (2009) Expanded RNA-binding activities of mammalian Argonaute 2. Nucleic Acids Res 37:7533–7545

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Tay Y, Zhang J, Thomson AM, Lim B, Rigoutsos I (2008) MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation. Nature 455:1124–1128

    Article  CAS  PubMed  Google Scholar 

  105. Thomas MC, Chiang CM (2006) The general transcription machinery and general cofactors. Crit Rev Biochem Mol Biol 41:105–178

    Article  CAS  PubMed  Google Scholar 

  106. Tora L, Timmers HT (2010) The TATA box regulates TATA-binding protein (TBP) dynamics in vivo. Trends Biochem Sci 35:309–314

    Article  CAS  PubMed  Google Scholar 

  107. Turunen MP, Lehtola T, Heinonen SE, Assefa GS, Korpisalo P, Girnary R, Glass CK, Vaisanen S, Yla-Herttuala S (2009) Efficient regulation of VEGF expression by promoter-targeted lentiviral shRNAs based on epigenetic mechanism: a novel example of epigenetherapy. Circ Res 105:604–609

    Article  CAS  PubMed  Google Scholar 

  108. Umbach JL, Cullen BR (2009) The role of RNAi and microRNAs in animal virus replication and antiviral immunity. Genes Dev 23:1151–1164

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  109. Vasudevan S, Tong Y, Steitz JA (2007) Switching from repression to activation: microRNAs can up-regulate translation. Science 318:1931–1934

    Article  CAS  PubMed  Google Scholar 

  110. Verdel A, Jia S, Gerber S, Sugiyama T, Gygi S, Grewal SI, Moazed D (2004) RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303:672–676

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  111. Volpe TA, Kidner C, Hall IM, Teng G, Grewal SI, Martienssen RA (2002) Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297:1833–1837

    Article  CAS  PubMed  Google Scholar 

  112. Wang W, Gralla JD, Carey M (1992) The acidic activator GAL4-AH can stimulate polymerase II transcription by promoting assembly of a closed complex requiring TFIID and TFIIA. Genes Dev 6:1716–1727

    Article  CAS  PubMed  Google Scholar 

  113. Weinmann L, Hock J, Ivacevic T, Ohrt T, Mutze J, Schwille P, Kremmer E, Benes V, Urlaub H, Meister G (2009) Importin 8 is a gene silencing factor that targets argonaute proteins to distinct mRNAs. Cell 136:496–507

    Article  CAS  PubMed  Google Scholar 

  114. van Werven FJ, van Teeffelen HA, Holstege FC, Timmers HT (2009) Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome. Nat Struct Mol Biol 16:1043–1048

    Article  CAS  PubMed  Google Scholar 

  115. Westendorp MO, Frank R, Ochsenbauer C, Stricker K, Dhein J, Walczak H, Debatin KM, Krammer PH (1995) Sensitization of T cells to CD95-mediated apoptosis by HIV-1 Tat and gp120. Nature 375:497–500

    Article  CAS  PubMed  Google Scholar 

  116. White J, Brou C, Wu J, Lutz Y, Moncollin V, Chambon P (1992) The acidic transcriptional activator GAL-VP16 acts on preformed template-committed complexes. EMBO J 11:2229–2240

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Yang C, Bolotin E, Jiang T, Sladek FM, Martinez E (2007) Prevalence of the initiator over the TATA box in human and yeast genes and identification of DNA motifs enriched in human TATA-less core promoters. Gene 389:52–65

    Article  CAS  PubMed  Google Scholar 

  118. Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT (2009) Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid. Nucleic Acids Res 37:6575–6586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  119. Yi R, Qin Y, Macara IG, Cullen BR (2003) Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev 17:3011–3016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  120. Ylisastigui L, Archin NM, Lehrman G, Bosch RJ, Margolis DM (2004) Coaxing HIV-1 from resting CD4 T cells: histone deacetylase inhibition allows latent viral expression. AIDS 18:1101–1108

    Article  CAS  PubMed  Google Scholar 

  121. Younes SA, Yassine-Diab B, Dumont AR, Boulassel MR, Grossman Z, Routy JP, Sekaly RP (2003) HIV-1 viremia prevents the establishment of interleukin 2-producing HIV-specific memory CD4+ T cells endowed with proliferative capacity. J Exp Med 198:1909–1922

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  122. Younger ST, Corey DR (2011) Transcriptional gene silencing in mammalian cells by miRNA mimics that target gene promoters. Nucleic Acids Res 39:5682–5691

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  123. Yue X, Schwartz JC, Chu Y, Younger ST, Gagnon KT, Elbashir S, Janowski BA, Corey DR (2010) Transcriptional regulation by small RNAs at sequences downstream from 3′ gene termini. Nat Chem Biol 6:621–629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  124. Zhang H (2009) Reversal of HIV-1 latency with anti-microRNA inhibitors. Int J Biochem Cell Biol 41:451–454

    Article  CAS  PubMed  Google Scholar 

  125. Zhang Y, Fan M, Geng G, Liu B, Huang Z, Luo H, Zhou J, Guo X, Cai W, Zhang H (2014a) A novel HIV-1-encoded microRNA enhances its viral replication by targeting the TATA box region. Retrovirology 11:23

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  126. Zhang Y, Fan M, Zhang X, Huang F, Wu K, Zhang J, Liu J, Huang Z, Luo H, Tao L, Zhang H (2014b) Cellular microRNAs up-regulate transcription via interaction with promoter TATA-box motifs. RNA 20:1878–1889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  127. Zhang Y, Yin Y, Zhang S, Luo H, Zhang H (2016) HIV-1 infection-induced suppression of the Let-7i/IL-2 axis contributes to CD4(+) T cell death. Sci Rep 6:25341

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Zhang, Y., Zhang, H. (2017). RNAa Induced by TATA Box-Targeting MicroRNAs. In: Li, LC. (eds) RNA Activation. Advances in Experimental Medicine and Biology, vol 983. Springer, Singapore. https://doi.org/10.1007/978-981-10-4310-9_7

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