Replication competent HIV-1 viruses that express intragenomic microRNA reveal discrete RNA-interference mechanisms that affect viral replication
© Klase et al; licensee BioMed Central Ltd. 2011
Received: 9 November 2011
Accepted: 23 November 2011
Published: 23 November 2011
It remains unclear whether retroviruses can encode and express an intragenomic microRNA (miRNA). Some have suggested that processing by the Drosha and Dicer enzymes might preclude the viability of a replicating retroviral RNA genome that contains a cis-embedded miRNA. To date, while many studies have shown that lentiviral vectors containing miRNAs can transduce mammalian cells and express the inserted miRNA efficiently, no study has examined the impact on the replication of a lentivirus such as HIV-1 after the deliberate intragenomic insertion of a bona fide miRNA.
We have constructed several HIV-1 molecular clones, each containing a discrete cellular miRNA positioned in Nef. These retroviral genomes express the inserted miRNA and are generally replication competent in T-cells. The inserted intragenomic miRNA was observed to elicit two different consequences for HIV-1 replication. First, the expression of miRNAs with predicted target sequences in the HIV-1 genome was found to reduce viral replication. Second, in one case, where an inserted miRNA was unusually well-processed by Drosha, this processing event inhibited viral replication.
This is the first study to examine in detail the replication competence of HIV-1 genomes that express cis-embedded miRNAs. The results indicate that a replication competent retroviral genome is not precluded from encoding and expressing a viral miRNA.
KeywordsmiRNA HIV-1 RNA interference viral replication miR326 miR211
RNA interference (RNAi) is a regulatory mechanism conserved in organisms from protozoans to mammals [1–3]. This process employs a small single stranded RNA of 20-24 nucleotides in length which is used as a guide-RNA to direct an RNA-induced silencing complex (RISC) containing the argonaut protein and co-factors to the targeted RNA [4–8]. Human cells encode 1,527 miRNA genes  that are transcribed into precursor primary miRNAs (pri-miRNAs) which are processed in the nucleus by Drosha into shorter hairpin products called pre-miRNA. The pre-miRNAs are exported into the cytoplasm by Exportin-5, and cleaved by Dicer to generate 20-24 nucleotide RNA duplexes, one strand of which is loaded into the Argonaute containing RISC [10–14]. miRNA-RISC complexes can silence target mRNAs via imperfect complementarity with sequences located in the 5'-UTR [15–17], coding sequences [18, 19], and most commonly the 3'-UTR [2, 20, 21].
The RNAi pathway is pleotropically functional in many diverse biological processes; and its dysregulation leads to a plethora of pathologies including cancers, metabolic disorders, and infectious diseases [22–24]. In plants, RNAi as a host defense against viral infections has been well-established [25–27]. In vetebrates, the efficacy of RNAi based antiviral defense is debated [28–32], although several findings support the importance of this mechanism [33–40]. Additionally, there is substantial evidence that RNAi is employed by cells as a mean to keep mammalian endogenous retroviruses (i.e. retrotransposons) under check [41–46].
Several studies have reported that cellular miRNAs can modulate HIV-1 replication in human cells. For example, it was found that miR-28, miR-125b, miR-150, miR-223 and miR-382 function to induce HIV-1 latency in T-cells , and that these same miRNAs conferred resistance to HIV-1 infection in blood monocytes . Furthermore, miR-29 has been shown to silence HIV-1 mRNAs that contain Nef sequences [49–51]. Finally, there is accumulating evidence that some cellular miRNAs may indirectly affect HIV-1 through the regulation of cellular proteins, such as Cyclin T1 and PCAF, which are employed for viral replication [52, 53]. These findings are underscored by studies demonstrating, in models of spreading infection, that the over-expression of proteins involved in RNAi decreases viral replication while the knock-down of these proteins increases viral replication [52, 54–56]
Relevant to their interaction with host cells is the question whether retroviruses can encode viral miRNAs. Some have suggested that the potential vulnerability of RNA-genomes to processing by RNAse III enzymes such as Drosha and Dicer might preclude RNA-viruses from containing cis-embedded miRNAs [37, 57–59]. However, it has been shown that the infecting retroviral genome is apparently shielded by RNA-binding proteins rendering it inaccessible to targeting by RNAi factors . Thus, it remains an open question whether a replication competent retroviral genome can encode a viral miRNA. Relevant to this issue, multiple laboratories have reported the processing of the viral TAR RNA into a miRNA-like non-coding RNA in HIV-1 infected cells [61–65]. The complexity of this multitude of findings cautions that a full understanding of the functions of HIV-1 associated non-coding RNAs awaits further investigation .
The current study was undertaken to answer more clearly whether an HIV-1 genome encoding an intragenomic miRNA is precluded from replication competence. We approached this question by creating several HIV-1 molecular genomes that contain discrete cellular miRNAs positioned in the Nef gene. We asked whether the intragenomic presence of the inserted miRNA in HIV-1 prevents viral replication in human cells. Our results showed no absolute preclusion in human cells against the replication of an HIV-1 genome expressing an intragenomic miRNA.
Construction of five discrete HIV-1 molecular clones containing intragenomic miRNA
Expression of the inserted miRNA from the chimeric NL4-3 miR molecular clones
Intragenomic expression of miR28, miR211 and miR326 reduced single cycle HIV-1 infectivity
Reduced infectivity of NL4-3 miR211 and NL4-3 miR326 arises from different mechanisms
The NL4-3 miR21, the NL4-3 miR326 and the NL4-3 miR28 viruses displayed reduced infectivity. We noted that the NL4-3 miR211 virus expressed its corresponding miRNA at a much higher level (>11,000 copies of miR211 per cell) than the NL4-3 miR326 virus (Figure 3). It is possible that an overly efficient processing of a cis-embedded miRNA within a viral RNA genome may deleteriously affect viral replication. Potentially, the reduced replication of the NL4-3 miR211 virus may be explained by this mechanism. By contrast the reduced replication of the NL4-3 miR326 virus may be because the miR326 expressed from Nef led to the silencing of its complementary NL4-3 target sequence (Figure 1A).
We performed a similar analysis using the NL4-3 miR211 virus. In these experiments, 293T cells were transfected with pNL4-3 let7 scr with or without 100 pM of synthetic miR211, and pNL4-3 miR211 was separately transfected into 293T cells with or without 100 pM anti-miR211 antagomir. Next, cell culture supernatants were harvested and measured for infectivity using TZMbl cells (Figure 5B). Interestingly, the production of the NL4-3 let7 scr virus was not silenced by co-transfected synthetic miR211; nor was the infectivity of NL4-3 miR211 virus increased by co-transfected synthetic anti-miR211 antagomirs. These results suggest that the observed reduction in replication of the NL4-3 miR211 virus is unlikely due to miR211-mediated silencing of a putative complementary HIV-1 RNA target sequence (Figure 1A). Further experiments are needed to determine whether the predicted miR211 complementary viral sequence (Figure 1A) is not a competent target or if synthetic miR211 is not efficiently employed as a guide RNA by RISC.
Chimeric NL4-3 miR viruses produce a spreading viral infection in cultured cells
The ability of mammalian DNA viruses to encode viral miRNAs is well accepted. By contrast, it remains debated whether RNA viruses or retroviruses can encode and express viral miRNAs and remain replication competent. The current study tested the hypothesis that an HIV-1 genome with a cis-embedded miRNA can express the miRNA and propagate a spreading infection in cultured T cells.
To check this hypothesis, we constructed several chimeric HIV-1-miRNA molecular genomes with discrete cellular miRNAs cassetted into the viral Nef gene (Figure 2). For most of these chimeric genomes (NL4-3 miR28, NL4-3 miR29b, NL4-3 miR138, NL4-3 miR326 and NL4-3 miR329), the expression of the Nef-inserted miRNAs was several hundred copies per cell (Figure 3). One of the chimeric HIV-1 miRNA virus, NL4-3 miR211, had an unusually high level (>11,000 copies) of miRNA expression (Figure 3). When the viruses were tested for viral infectivity, three (NL4-3 miR28, NL4-3 miR211, and NL4-3 miR326) showed significantly reduced infectivity when compared to the NL4-3 let 7 scr and NL4-3 let7a control viruses (Figure 4).
The NL4-3 miR211 and NL4-3 miR326 viruses were studied in greater detail to understand the reason(s) for reduced infectivity. We explored two possible explanations. One possibility was that the expressed intragenomic miR211 or miR326 miRNAs recognize a cis-HIV-1 target sequence (Figure 1A) and that this miRNA-viral RNA interaction resulted in silencing, reducing viral infectivity. This explanation could be confirmed if an antagomir targeted against either miR211 or the miR326 would rescue the infectivity of the respective NL4-3 miR211 or pNL4-3 miR326 virus. That the infectivity of NL4-3 miR326, but not NL4-3 miR211, was rescued by a sequence-specific antagomir (Figure 5A) supported the interpretation that miRNA-viral RNA silencing explains the reduced infectivity of the former, but not the latter, virus.
What might explain the reduced infectivity of the NL4-3 miR211 virus? A second possibility is that the decreased infectivity may be due to unusually high efficiency of processing miR211 from NL4-3 transcripts that contain cis-inserted miR211 sequence. It may be that some miRNAs are simply better than other miRNAs as substrates for Drosha, Dicer, or both. If all viral RNAs with embedded-miR211 sequence were cleaved by Drosha or Dicer or both, then such events would severely hamper viral protein expression and could explain the severely attenuated infectivity of the NL4-3 miR211 virus. Indeed, we noted that the knockout of Drosha, but not Dicer, rescued NL4-3 miR211 infectivity (Figure 6A) while either knock down improved the infectivity of the NL4-3 miR326 virus (Figure 6A). Taken together with the findings in Figure 5, the results support that two different mechanisms are operative in reducing NL4-3 miR326 and NL4-3 miR211 viral replication (Figure 8).
Our NL4-3 miR211 virus results agree with a similar observation made by Liu et al. in their study of miRNA expression using a single round lentiviral gene delivery vector . Liu et al. also found that the processing by Drosha of some miRNA-cassettes in lentivectors was one of several mechanisms that reduced particle titers. Because Drosha processing is a nuclear event, the likely scenario for reduced NL4-3 miR211 infectivity is the overly robust cleavage of miR211-embedded HIV-1 RNAs transcribed from the integrated proviral DNA genome (Figure 8), not from the cytoplasmic cleavage of miR211-embedded HIV-1 RNA genome. This interpretation agrees with the earlier observation made by Berkhout and colleagues that the infecting lentiviral RNA genome is well-protected from RNAi-mediated silencing .
Finally, we observed that the NL4-3 let7a and the NL4-3 miR326 viruses are capable of a spreading infection in cultured Jurkat T-cells. These results are consistent with no absolute preclusion against a replicating retrovirus encoding and expressing an intragenomic miRNA. Previously, it has been suggested that the proclivity of DNA viruses to replicate in the nucleus and RNA viruses to replicate mostly in the cytoplasm might explain why the former and latter have varying capacity for encoding viral miRNAs. Since a large part of the retroviral life cycle takes place in the nucleus and the genomic retroviral RNA in the cytoplasm is shielded by RNA-binding proteins , these processes may explain why some retroviruses like HIV-1 do produce modest levels of processed non-coding viral RNAs [61, 63, 64]. Other retroviruses like BLV are suggested to potentially encode more non-coding viral RNAs . A recent study reports the expression of a miRNA-like small RNA from the highly structured 3' UTR of West Nile Virus and found that this RNA is supportive of viral replication . If true, this report would represent another example of a miRNA or miRNA-like RNA encoded by an RNA virus. These reports, together with our currently demonstrated replication competence of HIV-1 genomes expressing inserted cellular miRNAs, encourage additional investigation into the nuanced miRNA-encoding capabilities of DNA viruses, RNA viruses, and retroviruses.
293T and TZMbl cells were maintained in DMEM supplemented with L-glutamine, Penicillin/Streptomycin and 10% fetal bovine serum. For transfections, cells were split 24 hours prior to transfection into 6-well plates at 500,000 cells/well. Cells were transfected with lipofectamine LTX (Invitrogen) according to manufacturer's instructions. For production of viral stocks, the supernatant was harvested at 48 hours after transfection. For siRNA transfections, the cells were first transfected with siRNAs and then re-transfected 24 hours later with proviral plasmids. Jurkat T-cell line was maintained in RPMI supplemented with L-glutamine, Penicillin/Streptomycin and 10% fetal bovine serum.
RNA isolation, qRT-PCR and miRNA measurement
RNA was extracted using Trizol reagent (Invitrogen) following manufacturer's protocol. For the determination of mRNA levels, 1 microgram of RNA was used to create cDNA using the SuperScript III First-Strand Synthesis kit (Invitrogen). Following reverse transcription, the samples were diluted 1:50, and 2.5 microliters were used for quantitative PCR in a BioRad CFX96 or CFX384 qPCR machine. All mRNA analyses were normalized to GAPDH. Nucleic acid amplification was tracked by SYBR Green method. For miRNA quantitation, 1 microgram of RNA was processed using QuantiMir (Systems Bioscience Inc.); the resulting tagged cDNA was quantified using miRNA specific primers via qPCR. All miRNA analyses were normalized to the cellular miRNA miR16.
Infections, RT and TZMbl assay
For infection of Jurkat cells, 6 × 106 cells were seeded in 2 ml of media and exposed to the indicated dose of virus supernatant for 24 hours. Cells were then washed and seeded in 10 ml of fresh RPMI, and sampled over time. Replication was measured through use of the RT activity assay: 5 μl of supernatant were added to 50 μl of RT reaction cocktail (60 mM TrisHCl, 75 mM KCl, 5 mM MgCl2, 1.04 mM EDTA, 0.1 NP-40, 5 μg/ml polyA and 0.16 μg/ml oligo dT) and incubated for two hours at 37°C. The reaction mix was spotted on DEAE membrane, washed with SSC, and dried before counting. For TZMbl assay, cells were seeded in a 96 well plate at 15,000 cells/well for 24 hours. Medium was then replaced with fresh RPMI containing serial dilutions of viral supernatant. Twenty-four hours post infection, the cells were washed, fixed and assayed for the presence of β-galactosidase by X-gal enzymatic assay. Blue cells were counted, and the number of infectious units per volume was computed based on the dilution of infecting supernatant.
Cellular DNA from Jurkat T-cells at 8 days post infection was extracted using Qiagen DNA easy kit. PCR for insertion sites was performed, and the resulting fragments were gel purified and cloned into Invitrogen's TopoTA cloning vector before being directly sequenced.
For cloning for miRNA into NL4-3, we followed a previously described procedure . In brief, the sequence of each pre-miRNA was determined by consulting the miRBase for the human miRNA [74, 75]. PCR primers were designed to amplify these sequences with the addition of Sal I (5' end) and Xho I (3' end) to each pre-miRNA. PCR products were cloned into TopoTA vector (Invitrogen) and excised with Sal I and Xho I. Pre-miRNA fragments were then inserted into the Xho I site of a ΔNef shuttle vector, screened for orientation and then moved into the full length pNL4-3 proviral vector to produce the NL4-3 miR clones. All clones were sequenced to verify the proper insertion of the pre-miRNA sequence.
Primers and oligonucleotides for cloning
Primers for generation of Sal I/Xho I miRNA precursors - let7a ATCGTCGACTGGGATGAGGTAGTAGGTTGTATAG/ACTCGAGTAGGAAAGACAGTAGATTGTATAG, miR28 ATCGTCGACGGTCCTTGCCCTCAAGGAGCTCACA/ACTCGAGAGTGCCTGCCCTCCAGGAGCTCACA, miR29b ATCGTCGACCUUCAGGAAGCUGGUUUCAUAUGGU/ACTCGAGCCCCCAAGAACACTGATTTCAAATG, miR138 ATCGTCGACCCCTGGCATGGTGTGGTGGGGCAGC/ACTCGAGCCTGTAGTGTGGTGTGGCCCTGGTG, miR211 ATCGTCGACUCACCUGGCCAUGUGACUUGUGGGC/ACTCGAGCTCCGTGCTGTGGGAAGTGACAACT, miR326 ATCGTCGACCTCATCTGTCTGTTGGGCTG/ACTCGAGTGAATCCGCCTCGGGGCTGG, miR329 ATCGTCGACGGTACCTGAAGAGAGGTTTTCTGGG/ACTCGAGGATACTGGAAAAGAGGTTAACCAGG
Oligonucleotides for the generation of let7 scr through annealing - ATCGTCGACGTTGTTTAGTATAGTTCTATTGCCCCAACTACGGCTAATAAGGTATCGTCC
- Agrawal N, Dasaradhi PV, Mohmmed A, Malhotra P, Bhatnagar RK, Mukherjee SK: RNA interference: biology, mechanism, and applications. Microbiol Mol Biol Rev. 2003, 67: 657-685. 10.1128/MMBR.67.4.657-685.2003PubMed CentralView ArticlePubMedGoogle Scholar
- Bartel DP: MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004, 116: 281-297. 10.1016/S0092-8674(04)00045-5View ArticlePubMedGoogle Scholar
- Hannon GJ: RNA interference. Nature. 2002, 418: 244-251. 10.1038/418244aView ArticlePubMedGoogle Scholar
- Cenik ES, Zamore PD: Argonaute proteins. Curr Biol. 21: R446-449.
- Chendrimada TP, Gregory RI, Kumaraswamy E, Norman J, Cooch N, Nishikura K, Shiekhattar R: TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature. 2005, 436: 740-744. 10.1038/nature03868PubMed CentralView ArticlePubMedGoogle Scholar
- Chi YH, Semmes OJ, Jeang KT: A proteomic study of TAR-RNA binding protein (TRBP)-associated factors. Cell Biosci. 1: 9.
- Ghildiyal M, Zamore PD: Small silencing RNAs: an expanding universe. Nat Rev Genet. 2009, 10: 94-108. 10.1038/nrg2504PubMed CentralView ArticlePubMedGoogle Scholar
- Haase AD, Jaskiewicz L, Zhang H, Laine S, Sack R, Gatignol A, Filipowicz W: TRBP, a regulator of cellular PKR and HIV-1 virus expression, interacts with Dicer and functions in RNA silencing. EMBO Rep. 2005, 6: 961-967. 10.1038/sj.embor.7400509PubMed CentralView ArticlePubMedGoogle Scholar
- miRBase: the microRNA database. http://www.mirbase.org/index.shtml
- Bernstein E, Caudy AA, Hammond SM, Hannon GJ: Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 2001, 409: 363-366. 10.1038/35053110View ArticlePubMedGoogle Scholar
- Gregory RI, Yan KP, Amuthan G, Chendrimada T, Doratotaj B, Cooch N, Shiekhattar R: The Microprocessor complex mediates the genesis of microRNAs. Nature. 2004, 432: 235-240. 10.1038/nature03120View ArticlePubMedGoogle Scholar
- Lee Y, Ahn C, Han J, Choi H, Kim J, Yim J, Lee J, Provost P, Radmark O, Kim S, Kim VN: The nuclear RNase III Drosha initiates microRNA processing. Nature. 2003, 425: 415-419. 10.1038/nature01957View ArticlePubMedGoogle Scholar
- Sigova A, Rhind N, Zamore PD: A single Argonaute protein mediates both transcriptional and posttranscriptional silencing in Schizosaccharomyces pombe. Genes Dev. 2004, 18: 2359-2367. 10.1101/gad.1218004PubMed CentralView ArticlePubMedGoogle Scholar
- Sontheimer EJ: Assembly and function of RNA silencing complexes. Nat Rev Mol Cell Biol. 2005, 6: 127-138. 10.1038/nrm1568View ArticlePubMedGoogle Scholar
- Easow G, Teleman AA, Cohen SM: Isolation of microRNA targets by miRNP immunopurification. Rna. 2007, 13: 1198-1204. 10.1261/rna.563707PubMed CentralView ArticlePubMedGoogle Scholar
- Lytle JR, Yario TA, Steitz JA: Target mRNAs are repressed as efficiently by microRNA-binding sites in the 5' UTR as in the 3' UTR. Proc Natl Acad Sci USA. 2007, 104: 9667-9672. 10.1073/pnas.0703820104PubMed CentralView ArticlePubMedGoogle Scholar
- Orom UA, Nielsen FC, Lund AH: MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell. 2008, 30: 460-471. 10.1016/j.molcel.2008.05.001View ArticlePubMedGoogle Scholar
- Hafner M, Landthaler M, Burger L, Khorshid M, Hausser J, Berninger P, Rothballer A, Ascano M, Jungkamp AC, Munschauer M: Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell. 141: 129-141.
- Rigoutsos I: New tricks for animal microRNAS: targeting of amino acid coding regions at conserved and nonconserved sites. Cancer Res. 2009, 69: 3245-3248. 10.1158/0008-5472.CAN-09-0352View ArticlePubMedGoogle Scholar
- Olsen PH, Ambros V: The lin-4 regulatory RNA controls developmental timing in Caenorhabditis elegans by blocking LIN-14 protein synthesis after the initiation of translation. Dev Biol. 1999, 216: 671-680. 10.1006/dbio.1999.9523View ArticlePubMedGoogle Scholar
- Doench JG, Sharp PA: Specificity of microRNA target selection in translational repression. Genes Dev. 2004, 18: 504-511. 10.1101/gad.1184404PubMed CentralView ArticlePubMedGoogle Scholar
- Nicolas FE, Lopez-Martinez AF: MicroRNAs in human diseases. Recent Pat DNA Gene Seq. 4: 142-154.
- Sayed D, Abdellatif M: MicroRNAs in development and disease. Physiol Rev. 91: 827-887.
- Yeung ML, Jeang KT: MicroRNAs and Cancer Therapeutics. Pharm Res. 3000.
- Llave C: Virus-derived small interfering RNAs at the core of plant-virus interactions. Trends Plant Sci. 15: 701-707.
- Pantaleo V: Plant RNA silencing in viral defence. Adv Exp Med Biol. 722: 39-58.
- Qu F: Antiviral role of plant-encoded RNA-dependent RNA polymerases revisited with deep sequencing of small interfering RNAs of virus origin. Mol Plant Microbe Interact. 23: 1248-1252.
- Grundhoff A, Sullivan CS: Virus-encoded microRNAs. Virology. 411: 325-343.
- Lei X, Bai Z, Ye F, Huang Y, Gao SJ: Regulation of herpesvirus lifecycle by viral microRNAs. Virulence. 1: 433-435.
- Dhuruvasan K, Sivasubramanian G, Pellett PE: Roles of host and viral microRNAs in human cytomegalovirus biology. Virus Res. 157: 180-192.
- Plaisance-Bonstaff K, Renne R: Viral miRNAs. Methods Mol Biol. 721: 43-66.
- Boss IW, Renne R: Viral miRNAs: tools for immune evasion. Curr Opin Microbiol. 13: 540-545.
- Bivalkar-Mehla S, Vakharia J, Mehla R, Abreha M, Kanwar JR, Tikoo A, Chauhan A: Viral RNA silencing suppressors (RSS): novel strategy of viruses to ablate the host RNA interference (RNAi) defense system. Virus Res. 155: 1-9.
- de Vries W, Berkhout B: RNAi suppressors encoded by pathogenic human viruses. Int J Biochem Cell Biol. 2008, 40: 2007-2012. 10.1016/j.biocel.2008.04.015View ArticlePubMedGoogle Scholar
- Ding SW: RNA-based antiviral immunity. Nat Rev Immunol. 10: 632-644.
- Grassmann R, Jeang KT: The roles of microRNAs in mammalian virus infection. Biochim Biophys Acta. 2008, 1779: 706-711.PubMed CentralView ArticlePubMedGoogle Scholar
- Haasnoot J, Berkhout B: RNAi and cellular miRNAs in infections by mammalian viruses. Methods Mol Biol. 721: 23-41.
- Haasnoot J, Westerhout EM, Berkhout B: RNA interference against viruses: strike and counterstrike. Nat Biotechnol. 2007, 25: 1435-1443. 10.1038/nbt1369View ArticlePubMedGoogle Scholar
- Houzet L, Jeang KT: MicroRNAs and human retroviruses. Biochim Biophys Acta. 3000.
- Song L, Gao S, Jiang W, Chen S, Liu Y, Zhou L, Huang W: Silencing suppressors: viral weapons for countering host cell defenses. Protein Cell. 2: 273-281.
- Yang N, Kazazian HH: L1 retrotransposition is suppressed by endogenously encoded small interfering RNAs in human cultured cells. Nat Struct Mol Biol. 2006, 13: 763-771. 10.1038/nsmb1141View ArticlePubMedGoogle Scholar
- Hakim ST, Alsayari M, McLean DC, Saleem S, Addanki KC, Aggarwal M, Mahalingam K, Bagasra O: A large number of the human microRNAs target lentiviruses, retroviruses, and endogenous retroviruses. Biochem Biophys Res Commun. 2008, 369: 357-362. 10.1016/j.bbrc.2008.02.025View ArticlePubMedGoogle Scholar
- Watanabe T, Takeda A, Tsukiyama T, Mise K, Okuno T, Sasaki H, Minami N, Imai H: Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. Genes Dev. 2006, 20: 1732-1743. 10.1101/gad.1425706PubMed CentralView ArticlePubMedGoogle Scholar
- Carmell MA, Girard A, van de Kant HJ, Bourc'his D, Bestor TH, de Rooij DG, Hannon GJ: MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev Cell. 2007, 12: 503-514. 10.1016/j.devcel.2007.03.001View ArticlePubMedGoogle Scholar
- Calabrese JM, Seila AC, Yeo GW, Sharp PA: RNA sequence analysis defines Dicer's role in mouse embryonic stem cells. Proc Natl Acad Sci USA. 2007, 104: 18097-18102. 10.1073/pnas.0709193104PubMed CentralView ArticlePubMedGoogle Scholar
- De Fazio S, Bartonicek N, Di Giacomo M, Abreu-Goodger C, Sankar A, Funaya C, Antony C, Moreira PN, Enright AJ, O'Carroll D: The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements. Nature.
- Huang J, Wang F, Argyris E, Chen K, Liang Z, Tian H, Huang W, Squires K, Verlinghieri G, Zhang H: Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nat Med. 2007, 13: 1241-1247. 10.1038/nm1639View ArticlePubMedGoogle Scholar
- Wang X, Ye L, Hou W, Zhou Y, Wang YJ, Metzger DS, Ho WZ: Cellular microRNA expression correlates with susceptibility of monocytes/macrophages to HIV-1 infection. Blood. 2009, 113: 671-674. 10.1182/blood-2008-09-175000PubMed CentralView ArticlePubMedGoogle Scholar
- Ahluwalia JK, Khan SZ, Soni K, Rawat P, Gupta A, Hariharan M, Scaria V, Lalwani M, Pillai B, Mitra D, Brahmachari SK: Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication. Retrovirology. 2008, 5: 117. 10.1186/1742-4690-5-117PubMed CentralView ArticlePubMedGoogle Scholar
- Hariharan M, Scaria V, Pillai B, Brahmachari SK: Targets for human encoded microRNAs in HIV genes. Biochem Biophys Res Commun. 2005, 337: 1214-1218. 10.1016/j.bbrc.2005.09.183View ArticlePubMedGoogle Scholar
- Nathans R, Chu CY, Serquina AK, Lu CC, Cao H, Rana TM: Cellular microRNA and P bodies modulate host-HIV-1 interactions. Mol Cell. 2009, 34: 696-709. 10.1016/j.molcel.2009.06.003PubMed CentralView ArticlePubMedGoogle Scholar
- Triboulet R, Mari B, Lin YL, Chable-Bessia C, Bennasser Y, Lebrigand K, Cardinaud B, Maurin T, Barbry P, Baillat V: Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science. 2007, 315: 1579-1582. 10.1126/science.1136319View ArticlePubMedGoogle Scholar
- Sung TL, Rice AP: miR-198 inhibits HIV-1 gene expression and replication in monocytes and its mechanism of action appears to involve repression of cyclin T1. PLoS Pathog. 2009, 5: e1000263. 10.1371/journal.ppat.1000263PubMed CentralView ArticlePubMedGoogle Scholar
- Chable-Bessia C, Meziane O, Latreille D, Triboulet R, Zamborlini A, Wagschal A, Jacquet JM, Reynes J, Levy Y, Saib A: Suppression of HIV-1 replication by microRNA effectors. Retrovirology. 2009, 6: 26. 10.1186/1742-4690-6-26PubMed CentralView ArticlePubMedGoogle Scholar
- Matskevich AA, Moelling K: Dicer is involved in protection against influenza A virus infection. J Gen Virol. 2007, 88: 2627-2635. 10.1099/vir.0.83103-0View ArticlePubMedGoogle Scholar
- Otsuka M, Jing Q, Georgel P, New L, Chen J, Mols J, Kang YJ, Jiang Z, Du X, Cook R: Hypersusceptibility to vesicular stomatitis virus infection in Dicer1-deficient mice is due to impaired miR24 and miR93 expression. Immunity. 2007, 27: 123-134. 10.1016/j.immuni.2007.05.014View ArticlePubMedGoogle Scholar
- Liu YP, Vink MA, Westerink JT, Ramirez de Arellano E, Konstantinova P, Ter Brake O, Berkhout B: Titers of lentiviral vectors encoding shRNAs and miRNAs are reduced by different mechanisms that require distinct repair strategies. Rna. 2010, 16: 1328-1339. 10.1261/rna.1887910PubMed CentralView ArticlePubMedGoogle Scholar
- Poluri A, Sutton RE: Titers of HIV-based vectors encoding shRNAs are reduced by a dicer-dependent mechanism. Mol Ther. 2008, 16: 378-386. 10.1038/sj.mt.6300370View ArticlePubMedGoogle Scholar
- ter Brake O, Berkhout B: Lentiviral vectors that carry anti-HIV shRNAs: problems and solutions. J Gene Med. 2007, 9: 743-750. 10.1002/jgm.1078View ArticlePubMedGoogle Scholar
- Westerhout EM, ter Brake O, Berkhout B: The virion-associated incoming HIV-1 RNA genome is not targeted by RNA interference. Retrovirology. 2006, 3: 57. 10.1186/1742-4690-3-57PubMed CentralView ArticlePubMedGoogle Scholar
- Klase Z, Kale P, Winograd R, Gupta MV, Heydarian M, Berro R, McCaffrey T, Kashanchi F: 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. 2007, 8: 63. 10.1186/1471-2199-8-63PubMed CentralView ArticlePubMedGoogle Scholar
- Klase Z, Winograd R, Davis J, Carpio L, Hildreth R, Heydarian M, Fu S, McCaffrey T, Meiri E, Ayash-Rashkovsky M: HIV-1 TAR miRNA protects against apoptosis by altering cellular gene expression. Retrovirology. 2009, 6: 18. 10.1186/1742-4690-6-18PubMed CentralView ArticlePubMedGoogle Scholar
- Ouellet DL, Plante I, Landry P, Barat C, Janelle ME, Flamand L, Tremblay MJ, Provost P: Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res. 2008, 36: 2353-2365. 10.1093/nar/gkn076PubMed CentralView ArticlePubMedGoogle Scholar
- Yeung ML, Bennasser Y, Watashi K, Le SY, Houzet L, Jeang KT: 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. 2009, 37: 6575-6586. 10.1093/nar/gkp707PubMed CentralView ArticlePubMedGoogle Scholar
- Purzycka KJ, Adamiak RW: The HIV-2 TAR RNA domain as a potential source of viral-encoded miRNA. A reconnaissance study. Nucleic Acids Symp Ser (Oxf). 2008, 511-512.
- Smith SM, Markham RB, Jeang KT: Conditional reduction of human immunodeficiency virus type 1 replication by a gain-of-herpes simplex virus 1 thymidine kinase function. Proc Natl Acad Sci USA. 1996, 93: 7955-7960. 10.1073/pnas.93.15.7955PubMed CentralView ArticlePubMedGoogle Scholar
- Kim S, Ikeuchi K, Byrn R, Groopman J, Baltimore D: Lack of a negative influence on viral growth by the nef gene of human immunodeficiency virus type 1. Proc Natl Acad Sci USA. 1989, 86: 9544-9548. 10.1073/pnas.86.23.9544PubMed CentralView ArticlePubMedGoogle Scholar
- Bartel DP: MicroRNAs: target recognition and regulatory functions. Cell. 2009, 136: 215-233. 10.1016/j.cell.2009.01.002PubMed CentralView ArticlePubMedGoogle Scholar
- Miura S, Nozawa M, Nei M: Evolutionary changes of the target sites of two microRNAs encoded in the Hox gene cluster of Drosophila and other insect species. Genome Biol Evol. 3: 129-139.
- Vella MC, Choi EY, Lin SY, Reinert K, Slack FJ: The C. elegans microRNA let-7 binds to imperfect let-7 complementary sites from the lin-41 3'UTR. Genes Dev. 2004, 18: 132-137. 10.1101/gad.1165404PubMed CentralView ArticlePubMedGoogle Scholar
- Wei X, Decker JM, Liu H, Zhang Z, Arani RB, Kilby JM, Saag MS, Wu X, Shaw GM, Kappes JC: Emergence of resistant human immunodeficiency virus type 1 in patients receiving fusion inhibitor (T-20) monotherapy. Antimicrob Agents Chemother. 2002, 46: 1896-1905. 10.1128/AAC.46.6.1896-1905.2002PubMed CentralView ArticlePubMedGoogle Scholar
- Martin F, Bangham CR, Ciminale V, Lairmore MD, Murphy EL, Switzer WM, Mahieux R: Conference Highlights of the 15th International Conference on Human Retrovirology: HTLV and Related Retroviruses, 4-8 June 2011, Leuven, Gembloux, Belgium. Retrovirology. 8: 86.
- Hussain M, Torres S, Schnettler E, Funk A, Grundhoff A, Pijlman GP, Khromykh AA, Asgari S: 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. PMID: 22080551.
- Griffiths-Jones S: The microRNA Registry. Nucleic Acids Res. 2004, 32: D109-111. 10.1093/nar/gkh023PubMed CentralView ArticlePubMedGoogle Scholar
- Kozomara A, Griffiths-Jones S: miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 39: D152-157.
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.