Understanding HIV‑1 latency provides
clues for the eradication of long-term
Mayte Coiras, María Rosa L...
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Box 1 | Lymphocyte subpopulations and HIV‑1 replication
• Naive T cells are a population of T cells that have not ...


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Box 2 | Mechanisms for the generation of HIV‑1 latency
• Transcriptional interference, owing to the site and orien...
a Location of integrated HIV-1 genomes

c Transcriptional interference
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114.	 Marban, C. et al. Recruitment of chromatin-modifying
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VH1 latente proporciona pistas para la erradicación de depósitos a largo plazo
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VH1 latente proporciona pistas para la erradicación de depósitos a largo plazo


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VH1 latente proporciona pistas para la erradicación de depósitos a largo plazo

  1. 1. REVIEWS Understanding HIV‑1 latency provides clues for the eradication of long-term reservoirs Mayte Coiras, María Rosa López-Huertas, Mayte Pérez-Olmeda and José Alcamí Abstract | HIV‑1 can infect both activated and resting, non-dividing cells, following which the viral genome can be permanently integrated into a host cell chromosome. Latent HIV‑1 reservoirs are established early during primary infection and constitute a major barrier to eradication, even in the presence of highly active antiretroviral therapy. This Review analyses the molecular mechanisms that are necessary for the establishment of HIV‑1 latency and their relationships with different cellular and anatomical reservoirs, and discusses the current treatment strategies for targeting viral persistence in reservoirs, their main limitations and future perspectives. Highly active antiretroviral therapy A combination of three or more potent anti-HIV‑1 drugs that reduces viral load below detection limits by standard techniques. Reservoir A cell type or anatomical site in which a replication-competent virus persists for much longer than it does in the main pool of productive infected cells, thereby sustaining the infection. Integrated proviral genomes and cells that persistently replicate HIV‑1  in the presence of highly active antiretroviral therapy can be considered viral reservoirs. AIDS Immunopathology Unit, National Centre of Microbiology, Instituto de Salud Carlos III, 28220 Majadahonda, Madrid, Spain. e‑mails:;;; doi:10.1038/nrmicro2223 The HIV‑1 pandemic represents one of the great plagues in human history and a major challenge for medicine, public health and biological research. Infection with HIV‑1, which was first isolated in 1983 (REF. 1), causes AIDS, a syndrome that was first described in 1981 (REF. 2). Continuous research has allowed the devel‑ opment of effective treatments that have transformed HIV‑1 infection from a fatal illness into a chronic dis‑ ease3. Currently, 25 different active compounds belong‑ ing to 6 different drug families have been developed. However, regardless of the use of highly active antiretroviral therapy (HAART), a cure is not yet achievable, and HIV‑1 persistence in reservoirs represents the major obstacle for its eradication4,5. All lentiviruses can infect macrophage lineage cells, in which they generate a persistent infection6. HIV‑1 is a lenti­ irus that has developed a broader tropism, leading to v preferential infection of CD4+ T cells, which are severely destroyed during the illness7. This target provides two potential environments for the virus, allowing latency in resting CD4+ T cells and massive viral replication in activated cells8. The molecular mechanisms that lead to HIV‑1 reac‑ tivation have been characterized in detail, but the study of viral latency remains limited. Recently, the identifi‑ cation of factors that restrict retroviral infections9, the characterization of chromatin structure in the setting of viral integration10, the discovery of new systems that regulate gene expression (such as small interfering RNAs (siRNAs)11) and the development of new techniques for analysing HIV‑1 latency 12 have provided a new perspective on this concealed state. Indeed, latency should not be considered a merely passive event but, rather, an active process that is maintained by cellular elements. In this Review, the molecular mechanisms that are necessary for the establishment of HIV‑1 latency, their relationship with different cellular and anatomical reservoirs and the current treatment strategies to target viral persistence are analysed. HIV‑1 life cycle The life cycle of HIV-1 can be divided into two phases: the early stage occurs between entry into the host cell and integration into its genome, and the late phase occurs from the state of integrated provirus to full viral replication. Accordingly, two types of viral latency can be differentiated: pre-integration latency refers to the gen‑ eration of different forms of viral DNA before integra‑ tion, whereas post-integration latency refers to the lack of replication after the insertion of viral DNA into the host genome8,13. Viral entry involves the fusion of viral and cellular membranes through successive interactions with CD4 and CXC chemokine receptor type 4 (CXCR4) or CC chemokine receptor type 5 (CCR5)7 (FIG. 1). The HIV‑1 core, containing two single-stranded, plus-sense RNA genomes, tRNA primers, viral protease, retro‑ transcriptase and integrase, is released into the cytosol. This intracellular core is named the reverse transcrip‑ tion complex because most of the viral RNA genome is reverse transcribed by the retrotranscriptase to form a linear, mostly double-stranded cDNA (dscDNA) molecule with terminal direct repeats and blunt ends14. 798 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  2. 2. REVIEWS Microtubule network and actin filaments gp41 and gp120 Proviral DNA synthesis Full- and shortlength dscDNA Reverse transcription complex Pre-integration complex Pre-integration latency Circular, nonintegrated DNA Linear dscDNA NPC Nuclear import Integration Post-integration latency Provirus Nuclear export NF-κB, SP1, NFAT, Tat Unspliced mRNA Genomic RNA Transcription Assembly Nuclear export Rev Budding and maturation Translation of viral proteins Multiple spliced mRNA Nucleus Provirus Viral genomic double-stranded cDNA that has permanently integrated into the host cell genome and that acts as a template for the synthesis of viral RNAs. Direct repeats Two or more identical or nearly identical repeats of specific nucleotide sequences that are in the same direction in the DNA molecule. Blunt end The end of a double-stranded DNA molecule that terminates in paired bases, rather than with uneven ends, such that one strand overhangs. Enhancer element A DNA consensus site, usually located 5′ from the basal gene promoter, that is bound to by specific transcription factors to increase the rate of transcription of the gene that it controls. An enhancer element may be placed thousands of bases upstream or downstream of the transcription initiation site of this gene. Figure 1 | HIV‑1 life cycle and viral latency. Viral fusion and entry requires the binding of glycoprotein gp120 to CD4 Nature Reviews | Microbiology receptors at the cell surface as well as to CC chemokine receptor type 5 (CCR5) or CXC chemokine receptor type 4 (CXCR4). The viral nucleocapsid enters the cytoplasm and uses cytoplasmic dynein to move toward the nuclear pore complex (NPC). The viral RNA is retrotranscribed into proviral double-stranded cDNA (dscDNA), which can stay in the cytosol, where it is highly unstable and exists in a transient, reversible pre-integration latent state, or can form a pre-integration complex consisting of dscDNA, viral proteins and some host cell proteins. When ATP levels are adequate, the pre-integration complex is transported into the nucleus through the NPC, and the dscDNA either circularizes as one or two long terminal repeat-containing circles or is integrated into a host cell chromosome. After integration, the provirus remains quiescent, existing in a permanent post-integration latent state. On activation, the viral genome is transcribed by the synergic interaction of cellular transcription factors (nuclear factor-κB (NF-κB), nuclear factor of activated T cells (NFAT) and specificity protein 1 ( SP1)) and the viral transactivator, Tat. Rev, a viral protein, regulates the splicing and cytosolic transport of some of the viral mRNAs, which are translated into regulatory and structural viral proteins. New virions assemble and bud through the cell membrane, maturing through the activity of the viral protease. Once in the cytoplasm, the reverse transcriptase complex progressively disassembles to form the pre-integration complex (PIC), which is composed of linear dscDNA, integrase, matrix protein, retrotranscriptase, viral protein r (Vpr) and various hosts proteins, such as the high-mobility group protein B1 (HMG1) or the lens epithelium-derived growth factor (LEDGF; also known as PSIP1)15–18. Viral trafficking is mediated through microtubules by retrograde transport and uses dynein to move towards the nuclear pore complex19. At the nuclear pore complex, the PIC enables the transport of dscDNA through the intact nuclear envelope, thereby allowing the infection of resting, non-dividing cells. Linear dscDNA either integrates into the host cell chromosomes or circularizes as one or two long terminal repeat (LTR)containing circles16. Host factors such as emerin and LEDGF are key molecules that facilitate HIV‑1 integra‑ tion20,21. Emerin is an inner nuclear envelope protein that seems to increase the efficiency of viral integration in macrophages by improving the localization of viral DNA to the chromatin before integration22, whereas LEDGF is a transcriptional co-activator that binds integrase and acts as a tethering factor to promote viral integration18. After integration, the LTR-flanked provirus behaves as a cellular gene: the 5′ LTR operates like any eukaryotic promoter and the 3′ LTR acts as the polyadenylation and termination site23. Activation of the T cell induces binding of the tran‑ scriptional pre-initiation complex to enhancer elements in the 5′ LTR proximal promoter (FIG. 1). This complex gathers essential host transcription factors, such as nuclear factor-κB (NF-κB)24, nuclear factor of activated nature reviews | Microbiology Volume 7 | november 2009 | 799 © 2009 Macmillan Publishers Limited. All rights reserved.
  3. 3. REVIEWS Box 1 | Lymphocyte subpopulations and HIV‑1 replication • Naive T cells are a population of T cells that have not yet contacted the foreign antigens that they are committed to identify and therefore are not activated. • Activated T cells are those that initiate clonal proliferation after their T cell receptors recognize non-self peptides that are presented by the class II major histocompatibility complex. T cells can also be activated by inflammatory mediators, in particular cytokines and chemokines, and through the engagement of Toll-like receptors that recognize pathogen-associated molecular patterns65,177. • Effector T cells are naive T cells than have been activated. • Memory T cells are those effector T cells that do not die in the process of the immune response but return to an arrested state, waiting for the same antigen to reappear. • Resting T cells are naive or memory T cells that are at the G0 state of the cell cycle, that have an extended lifespan and that lack T cell activation markers on the cell surface. Tat A regulatory HIV‑1 protein that is essential for viral transcript elongation through its interaction with the Tat response element and several host factors, such as the positive transcription elongation factor b. Rev A regulatory HIV‑1 protein that controls the nuclear export of viral mRNA species through its interaction with the Rev response element that is found in unspliced or incompletly spliced HIV‑1 RNAs. Naive T cell A mature T cell from the acquired immune system that has not yet made contact with its cognate antigen and that therefore lacks both activation and memory markers on the cell surface. Memory T cell A T cell that persists for a long time after its exposure to a specific foreign antigen and that can be promptly expanded to effector T cells after contact with the same antigen to initiate a faster and stronger immune response. Retroviral restriction factor A component of the innate immune system that aids the survival of a host cell after retroviral infection by interfering with viral replication at different steps of the viral life cycle. T  cells (NFAT) 25 and specificity protein 1 (SP1) 26. These enhancer proteins transmit activation signals to basal factors belonging to the general transcription machinery and promote binding of RNA polymerase II (RNAPII) to the TATA box to initiate mRNA transcrip‑ tion. A 59-nucleotide stem-loop structure termed the transactivation response element (TAR) is then formed at the 5′ end of the nascent viral transcript, creating a binding site for the viral transactivator Tat27. The Tat– TAR interaction promotes efficient elongation of viral transcripts by recruiting cellular factors that increase the functional capacity of RNAPII, such as positive transcription elongation factor b (PTEFb), which is composed of cyclin-dependent kinase 9 (CDK9) and cyclin T1 (Refs 28,29). Efficient elongation of viral tran‑ scripts allows the synthesis of mRNA, which is further processed by the regulatory protein Rev. Rev is a viral RNA-binding factor that regulates the nucleo-cytosolic transport and splicing of viral mRNA species30. Once in the cytoplasm, HIV‑1 proteins are synthesized as large precursor polyproteins that must be processed into mature viral proteins and then assemble to create viable particles that will bud off the cell and infect new cells31 (FIG. 1). Cellular environment and HIV‑1 replication Resting lymphocytes: the territory of latency. The acti‑ vation of resting naive T cells gives rise to effector T cells (BOX 1). Most of these die during the immune response, but some return to a resting state and become memory T cells (FIG. 2a). Both naive and memory subpopula‑ tions of resting lymphocytes represent an extremely restrictive environment for HIV‑1 replication, owing to several mechanisms. First, CCR5 expression is low or absent, which limits the number of targets available to the virus32, and second, low nucleotide pools and ATP levels in these cells cause inefficient retrotranscrip‑ tion33,34 and limited nuclear PIC import, respectively 35. Moreover, the virus must overcome several cellular retroviral restriction factors , such as the cytoplasmic APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G). This cytidine deami‑ nase exists in resting CD4+ T cells as an enzymatically active, low‑molecular-mass complex and interferes with reverse transcription through the induction of non-viable viruses with G‑to‑A-hypermutated genomes36. Owing to integration restraints, both linear and circular forms of unintegrated viral dscDNA accu‑ mulate in resting CD4+ T cells. Linear, unintegrated DNA is susceptible to integration on cell activation and is considered to be a source of potential viral reser‑ voirs14,33 (FIG. 2b). However, its short half-life — 24 hours to a few days — limits its impact in the generation of a stable pool of infected T cells that carry integrated proviruses37,38. Although non-integrated viral DNA cannot produce viable particles39, it can generate some RNA transcripts and produce the HIV‑1 negative fac‑ tor (Nef) in resting CD4+ T cells40 and macrophages41. This could increase cell activation and therefore facili‑ tate HIV‑1 replication, either in the same cell40 or in surrounding cells (through the production of soluble factors by Nef-expressing macrophages)42. Stable post-integration latency is more relevant for HIV‑1 persistence and it has been widely documented in different groups of patients, including naive and treated adults, children and elite controllers43–46. The reservoir of latently infected CD4+ T cells carrying replicationcompetent HIV‑1 genomes is established in primary infection47. It has been estimated to comprise 106–107 cells in asymptomatic patients48, whose infected naive CD4+ T cells can harbour an average of 3–4 copies of the integrated provirus per cell49. These cells do not progress to complete viral replication unless they are activated50, and their stability and long half-lives represent major obstacles to HIV‑1 eradication51,52. The activation of resting CD4+ T cells harbouring linear, non-integrated DNA14,33 and the persistence of proviral DNA in memory T cells that return to a quies‑ cent state after activation are the two proposed sources of integrated proviral DNA in latently infected cells53,54. However, it is difficult to conceive that cells could sur‑ vive the massive viral replication that is induced in activated CD4 + T cells. As an alternative, memory T cells could become infected during the decay phase of activation, therefore allowing viral integration with no further progression to active replication55. Recently, it has been proposed that infected memory T cells can be expanded by homeostatic proliferation driven by interleukin‑7 (IL‑7) or low-level proliferation driven by antigens 56. As only a fraction of latently infected cells are naive T cells57, alternative mechanisms for latent integration must exist. One possible explana‑ tion could be the contribution of infected thymocytes and suboptimal activation pathways58. Viral replication in activated T cells. The phenotypic changes that are induced by immune activation in CD4 + T cells provide an optimal environment for robust HIV‑1 replication59. Expression of CCR5 allows viral entry, and efficient retrotranscription takes place owing to high nucleotide pools and APOBEC3G inhi‑ bition36. Following integration into the host genome, the expression of cellular transcription factors and viral Tat increases transcription and elongation of the provirus, respectively, through the recruitment of PTEFb to the LTR promoter 29. CD4+ T cells that are 800 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  4. 4. REVIEWS a Apoptosis Antigen Antigen Naive CD4+ T cell Memory CD4+ T cell Clonal proliferation b Apoptosis Antigen Naive CD4+ T cell Pre-integration latency Suboptimal activation Antigen Clonal proliferation and viral replication Suboptimal activation Memory CD4+ T cell Pre-integration latency Macrophage Memory CD4+ T cell Post-integration latency Suboptimal activation Post-integration latency HIV-infected macrophage Low ongoing replication Persistent replication Figure 2 | HIV‑1 replication in different cellular environments.Reviews | Microbiology Nature a | After stimulation with specific antigens, naive CD4+ T cells begin clonal proliferation to produce effector T cells in an attempt to destroy the pathogen. As the antigen wanes, T cells undergo apoptosis or turn into memory cells that remain quiescent until they contact the same antigen, eliciting a more robust immune response. b | After HIV‑1 infects resting, naive T cells, these cells can carry partially transcribed, unintegrated viral double-stranded cDNA (dscDNA) that can be degraded in the absence of activation. However, if these cells are stimulated by their cognate antigen they begin clonal proliferation, which allows the integration of viral dscDNA into the host cell genome and active HIV‑1 replication. As the antigen fades, most HIV-infected effector T cells die by apoptosis, but some remain as memory T cells, carrying a permanent provirus in their genome that undergoes viral replication if the cell is stimulated again with the same antigen. In the case of suboptimal activation, the partially transcribed, unintegrated viral dscDNA can be completed and successfully integrated into the host cell genome, inducing a post-integration latent state. Moreover, a continuous low-level replication occurs in these cells even in the absence of activation, as is also the case in highly stable cells such as macrophages. Elite controller A patient infected with HIV whose immune system can limit viral RNA to below 50 copies per ml for at least 12 months in the absence of highly active antiretroviral therapy. activated by HIV‑1, other foreign antigens, inflamma‑ tory mediators or Toll-like receptors become particu‑ larly susceptible to HIV‑1 infection60,61. In this context, a vicious cycle of immune activation and HIV‑1 spreading is established (FIG. 2b), and activated CD4+ T cells that are largely located in the gut-associated lymphoid tissue become severely depleted during the course of the disease62–65. Low-level viral replication in resting T cells. Low-level HIV‑1 replication in CD4+ T cells that lack activation markers has been described in tissues from macaques and patients infected with the virus66,67. Therefore, unlike peripheral blood CD4+ T cells68, mucosal naive T cells can be productively infected by HIV‑1. Several findings support the role for suboptimal activation in driving the increased susceptibility to HIV‑1 infection and the lowlevel replication in resting CD4+ T cells. In the absence of T cell receptor (TCR) engagement, a combination of inflammatory cytokines can trigger HIV‑1 replication69,70, and a similar role has been proposed for IL‑7 (REFS 56,71). In addition, macrophages expressing Nef or activated through CD40 ligand (CD40L) can produce soluble intra‑ cellular adhesion molecules (ICAMs) and CD23, which in turn increase the susceptibility of resting CD4+ T cells to infection42. Recently, it has been reported that conditioned medium from ex vivo-cultured tonsil tissue enhances the infection of naive-tissue CD4+ T cells by preventing APOBEC3G inhibition72. These findings emphasize the potential role of soluble factors and cytokines that are produced in the tissue environment in modifying sur‑ rounding lymphocytes and increasing their susceptibility to HIV‑1 infection. Dendritic cells and macrophages as viral reservoirs. The existence of unrecognized in vivo reservoirs that contrib‑ ute to persistent viral replication has renewed the inter‑ est in the study of HIV‑1 infection in macrophages and dendritic cells. Macrophages are susceptible to HIV‑1 infection and are productively infected in both HAARTtreated and untreated patients73,74. Viral replication in macrophages is characterized by longer persistence of unintegrated DNA41, production of chemokines and soluble mediators75 and generation of infective viral par‑ ticles76. Interestingly, in macrophages HIV‑1 assembly can occur both at the plasma membrane and in intracellular compartments, such as late endosomes and multivesicu‑ lar bodies. The relevance of these compartments for viral production in vivo is still unknown77–79. Dendritic cells (DCs) also play a key part in HIV‑1 propagation, through the capture of viruses by the receptor DC-SIGN (DC‑specific ICAM3-grabbing non-integrin) as well as through efficient HIV‑1 transmission to T cells at the virological synapse. In addition, DCs can be infected in vitro and lead to DC‑SIGN-mediated transinfection of CD4+ T cells. However, the role of infected DCs as poten‑ tial reservoirs in vivo remains controversial80. Finally, fol‑ licular DCs in lymphoid tissues are specialized in trapping and retaining antigens, including HIV‑1 virions, on their surfaces in the form of immune complexes81. Accordingly, follicular DCs may archive HIV‑1 viruses for months or years and provide another mechanism for viral persist‑ ence82. Unfortunately, research on DCs and macrophages is beset with technical limitations, and their precise roles as long-term reservoirs are still unknown. Molecular mechanisms of HIV‑1 latency Site and orientation of the integrated provirus. Most mechanisms to maintain HIV‑1 latency operate at the transcriptional level; for example, the chromosome nature reviews | Microbiology Volume 7 | november 2009 | 801 © 2009 Macmillan Publishers Limited. All rights reserved.
  5. 5. REVIEWS Box 2 | Mechanisms for the generation of HIV‑1 latency • Transcriptional interference, owing to the site and orientation of the provirus in the cell chromosome. • Epigenetic silencing, by post-transcriptional modifications (for example, hypoacetylation or trimethylation) of the histone tails that form the nucleosome core and modulate the chromatin structure. • The absence of nuclear host transcription activators for HIV‑1 expression, for example, nuclear factor-κB (NF‑κB), nuclear factor of activated T cells (NFAT) and specificity protein 1 (SP1). • The presence of cellular transcriptional repressors, such as yin and yang 1 (YY1), late SV40 factor (LSF; also known as TFCP2), C‑promoter binding factor 1 (CBF1; also known as RBPJ), APOBEC3G (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3G), inhibitor of NF-κB α-subunit (IκBα) and COMMD1 (copper metabolism (Murr1) domain-containing protein 1). • Inefficient elongation of HIV‑1 transcripts, owing to the absence of the viral protein Tat and Tat-associated viral factors. • Unproductive control of viral RNA splicing, owing to the absence of the viral protein Rev. • Innate host antiviral processes (for example, short interfering RNAs and microRNAs). Gut-associated lymphoid tissue The intestinal mucosaassociated lymphoid tissue that constitutes 70% of the whole immune system and may be the main site of HIV‑1 activity, despite the use of highly active antiretrovial therapy. Transcriptional interference Interruption of RNA transcription that is caused by adjacent active promoters owing to the competition for transcription factors or the collision of RNA polymerase II elongation complexes. environment at the site of integration and the avail‑ ability of viral and host factors can have substantial influences on viral latency (BOX 2). Proviral integration can occur at different sites and not entirely at random. Specific sequences at the ends of dscDNA are required to generate an efficient PIC15 that seems to be preferen‑ tially integrated into chromosomal regions that are rich in expressed genes83. However, there are strong biases that obstruct the access of the PIC to target DNA, such as the wrapping of host DNA in nucleosomes or the presence of already bound transcription complexes84. Integration into outward-facing DNA major grooves in chromatin is favoured85, and most inducible HIV‑1 proviruses can be found in intronic regions of the most highly expressed host genes86,87, probably owing to the increased chromatin accessibility of these regions84 (FIG. 3a) . However, viral replication from these pro‑ viruses can suffer intense transcriptional interference because of the orientation of the proviruses or their proximity to a stronger, host gene promoter 88 (FIG. 3b,c). Transcriptional interference of HIV‑1 gene expression may have a role in the establishment of latency 89,90 and can occur between active divergent promoters, owing to the lack of factor recruitment to the pre-initiation complex 88, and between active convergent promoters, owing to the collision of two RNAPII complexes during elongation, which can lead to the premature termina‑ tion of the transcription of one or both complexes89,90. Convergent transcription could also result in elonga‑ tion of both viral DNA strands and the subsequent for‑ mation of double-stranded RNA (dsRNA), which might silence proviral transcription through RNA interfer‑ ence (RNAi) 91, RNA-directed DNA methylation 92 or the generation of antisense RNA93. By contrast, when the provirus is in a parallel orien‑ tation to the host gene, read-through transcription may repress viral replication by two mechanisms (FIG. 3c). Firstly, it can block the access of transcription factors or displace already bound proteins87,94. Secondly, ongoing transcription from an upstream host promoter can pre‑ vent the assembly of the pre-initiation complex on the 5′ LTR95: the upstream transcription fails to terminate, and RNAPII reads through into the downstream HIV‑1 promoter, interfering with initiation. HIV‑1 sequences are included in the primary transcript of the host gene and degraded with the rest of the intron 86. Despite the universal inhibitory effect between two conver‑ gent or divergent promoters, results from two parallel promoters can vary depending on the system 87,88,95,96. Read-through transcription may also increase gene expression of proviruses, owing to the effect of splicing complexes on adjacent parallel promoters, the removal of repressors upstream of the viral transcription start site or alterations in DNA topology 88. Together, these data imply that the orientation-dependent regulation is highly variable and relies on the rate of 5′ LTR occupancy and on the rate of host gene elongation89,97. Inducible proviruses can also be integrated outside genes into long intergenic regions or gene deserts, which are expected to be heterochromatic or enriched in binding sites for transcriptional repressors98. In fact, integration into alphoid repeats located in centromeric heterochromatin regions is a rare event in primary cells84,99 and strongly disfavours HIV‑1 gene expres‑ sion100, promoting pre-integration latency 101. By con‑ trast, short intergenic regions commonly host stably expressed proviruses87. Epigenetic silencing of HIV‑1 transcription. Dynamic modifications of chromatin structure and nucleosome remodelling near the 5′ LTR also influence HIV‑1 repli‑ cation. Post-translational modifications of histone tails modulates chromatin rearrangements, with a highorder chromatin structure reducing the accessibility of transacting factors and RNAPII. Hypoacetylation of histones by histone deacetylases (HDACs) correlates with transcription repression, whereas hyperacetyla‑ tion by histone acetyltransferases (HATs) induces transcription activation102 (FIG. 4a). Accordingly, the nucleosome structure may lead to viral latency in CD4+ T cells with integrated proviruses. Deacetylation of histones may remodel nucleosome 1, resulting in HIV‑1 transcriptional repression. Transcription factors such as yin and yang 1 (YY1)103 and late SV40 factor (LSF; also known as TFCP2)104 repress HIV‑1 replication in infected CD4+ T cells by recruiting HDAC1 to the repressor complex sequence located at position –10 to +27 nucleotides in the LTR. Other host transcription factors, such as NF‑κB subunit p50 homodimers105 or the C‑promoter binding factor 1 (CBF1; also known 802 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  6. 6. REVIEWS a Location of integrated HIV-1 genomes c Transcriptional interference • Divergent promoters: lack of factor recruitment HIV-1 LTR HIV-1 LTR Host promoter HIV-1 LTR • Convergent promoters: collision of RNA polymerase complexes b Efficient HIV-1 transcription in activated CD4+ T cells PTEFb AF PC BP C Ac P Tat Tar CTD HIV-1 LTR Ac Host promoter RNAPII P P DSIF NELF P HIV-1 LTR • Parallel promoters: occlusion by read-through transcription of the host gene Host promoter HIV-1 LTR Figure 3 | Influence of provirus integration site and orientation into the host cell genome on HIV‑1 replication Nature Reviews | Microbiology efficiency. a | Most inducible HIV‑1 proviruses can be found in intronic regions of the most highly expressed host genes, in obverse or reverse orientation. b | Efficient HIV‑1 transcription is achieved by the formation of an elongation complex that binds to the transactivation response element (TAR), a 59-nucleotide stem-loop structure formed at the 5′ end of the nascent viral transcript. The viral protein Tat interacts directly with TAR and recruits cellular factors that increase the functional capacity of RNA polymerase II (RNAPII), such as positive transcription elongation factor b (PTEFb), composed of cyclindependent kinase 9 (CDK9) and cyclin T1. Cyclin T1 binds directly to Tat and allows its interaction with TAR, and CDK9 hyper‑ phosphorylates RNAPII at the carboxy-terminal domain (CTD) to induce a sustained viral mRNA synthesis. Acetylation (Ac) of Tat by cellular acetyl transferases, such as CREB-binding protein (CBP) and CBP-associated factor (PCAF), enhances its activity. c | Viral replication can undergo transcriptional interference, which occurs by different means depending on the orientation of the provirus in relation to a strong host promoter and induces viral latency. The viral transcript is shown in orange and the cellular gene transcript is in blue. DSIF, 5,6-dichloro‑1‑β‑d-ribofuranosylbenzimidazole sensitivity inducing factors; LTR, long terminal repeat; NELF, negative elongation factor. as RBPJ)106, can also recruit HDACs to the LTR and inhibit viral transcription similarly to YY1 in several cell lines. By contrast, Tat and several cytokines and HDAC inhibitors, such as trichostatin A, decrease HDAC1 occupancy at the repressor complex sequence, induc‑ ing nucleosome 1 rearrangement, which activates tran‑ scription at the 5′ LTR95 (FIG. 4b). Tat can recruit factors with HAT activity, such as CREB binding protein (CBP; also known as CREBBP), CBP-associated fac‑ tor (PCAF; also known as KAT2B) and human general control of amino acid synthesis protein 5 (hGCN5; also known as KAT2A), to the 5′ LTR, which induces nucle‑ osome hyperacetylation in cell lines and in peripheral blood mononuclear cells107 (FIG. 4b). Accordingly, in the absence of Tat, LTR-associated nucleosomes are hypoacetylated and viral gene expression is silenced, contributing to viral latency in both U1 and HL3T1 cell lines108. However, reversion to a permissive chro‑ matin arrangement by HDAC inhibitors is not enough to induce transcription. Host factors such as NF-κb, NF-AT and SP1 must also be recruited to the LTR, forming a complex that recruits other co-factors includ‑ ing HATs, although SP1 has been reported to interact with HDACs in cell lines and in primary resting CD4+ T cells from patients infected with HIV109. Moreover, both NF‑κB and SP1 are also regulated by reversible acetylation110,111. Although histone acetylation is generally associated with gene activation, histone methylation can be asso‑ ciated with both activation and silencing. Accordingly, methylation of H3 at lysine 4 (H3K4) and H3K36 is found in active genes, whereas methylation of H3K9, H3K27 and H4K20 is associated with gene silencing 112. In particular, H3K9 trimethylation, mediated by the histone-lysine N-methyltransferase suppressor of variega‑ tion 3–9 homologue 1 (SUV39H1), has been correlated nature reviews | Microbiology Volume 7 | november 2009 | 803 © 2009 Macmillan Publishers Limited. All rights reserved.
  7. 7. REVIEWS a HAT DNMT1 Ac Ac HDAC1 SUV39H1 Ac Transcription factors Ac Nucleosomes Ac Ac Ac Ac Ac Inaccessible chromatin Ac Ac HAT SUV39H1 Activation of gene transcription Transcription factors HIV-1 LTR Repressive HDAC–TF complex Transcriptional silencing HAT HDAC MTase Nuc0 Ac Ac Pre-initiation complex LEF1 NF-κB AF PC BP C Ac PTEFb TFs TFIID complex Basal transcription machinery The complex that regulates the initiation and elongation of transcription by binding to a core promoter that is located ~50 bp upstream of the transcription initiation site and contains the highly conserved TATA box. The complex consists of RNA polymerase II and several transcription factors and co-activators. AP1 H3 Ac H4 Tat TAR INR Nucleosomes PTEFb RNAPII P Ac Ac Ac Ets1 NFAT TATA TBP Ac HIV-1 LTR Open chromatin DNMT1 HDAC1 SP1 Transcription factors Ac Ac Ac b Ac Ac HAT Transactive HAT–TF complex Nuc1 P NELF DSIF P P CTD Host genome Elongation complex Figure 4 | Epigenetic modifications that regulate chromatin accessibility and influence HIV‑1 latency. a | Histone Nature Reviews Microbiology acetyltransferases (HATs) form a multimolecular complex with histone deacetylases (HDACs) that is recruited| to the target promoters and modifies nucleosome conformation around the binding site, along with methyl transferases (MTases) such as SUV39H1 (suppressor of variegation 3–9 homologue 1) and DNA methyltransferase 1 (DNMT1). The balance between HDACs and HATs modifies viral transcription, because recruitment of HATs makes chromatin permissive for HIV‑1 replication, whereas recruitment of HDACs and MTases and the consequent release of HATs leads to a higher-order chromatin structure that causes transcriptional silencing and latency. b | Disruption of nucleosome 1 (nuc1) by HATs, Tat or HDAC inhibitors unlocks chromatin to allow the binding of the pre-initiation complex, formed by cellular transcription factors such as nuclear factor of activated T cells ( NFAT), nuclear factor-κB (NF‑κB), specificity protein 1 (SP1) and activator protein 1 (AP1), along with the basal transcription machinery. The distal HIV‑1 enhancer contains consensus sites for lymphoid enhancer-binding factor 1 (LEF1) and Ets1 (v‑Ets erythroblastosis virus E26 oncogene homologue 1). The initiation of transcription allows the binding of the elongation complex (formed by Tat, positive transcription elongation factor b (PTEFb) and HATs (CREB-binding protein (CBP) and CBP-associated factor (PCAF)). Conversely, deacetylation or methylation of histones may remodel nuc1, resulting in HIV‑1 transcription repression. Elongation is also restricted by negative factors DSIF (5,6-dichloro‑1‑β‑d-ribofuranosylbenzimidazole sensitivity-inducing factors) and negative elongation factor (NELF). PTEFb phosphorylates DSIF, NELF and the carboxy-terminal domain (CTD) of RNA polymerase II (RNAPII), resulting in enhanced RNAPII processivity and transcription of the full HIV‑1 genome. Ac, acetyl group; H3, histone 3; INR, initiation element; LTR, long terminal repeat; TF, transcription factor; TFIID, transcription factor II D complex; TAR, transactivation response element; TBP, TATA binding protein. with heterochromatin assembly and with mediating HIV‑1 silencing113 by recruiting heterochromatin protein 1 homologue-γ (HP1γ; also known as CBX3)107. The co-repressor CTIP2 (chicken ovalbumin upstream promoter-transcription factor (COUPTF)-interacting protein 2; also known as BCL-11B) also recruits HDAC1, HDAC2, SUV39H1 and the HP1 proteins to establish a heterochromatic environment that leads to HIV‑1 silencing in several cell lines114. Consequently, latently infected Jurkat cells show highly deacetylated and trimethyl‑ ated histones115. On activation, trimethylated H3 levels and the occupancy of the LTR by the HP1 proteins and HDACs fall rapidly, inducing HIV‑1 replication from the reservoirs. 804 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  8. 8. REVIEWS Proviral integration can also be affected by histone modifications. In fact, integration favours regions rich in H3 and H4 acetylation as well as H3K4 methylation and disfavours regions rich in H3K27 trimethylation and CpG island methylation85. Host cell factors with restrictive activity against HIV‑1. HIV‑1 gene expression is strongly dependent on host cell transcription factors. One example of such a transcription factor is inhibitor of NF‑κB α-subunit (IκBα), which seques‑ ters NF‑κB dimers in the cytoplasm by a non-covalent interaction. On cellular activation, the IκBα kinase com‑ plex is activated through the protein kinase C (PKC) signalling pathway and phosphorylates IκBα, resulting in its ubiquitin-mediated degradation. This allows the now free NF‑κB to enter the nucleus and bind cognate sequences in the proviral 5′ LTR116. Accordingly, over‑ expression of IκBα inhibits HIV‑1 replication and can be responsible for the maintenance of latency in resting T cells117,118. Another example is the transcriptional regula‑ tor MYC, which binds SP1 at the LTR , forming a complex that recruits HDAC1 to repress HIV‑1 gene expression, thereby maintaining viral latency (REF. 109). SP1 also inter‑ acts with Vpr to increase the transcriptional activity of the cyclin-dependent kinase inhibitor p21, a key regulator of the cell cycle119. Induction of p21 prevents integration of the viral genome and establishes pre-integration latency by binding to HIV‑1 integrase120. The inhibition of Tat may also induce latency. Tat activity is regulated mainly through the acetylation of Lys28 and Lys50. Acetylation of Lys28 by PCAF stimu‑ lates Tat association with PTEFb121, whereas acetylation of Lys50 by CBP122 promotes the dissociation of Tat from the Tat–TAR–cyclin T1 complex123 and causes it to bind instead to PCAF during early phases of transcript elon‑ gation124. This Tat–PCAF complex is then recruited to the elongating RNAPII. Some cellular proteins can affect the acetylation state of Tat, modulating its activity. Tumour protein p73 binds to Tat, preventing its acetyla‑ tion at Lys28 by PCAF124, whereas sirtuin 1 (SIRT1)125, a class III HDAC, acts as a specific Tat deacetylase, increas‑ ing the quantity of Tat that is available to act as a tran‑ scriptional activator. In addition, CDK9 acetylation by hGCN5 and PCAF notably reduces the transcriptional activity of PTEFb, promoting HIV-1 latency126. CDK9 is deacetylated on T cell activation, inducing RNAPII hyperphosphorylation and HIV-1 replication. Other post-transcriptional modifications of Tat, such as the methylation of residues Arg52 and Arg53 by the arginine N-methyltransferase 6 (PRMT6)127,128 negatively affect the formation of the Tat–TAR–cyclin T1 complex128. Finally, specific restriction factors exist to defend the host cell against viral infection. Innate cellular fac‑ tors such as COMMD1 (copper metabolism (Murr1) domain-containing protein 1) 129 and APOBEC3G 36 impair various early phases of the HIV‑1 life cycle, inducing latency. COMMD1 not only interferes with both basal and tumour necrosis factor-induced NF‑κB activity, blocking HIV‑1 replication in resting lym‑ phocytes, but also directly interacts with NF‑κB. Rather than interfering with NF‑κB nuclear translocation, as IκBα does130, COMMD1 seems to control the duration of NF‑κB recruitment to open chromatin131. APOBEC3G strongly inhibits HIV-1 replication in CD4+ T cells by inducing C‑to‑U conversions in the viral minus strand DNA during reserve transcription132,133. This inhibitory effect is limited to resting cells, in which APOBEC3G exists as an active, low-molecular-mass ribonucleopro‑ tein complex 134. T cell activation induces the shift from active APOBEC3G to an inactive, high-molecular-mass complex that cannot restrict viral infection36. Inactive APOBEC3G can be found in tissue-resident naive T cells, which are permissive to HIV‑1 infection72. This correlates with the fact that HIV‑1 can infect resting CD4+ T cells residing in lymphoid tissues but not those circulating in peripheral blood. RNAi pathway. The RNAi pathway acts as a barrier against viral replication135 and introduces a new level of complexity to virus–host interplay 136 (FIG. 5). First, several cellular microRNAs (miRNAs), namely, miR‑28, miR‑125b, miR‑150, miR‑223 and miR‑382, seem to control HIV‑1 replication by targeting all spliced or unspliced HIV‑1 mRNAs except Nef-coding mRNA137. These cellular miRNAs are overexpressed in resting CD4+ T cells and inhibit the translation of almost all HIV‑1encoded proteins that contribute to viral latency, includ‑ ing Tat and Rev 138. Second, viral genomes produce viral interference RNAs (viRNAs) that can target viral RNAs (such as LTR139, Nef 140 and Env 141), cellular mRNAs and even cellular miRNAs. By targeting its own mRNAs, the virus induces its own latency. Targeting cellular genes such as CD28 (REFS 142–145) leads to modification of the environment in infected cells. However, some of these data remain controversial, as they have been gen‑ erated by overexpression of miRNA or viRNA but have not been confirmed in more physiological conditions146. Finally, cellular miRNAs can target factors involved in HIV‑1 replication; for example, miR‑17, miR-5p and miR‑20 silence PCAF, resulting in the downregulation of HIV‑1 expression. Overall, these RNAi mechanisms cause inhibition of viral gene expression or deficient HIV‑1 propagation. As is the case with other immune defence mechanisms, HIV‑1 has to counteract RNAi pathways to ensure its own replication. Viral products interfere directly with the cellular RNAi machinery through three different mechanisms. The first is the Tat-mediated partial repression of the ability of Dicer to process precursor dsRNAs into small interfering RNAs (siRNAs)147 through a physical interaction between the Dicer helicase domain and a 30–72-amino-acid region of Tat 148, leading to the suppression of the RNAi pathway 147. However, the upregulation in cellular miRNA expression that is triggered following HIV-1 infec‑ tion seems to contradict the inhibition of Dicer by Tat. Furthermore, the change in miR‑17 levels that is induced by Tat in infected cells has not been confirmed by other authors146. The second mechanism involves the viral TAR sequence, which sequesters the Dicer-interacting protein TAR RNA-binding protein 2 (TRBP2), preventing the for‑ mation of a functional RNA-induced silencing complex (RISC) 141,149,150. The third mechanism involves the nature reviews | Microbiology Volume 7 | november 2009 | 805 © 2009 Macmillan Publishers Limited. All rights reserved.
  9. 9. REVIEWS PACT Dicer TRBP 21-23 nucleotide miRNA duplex Nucleus 4 pre-miRNA Tat Exportin 5 viRNAs TRBP RISC AGO2 P 2 TAR HIV-1 RNA P TRBP miRISC PACT 4 AGO2 Multiple spliced viral mRNAs TRBP TRBP Inactive RISC AGO2 AAAA PACT Provirus AGO2 Dicer Inactive Pri-miRNA transcription Host cell DNA P P 1 Drosha 1 Tat/Rev mRNAs AAAA 3 Cellular factors involved in HIV-1 expression miR-28 miR-125b miR-150 miR-223 miR-382 viRNA AGO2 P Active RISC PACT DGCR8 PACT Cellular miRNAs PACT Nuclear membrane Cytosol TRBP Translational repression P AAAA Degradation of target mRNA Figure 5 | The microRNA pathway can modulate both cellular and viral gene expression. DNA from intergenic Nature Reviews | Microbiology regions, introns or exons encodes pre-microRNAs (pri-miRNAs) that are cleaved in the nucleus by the microprocessor complex (consisting of the RNase III endonuclease Drosha (also known as ribonuclease III) and the co-factor DGCR8 (DiGeorge syndrome critical region 8 gene)) to produce a precursor hairpin structure of 60–70 nucleotides, termed pre-miRNA, which encodes a single miRNA sequence. This is exported to the cytoplasm by exportin 5. Cytoplasmic pre-miRNAs are further cleaved by an RNase III endonuclease, Dicer, in concert with the co-factors transactivation response element-RNA-binding protein (TRBP) and protein kinase R-activating protein (PACT), which remove the loop sequence and form a 21–23 nulceotide miRNA asymmetric duplex. This mature duplex binds the RNA-induced silencing complex (RISC), which degrades one strand to produce an active, single-stranded miRNA that can target mRNAs with sequence homology. Targets are marked for full degradation when the complementarity is complete and for translation inhibition when the complementarity is partial. The miRNA pathway can influence HIV‑1 latency through four mechanisms. Cellular miRNAs can target and degrade viral mRNA (step 1). Viral genomes produce miRNAs, called viRNAs, which can target viral RNAs and cellular mRNAs or miRNAs (step 2). Cellular miRNAs can target cellular factors that are involved in HIV‑1 replication (step 3). Finally, viral products can interfere directly with cellular siRNA machinery by hijacking Dicer (mediated by Tat) and TRBP (mediated by TAR). AGO2, argonaute 2. modification of some miRNAs151,152. In particular, miRNAs derived from TAR following asymmetrical processing of Dicer can regulate gene expression in vivo153. In conclusion, HIV‑1 seems to modify the host cell miRNA expression profile, but the ultimate consequences of these changes and the underlying mechanisms are still undefined. Both cellular and viral miRNAs could be involved in maintaining HIV‑1 latency or in control‑ ling low ongoing viral replication. In addition, HIV‑1 has developed strategies to overcome the cellular miRNA restriction machinery or enhance the expression of certain favourable miRNAs to achieve full replication154. Sources of plasma viraemia In patients who have not been treated with HAART, viraemia is mainly generated by repeated cycles of infection–replication in activated CD4 + T cells. Activation of latently infected T cells and replication 806 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  10. 10. REVIEWS Homeostatic cell division Viral replication in non-treated patients with HIV infection Potential sources of residual viraemia in HAART IM SUPP Latently infected T cells REACT + HAART High-level viraemia Residual viraemia Reactivation Activated T cells IM SUPP Low level ongoing replication Robust replication T cell destruction Viral propagation Infection of new targets HAART INT New cycles of infection Other infected cell types TOXIN ? T cell Macrophage DC Persistent replications Nature Reviews | Microbiology Figure 6 | Sources of viral replication in patients infected with HIV-1 and strategies to control residual viraemia. (Left panel) Plasma viraemia in non-treated patients infected with HIV-1 is mainly generated by repeated cycles of infection–replication in activated CD4+ T cells; robust replication occurs in these cells, and they are highly susceptible to de novo infection. Reactivation of latently infected T cells, persistent replication in other cell types such as macrophages and dendritic cells (DCs) or viruses being trapped in follicular DCs contribute in lower proportions to viraemia. (Right panel) CD4+ T cells carrying latent proviruses can become activated and contribute to residual viraemia in patients treated with highly active antiretroviral therapy (HAART). Reactivation of latent reservoirs (REACT) has been proposed to purge latent viruses and force HIV‑1 eradication. But this reactivation should always be combined with HAART to block the spread of infection by new viral particles that are produced from the activated reservoirs. The use of immunosuppressive drugs (IM SUPP) can contribute to the maintenance of T cells in a resting state, to avoid the expansion of reservoirs through the proliferation that occurs in latently infected T cells. HAART intensification (HAART INT) could achieve complete suppression of the residual viraemia that is caused by ongoing replication in T cells that escape from HAART control. Finally, the use of antibodies coupled to drugs or treatment with immunotoxins (TOXIN) are potential strategies for selective killing of the remaining unidentified cellular reservoirs that produce residual viraemia even in patients treated with fully suppressive HAART regimens. In this case, although intensification of HAART could potentially control long-lasting viral replication from this reservoir, resistance to cytopathic effects in these persistent cells would be a major obstacle to complete viral eradication. in other cell types contribute to only a low proportion of the viral load (FIG. 6). This scenario is supported by classical studies on viral replication kinetics 155 that show a two-phase decay in viraemia after initi‑ ating HAART. The first phase reflects viral produc‑ tion by activated CD4+ T cells with short half-lives (roughly 1 day), which are responsible for more than 90% of plasma viral load. The second phase of viraemia corresponds to viral replication from reservoirs with an estimated half-life of a few weeks, which produce HIV‑1 at lower rates155. It has been proposed that this second reservoir comprises macrophages, resting T cells, infected DCs or viruses trapped in follicular DCs. A third phase of persistent residual viraemia (1–5 copies per ml) can also be detected in patients undergoing long-term HAART156,157. The origin of residual viraemia is a matter of con‑ troversy, and three hypotheses have been proposed. In the first, low-level, ongoing replication is suggested to occur as a consequence of non-fully suppressive HAART158,159 (FIG. 6). In the second, reactivation from a long-lived reservoir of latently infected T cells is sug‑ gested as the cause. The third hypothesis proposes that virus release from a stable, unrecognized reser‑ voir leads to low-level, persistent production of viral particles without additional cycles of infection but leading to the detection of viral RNA160. Residual viraemia 157,161 has been suggested as a proof of ongoing viral replication cycles, but its control following HAART intensification 162,163 has not been confirmed in recent studies164. Current pharmacody‑ namic models that assess the antiretroviral inhibitory potential in single-round infections165 indicate that current HAART regimens can fully control ongo‑ ing cycles of HIV‑1 replication. Nevertheless, low pharmacological activity due to reservoirs located in anatomical sites with limited penetration for anti­ retrovirals, such as the gut or central nervous system, cannot be excluded. In fact, HIV‑1 RNA has been found in the lymph nodes166 and the gut 167,168 despite undetectable plasma viraemia. It has been argued that the maintenance of viral DNA in peripheral blood mononuclear cells and gut-associated lymphoid tissue after an initial decay supports ongoing HIV‑1 replication 158,169,170. A good correlation between DNA levels and viral suppres‑ sion has been found in different situations162,171–173; therefore, stable DNA could possibly be viewed as a marker of persistent viral replication despite HAART. However, maintained DNA levels could also be a consequence of the stability of the latent reservoir in resting CD4 + T cells 51,52, including replicationincompetent integrated DNA copies 48. In fact, the initial decay of total viral DNA levels is mainly due to a decrease in linear non-integrated DNA, whereas integrated proviral DNA remains stable and repre‑ sents the larger DNA reservoir in patients treated with HAART170. Conflicting results regarding the origin of residual viraemia have been obtained from viral evolution studies and comparisons of plasma viruses and proviral DNA nature reviews | Microbiology Volume 7 | november 2009 | 807 © 2009 Macmillan Publishers Limited. All rights reserved.
  11. 11. REVIEWS in CD4 + T cells. Viral evolution in proviral DNA and cross-infection among different lymphocytic compartments were detected 158,163,168 , suggesting that replication occurs in CD4+ T cells. By contrast, characterization of residual viraemia at the clonal level160,174 has shown that although some plasma viral clones share sequences with proviruses that are inte‑ grated in resting T cells, most plasma clones (termed predominant plasma clones) do not come from circulat‑ ing CD4+ T cells. In addition, predominant plasma clones are homogeneous populations that remain genetically stable for years, suggesting that they are not produced by ongoing cycles of viral replication but originate instead from long-lasting cells that never enter blood circulation, such as tissue CD4+ T cells, chronically infected tissue macrophages or dividing monocyte–macrophage-lineage stem cells160. In sum‑ mary, although low-level ongoing replication in CD4+ T cells cannot be fully excluded in all patients treated with HAART, residual viraemia seems to be fuelled by a different reservoir. Based on these hypotheses, several strategies have been proposed to tackle viral reservoirs (see below) (FIG. 6). Therapeutic strategies for eradication HAART intensification. The aim of the HAART inten‑ sification strategy is to achieve a complete suppression of residual viraemia. However, recent intensification studies failed to decrease residual viraemia any more than normal HAART 164 , suggesting that current regimens can halt ongoing cycles of viral replica‑ tion effectively. Nevertheless, the approval of potent drugs targeting CCR5 (REF. 175) and integrase 176 has raised new expectations for successfully decreasing the reservoir size in patients with primary infection in particular 167,173. This strategy must be analysed in clinical trials before we can conclude whether current HAART combinations have achieved the maximal effect in controlling HIV‑1 replication or whether an intensification of the effect is still possible. Predominant plasma clone The main plasma clone of infected cells that is responsible for most of the residual viraemia in patients on highly active antiretroviral therapy. This clone is replication competent and shows a specific sequence for each patient that cannot be easily found in the patient’s activated or resting CD4+ T cells. Immunosuppressants. The addition of immunosup‑ pressants to HAART combinations has been pro‑ posed to decrease the activation of CD4+ T cells and reduce their susceptibility to viral infection and rep‑ lication. Corticosteroids 177, mycophenolic acid 178,179, cyclosporine A 180, hydroxyurea 181,182 and thalido‑ mide 183 have been assayed in several clinical trials. These compounds directly decrease the activity of transcription factors such as NF‑κB or NFAT, protect the cell from apoptosis or reduce the production of pro-inflammatory cytokines such as tumour necrosis factor, thereby reducing immune stimuli, HIV‑1 rep‑ lication and cell destruction. Some benefit from their application has been observed in small trials, but drug withdrawal causes viral load to return to basal levels. The most interesting results were found in patients who were recently infected with the virus and treated with cyclosporin A, because CD4+ counts were higher than in patients treated only with HAART (although no changes in viral load were observed)180. However, the general use of immunosuppressants is not justi‑ fied because of their toxicity, although their efficacy in certain situations, for example primary infection, should be studied in controlled clinical trials. Reactivation of latent reservoirs. The combination of HAART with new therapeutic agents that can reacti‑ vate latent reservoirs would lead to HIV‑1 eradication. However, the use of cytokines, antibodies against CD3, non-tumorigenic phorbol ester derivatives and HDAC has shown limited success. Despite initial optimistic findings184, combined treatment with IL‑2 and HAART has not reduced HIV‑1 reservoirs, and viral rebound has been systematically observed185. A combination of anti‑ bodies against CD3 and IL‑2 has proved to be highly toxic, without a clear benefit and is not further advised for HIV‑1 treatment 186. Interestingly, IL‑7 can reacti‑ vate HIV‑1 in latently infected cells in vitro through the induction of the Janus kinase–signal transducer and activator of transcription (JAK–STAT) signalling path‑ way 71. In vivo, IL‑7 increases the TCR repertoire and expands both naive187 and memory 56 T cells, making this cytokine an attractive candidate for future studies. The use of different chemical compounds targeting the PKC signalling pathway has also been proposed as a means of reactivating viral reservoirs. Prostratin increases HIV‑1 transcription in latently infected T cells through PKC activation and induction of NF‑κB and SP1 (REF. 188) . Prostratin also downregulates HIV‑1 recep‑ tors, which has the additional advantage of decreas‑ ing the risk of re-infection. This non-tumorigenic phorbol ester has been advanced in clinical develop‑ ment, and recent synthesis made the drug available for clinical trials189. Other compounds, including phorbol13-monoesters190, the jatrophane diterpene SJ23B191 and hexamethylbisacetamide192, induce potent reactivation of HIV‑1 in vitro and could be future candidates for clinical development. The use of antibodies coupled to drugs and treatment with immunotoxins are other strategies proposed for the selective killing of infected cells. A combination of immunotoxins and agents that induce viral reactivation has proved to be useful for HIV‑1 eradication in cultures of lymphocytes from patients193 and in animal models194. Unfortunately, the failure of the initial phase I trial to reduce viral load and the toxic side effects of this treatment precluded its further development 195, but this approach could be envisaged in the context of minimal residual disease to selectively destroy hidden viral reservoirs that escapes from HAART. Finally, HDAC blocking is an attrac‑ tive potential means of inducing broad reactivation of HIV‑1 reservoirs. Although promising results in the reduction of HIV‑1 reservoirs were achieved using the HDAC inhibitor valproic acid196, these results have not been replicated197,198. Perspectives and future directions Despite its effectiveness, chronic treatment with antiret‑ rovirals is not devoid of long-term toxicity problems. Therefore, the challenge in the field of HIV‑1 treatment is to find a cure, which implies that either the virus must 808 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  12. 12. REVIEWS be eradicated or treatment must be able to be stopped without notable viral rebound. A better understanding of HIV‑1 latency and persistence can provide clues for the development of new strategies for viral eradication. The study of latency had been hampered by technical limita‑ tions, but new approaches have allowed the characteriza‑ tion of persistent viruses in patients treated with HAART and the study of infected CD4+ T cells at the singlecell level. The finding that residual viraemia does not come from circulating, latently infected CD4+ T cells but from an unknown reservoir represents a major obstacle for eradication strategies, including the use of drugs to reactivate latent viruses. Therefore, the identification of these cells is key for understanding HIV‑1 persistence. Knowledge of the cellular elements that restrict retroviral replication and actively inhibit the viral transcription machinery and an understanding of 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. Barré-Sinoussi, F. et al. Isolation of a T‑lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). Science 220, 868–871 (1983). Centers for Disease Control and Prevention. Pneumocystis pneumonia — Los Angeles. MMWR Morb. Mortal Wkly Rep. 30, 250–252 (1981). Pomerantz, R. J. & Horn, D. L. Twenty years of therapy for HIV‑1 infection. Nature Med. 9, 867–874 (2003). Pomerantz, R. J. Reservoirs of human immunodeficiency virus type 1: the main obstacles to viral eradication. Clin. Inf. Dis. 34, 91–97 (2002). Shen, L. & Siliciano, R. F. Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection. J. Allergy Clin. Immunol.122, 22–28 (2008). Goff, S. P. in Fields’ Virology (eds Knipe D. M. & Howley P. M.) 1871–1939 (Lippincott Williams & Wilkins, Philadelphia, 2001). Loetscher, P., Moser, B. & Baggiolini, M. Chemokines and their receptors in lymphocyte traffic and HIV infection. Adv. Immunol. 74, 127–180 (2000). Stevenson, M. HIV‑1 pathogenesis. Nature Med. 9, 853–860 (2003). Huthoff, H. & Towers, G. J. Restriction of retroviral replication by APOBEC3G/F and TRIM5α. Trends Microbiol. 16, 612–619 (2008). He, G., Ylisastigui, L. & Margolis, D. M. The regulation of HIV‑1 gene expression: the emerging role of chromatin. DNA Cell Biol. 21, 697–705 (2002). Du, T. & Zamore, P. D. Beginning to understand microRNA function. Cell Res. 17, 661–663 (2007). Han, Y., Wind-Rotolo, M., Yang, H. C., Siliciano, J. D. & Siliciano, R. F. Experimental approaches to the study of HIV‑1 latency. Nature Rev. Microbiol. 5, 95–106 (2007). Lassen, K., Han, Y., Zhou, Y., Siliciano, J. & Siliciano, R. F. The multifactorial nature of HIV‑1 latency. Trends Mol. Med. 10, 525–531 (2004). Bukrinsky, M. I., Stanwick, T. L., Dempsey, M. P. & Stevenson, M. Quiescent T lymphocytes as an inducible virus reservoir in HIV-1 infection. Science 254, 423–427 (1991). The identification of quiescent T cells as a source of extrachromosomal HIV‑1 DNA that retains the ability to integrate on T cell activation in vitro. Piller, S. C., Caly, L. & Jans, D. A. Nuclear import of the pre-integration complex (PIC): the Achilles heel of HIV? Curr. Drug Targets 4, 409–429 (2003). Arhel, N. J. et al. HIV-1 DNA Flap formation promotes uncoating of the pre-integration complex at the nuclear pore. EMBO J. 26, 3025–3037 (2007). The first observation, by scanning electron microscopy, that the uncoating of HIV‑1 is not an immediate post-fusion event but, instead, intact intracellular capsids can reach the nuclear pore. Farnet, C. & Bushman, F. D. HIV‑1 cDNA integration: requirement of HMG I(Y) protein for function of preintegration complexes in vitro. Cell 88, 1–20 (1997). Shun, M. C. et al. LEDGF/p75 functions downstream from preintegration complex formation to effect genespecific HIV‑1 integration. Genes Dev. 21, 1767–1778 (2007). the complex interactions between HIV‑1 and cellular and viral siRNAs provide a new paradigm for HIV‑1 latency. As a result, latency should be considered not merely a passive process but, rather, an active process that is tightly regulated by cellular and viral factors. New insights into the molecular mechanisms of HIV‑1 latency have led to the characterization of targets that will be useful for designing new drugs. In particular, the modification of chromatin conformation through HDAC inhibitors and the activation of kinase path‑ ways leading to the activation of transcription factors are both attractive possibilities for specific drug devel‑ opment. Finally, cellular factors that are involved in the maintenance of latency, such as APOBEC3G and miRNAs, or factors required by the virus to complete PIC transport and integration, such as emerin and LEDGF, are also new targets for drug development. 19. McDonald, D. et al. Visualization of the intracellular behavior of HIV in living cells. J. Cell Biol. 159, 441–452 (2002). 20. Llano, M. An essential role for LEDGF/p75 in HIV integration. Science 314, 461–464 (2006). 21. Jacque, J. M. & Stevenson, M. The inner‑nuclear‑envelope protein emerin regulates HIV‑1 infectivity. Nature 441, 641–645 (2006). 22. Shun, M. C., Daigle, J. E., Vandegraaff, N. & Engelman, A. Wild-type levels of human immunodeficiency virus type 1 infectivity in the absence of cellular emerin protein. J. Virol. 81, 166–172 (2007). 23. Guntaka, R. V. Transcription termination and polyadenylation in retroviruses. Microbiol. Rev. 57, 511–521 (1993). 24. Nabel, G. & Baltimore, D. An inducible transcription factor activates expression of human immunodeficiency virus in T cells. Nature 326, 711–713 (1987). The first description of the binding consensus sites for NF-κB in the HIV‑1 LTR promoter and of the synergic interaction of this factor with the viral protein Tat to enhance HIV‑1 transcription in T cells. 25. Corthésy, B. & Kao, P. N. Purification by DNA affinity chromatography of two polypeptides that contact the NF-AT DNA binding site in the interleukin 2 promoter. J. Biol. Chem. 269, 20682–20690 (1994). 26. Jones, K. A., Kadonaga, J. T., Luciw, P. A. & Tjian, R. Activation of the AIDS retrovirus promoter by the cellular transcription factor, Sp1. Science 232, 755–759 (1986). 27. Dingwall, C. et al. HIV-1 Tat protein stimulates transcription by binding to a U-rich bulge in the stem of the TAR RNA structure. EMBO J. 9, 4145–4153 (1990). 28. Garber, M. E., Wei, P. & Jones, K. A. HIV-1 Tat interacts with cyclin T1 to direct the P-TEFb CTD kinase complex to TAR RNA. Cold Spring Harb. Symp. Quant. Biol. 63, 371–380 (1998). 29. Zhou, M. et al. Tat modifies the activity of CDK9 to phosphorylate serine 5 of the RNA polymerase II carboxyl-terminal domain during human immunodeficiency virus type 1 transcription. Mol. Cell. Biol. 20, 5077–5086 (2000). 30. Pollard, V. W. & Malim, M. H. The HIV-1 Rev protein. Annu. Rev. Microbiol. 52, 491–532 (1998). 31. Ganser-Pornillos, B. K., Yeager. M. & Sundquist, W. I. The structural biology of HIV assembly. Curr. Opin. Struct. Biol. 18, 203–217 (2008). 32. Bleul, C. C., Wu, L., Hoxie, J. A. & Springer, T. A., Mackay, C. R. The HIV coreceptors CXCR4 and CCR5 are differentially expressed and regulated on human T lymphocytes. Proc. Natl Acad. Sci. USA 94, 1925–1930 (1997). 33. Zack, J. A. et al. HIV‑1 entry into quiescent primary lymphocytes: molecular analysis reveals a labile, latent viral structure. Cell 61, 213–222 (1990). The first description of pre-integration latency by an incomplete retrotranscription of the HIV‑1 genome in infected quiescent T cells that, despite its frailty, persists as a latent form. 34. Meyerhans, A. et al. Restriction and enhancement of human immunodeficiency virus type 1 replication by modulation of intracellular deoxynucleoside triphosphate pools. J. Virol. 68, 535–540 (1994). This work shows that resting blood CD4+ T cells are highly resistant to infection with HIV‑1 and that viral retrotranscrition results in incomplete, labile transcripts, thereby proving that successful HIV‑1 infection requires T cell activation. 35. Bukrinsky, M. I. et al. Active nuclear import of human immunodeficiency virus type 1 preintegration complexes. Proc. Natl Acad. Sci. USA 89, 6580–6584 (1992). 36. Chiu, Y. L. et al. Cellular APOBEC3G restricts HIV-1 infection in resting CD4+ T cells. Nature 435, 108–114 (2005). This study finds that low-molecular-mass APOBEC3G functions as a potent post-entry restriction factor for HIV‑1 in resting CD4+ T cells, whereas high-molecular-mass APOBEC3G is permissive for HIV‑1 infection in activated CD4+ T cells. 37. Pierson, T. C. et al. Molecular characterization of preintegration latency in human immunodeficiency virus type 1 infection. J. Virol. 76, 8518–8531 (2002). 38. Zhou, Y. et al. Kinetics of human immunodeficiency virus type 1 decay following entry into resting CD4+ T cells. J. Virol. 79, 2199–2210 (2005). 39. Sakai, H. et al. Integration is essential for efficient gene expression of human immunodeficiency virus type 1. J. Virol. 67, 1169–11174 (1993). 40. Wu, Y. & Marsh, J. W. Selective transcription and modulation of resting T cell activity by preintegrated HIV DNA. Science 293, 1503–1506 (2001). 41. Kelly, J. et al. Human macrophages support persistent transcription from unintegrated HIV‑1 DNA. Virology 3672, 300–312 (2008). 42. Swingler, S. et al. HIV‑1 Nef intersects the macrophage CD40L signalling pathway to promote resting-cell infection. Nature 424, 213–219 (2003). 43. Chun, T. W. et al. In vivo fate of HIV‑1‑infected T cells: quantitative analysis of the transition to stable latency. Nature Med. 1, 1284–1290 (1995). 44. Finzi, D. et al. Identification of a reservoir for HIV‑1 in patients on highly active antiretroviral therapy. Science 278, 1295–1300 (1997). 45. Persaud, D. et al. A stable latent reservoir for HIV‑1 in resting CD4+ T lymphocytes in infected children. J. Clin. Invest. 105, 995–1003 (2000). 46. Blankson, J. N. et al. Isolation and characterization of replication-competent human immunodeficiency virus type 1 from a subset of elite suppressors. J. Virol. 81, 2508–2518 (2007). 47. Chun, T. W. et al. Early establishment of a pool of latently infected resting CD4+ T cells during primary HIV‑1 infection. Proc. Natl Acad. Sci. USA 95, 8869–8873 (1998). 48. Chun, T. W. et al. Quantification of latent tissue reservoirs and total body viral load in HIV‑1 infection. Nature 387, 183–188 (1997). nature reviews | Microbiology Volume 7 | november 2009 | 809 © 2009 Macmillan Publishers Limited. All rights reserved.
  13. 13. REVIEWS 49. 50. 51. 52. 53. 54. 55. 56. 57. 58. 59. 60. 61. 62. 63. 64. 65. 66. 67. 68. 69. 70. 71. 72. In this investigation, the whole pool of latently infected resting CD4+ T cells containing a replica‑ tion-competent integrated provirus was quantified as ∼107 cells. Jung, A. et al. Multiply infected spleen cells in HIV patients. Nature 418, 144 (2002). Lassen, K. G., Bailey, J. R. & Siliciano, R. F. Analysis of human immunodeficiency virus type 1 transcriptional elongation in resting CD4+ T cells in vivo. J. Virol. 78, 9105–9114 (2004). Finzi, D. et al. Latent infection of CD4+ T cells provides a mechanism for lifelong persistence of HIV‑1, even in patients on effective combination therapy. Nature Med. 5, 512–517 (1999). Siliciano, J. D. et al. Long-term follow-up studies confirm the stability of the latent reservoir for HIV‑1 in resting CD4+ T cells. Nature Med. 9, 727–728 (2003). Haase, A. T. Population biology of HIV‑1 infection: viral and CD4+ T cell demographics and dynamics in lymphatic tissues. Annu. Rev. Immunol. 17, 625–656 (1999). Spina, C. A., Prince, H, E. & Richman, D. D. Preferential replication of HIV‑1 in the CD45RO memory cell subset of primary CD4 lymphocytes in vitro. J. Clin. Invest. 99, 1774–1785 (1997). Blaak, H. et al. In vivo HIV‑1 infection of CD45RA+CD4+ T cells is established primarily by syncytium-inducing variants and correlates with the rate of CD4+ T cell decline. Proc. Natl Acad. Sci. USA 97, 1269–1274 (2000). Chomont, N. et al. HIV reservoir size and persistence are driven by T cell survival and homeostatic – proliferation. Nature Med. 15, 893­ 900 (2009). Ostrowski, M. A. et al. Both memory and CD45RA+/ + + CD62L naive CD4 T cells are infected in human immunodeficiency virus type 1-infected individuals. J. Virol. 73, 6430–6435 (1999). Brooks, D. G., Kitchen, S. G. & Kitchen, C. M. Scripture-Adams, D. D., Zack, J. A. Generation of HIV latency during thymopoiesis. Nature Med. 7, 459–464 (2001). Williams, S. A. & Greene, W. C. Regulation of HIV‑1 latency by T‑cell activation. Cytokine 39, 63–74 (2007). Brenchley, J. M. et al. Microbial translocation is a cause of systemic immune activation in chronic HIV infection. Nature Med. 2, 1365–1371 (2006). Douek, D. C. et al. HIV preferentially infects HIVspecific CD4+ T cells. Nature 417, 95–98 (2002). Guadalupe, M. et al. Severe CD4+ T‑cell depletion in gut lymphoid tissue during primary human immunodeficiency virus type 1 infection and substantial delay in restoration following highly active antiretroviral therapy. J. Virol. 77, 11708–11717 (2003). Mehandru, S. et al. Primary HIV‑1 infection is associated with preferential depletion of CD4+ T lymphocytes from effector sites in the gastrointestinal tract. J. Exp. Med. 200, 761–770 (2004). Brenchley, J. M., Price, D. A. & Douek, D. C. HIV disease: fallout from a mucosal catastrophe?. Nature Immunol. 7, 235–239 (2006). Mattapallil, J. J. Massive infection and loss of memory CD4+ T cells in multiple tissues during acute SIV infection. Nature 434, 1093–1097 (2005). Zhang, Z. et al. Sexual transmission and propagation of SIV and HIV in resting and activated CD4+ T cells. Science 286, 1353–1357 (1999). Eckstein, D. A. et al. HIV‑1 actively replicates in naive CD4+ T cells residing within human lymphoid tissues. Immunity 15, 671–682 (2001). Chou, C. S., Ramilo, O. & Vitetta, E. S. Highly purified CD25– resting T cells cannot be infected de novo with HIV‑1. Proc. Natl Acad. Sci. USA 94, 1361–1365 (1997). Unutmaz, D., KewalRamani, V. N., Marmon, S. & Littman, D. R. Cytokine signals are sufficient for HIV‑1 infection of resting human T lymphocytes. J. Exp. Med. 189, 1735–1746 (1999). Chun, T. W., Engel, D., Mizell, S. B., Ehler, L. A. & Fauci, A. S. Induction of HIV‑1 replication in latently infected CD4+ T cells using a combination of cytokines. J. Exp. Med. 188, 83–91 (1998). Wang, F. X. et al. IL‑7 is a potent and proviral strainspecific inducer of latent HIV‑1 cellular reservoirs of infected individuals on virally suppressive HAART. J. Clin. Invest. 115, 128–137 (2005). Kreisberg, J. F., Yonemoto, W. & Greene, W. C. Endogenous factors enhance HIV-1 infection of tissue naive CD4 T cells by stimulating high molecular mass 73. 74. 75. 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 91. 92. 93. APOBEC3G complex formation. J. Exp. Med. 203, 865–870 (2006). Koenig, S. et al. Detection of AIDS virus in macrophages in brain tissue from AIDS patients with encephalopathy. Science 233, 1089–1093 (1986). Sharkey, M. E. et al. Persistence of episomal HIV‑1 infection intermediates in patients on highly active antiretroviral therapy. Nature Med. 6, 76–81 (2006). Swingler, S. et al. HIV‑1 Nef mediates lymphocyte chemotaxis and activation by infected macrophages. Nature Med. 5, 997–103 (1999). Sharova, N., Swingler, C., Sharkey, M. & Stevenson, M. Macrophages archive HIV‑1 virions for dissemination in trans. EMBO J. 24, 2481–2489 (2005). Deneka, M., Pelchen-Matthews, A., Byland, R., RuizMateos, E. & Marsh, M. In macrophages, HIV‑1 assembles into an intracellular plasma membrane domain containing the tetraspanins CD81, CD9, and CD53. J. Cell Biol. 177, 329–341 (2007). Welsch, S. et al. HIV‑1 buds predominantly at the plasma membrane of primary human macrophages. PLoS Pathog. 3, e36 (2007). Joshi, A., Ablan, S. D., Soheilian, F., Nagashima, K. & Freed, E. O. Evidence that productive human immunodeficiency virus type 1 assembly can occur in an intracellular compartment. J. Virol. 83, 5375–5387 (2009). Wu, L. & KewalRamani, V. N. Dendritic-cell interactions with HIV: infection and viral dissemination. Nature Rev. Immunol. 6, 859–868 (2006). Smith-Franklin, B. A. et al. Follicular dendritic cells and the persistence of HIV infectivity: the role of antibodies and Fcγ receptors. J. Immunol. 166, 690–696 (2002). Keele, B. F. et al. Characterization of the follicular dendritic cell reservoir of human immunodeficiency virus type 1. J. Virol. 82, 5548–5561 (2008). Mitchell, R. S. et al. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences. PLoS Biol. 2, E234 (2004). Schröder, A. R. et al. HIV-1 integration in the human genome favours active genes and local hotspots. Cell 110, 521–529 (2002). This work shows that HIV‑1 provirus integration is strongly favoured in active genes and preferentially those that are activated after viral infection. Wang, G. P., Ciuffi, A., Leipzig, J., Berry, C. C., Bushman, F. D. HIV integration site selection: analysis by massively parallel pyrosequencing reveals association with epigenetic modifications. Genome Res. 17, 1186–1194 (2007). Han, Y. et al. Resting CD4+ T cells from human immunodeficiency virus type 1 (HIV-1)-infected individuals carry integrated HIV-1 genomes within actively transcribed host genes. J. Virol. 78, 6122–6133 (2004). Lewinski, M. K. et al. Genome wide analysis of chromosomal features repressing human immunodeficiency virus transcription. J. Virol. 79, 6610–6619 (2005). Han, Y. et al. Orientation-dependent regulation of integrated HIV-1 expression by host gene transcriptional readthrough. Cell Host Microbe 4, 134–146 (2008). This study describes how read-through transcription of actively transcribed host genes may interfere with the gene expression of a nearby integrated HIV‑1 provirus, inducing viral latency depending on the site and orientation of the provirus. Callen, B. P., Shearwin, K. E. & Egan J. B. Transcriptional interference between convergent promoters caused by elongation over the promoter. Mol. Cell. 14, 647–656 (2004). Crampton, N., Bonass, W. A., Kirkham, J., Rivetti, C. & Thomson, N. H. Collision events between RNA polymerases in convergent transcription studied by atomic force microscopy. Nucleic Acids Res. 34, 5416–5425 (2006). Hu, W. Y., Bushman, F. D. & Siva, A. C. RNA interference against retroviruses. Virus Res. 102, 59–64 (2004). Morris, K. V., Chan, S. W., Jacobsen, S. E. & Looney D. J. Small interfering RNA-induced transcriptional gene silencing in human cells. Science 305, 1289–1292 (2004). Scherer, L. J. & Rossi, J. J. Approaches for the sequence-specific knockdown of mRNA. Nature Biotech. 21, 1457–1465 (2003). 94. Martens, J. A., Laprade, L. & Winston, F. Intergenic transcription is required to repress the Saccharomyes cerevisiae SER3 gene. Nature 429, 571–574 (2004). 95. Lenasi, T., Contreras, X. & Peterlin, B. M. Transcriptional interference antagonizes proviral gene expression to promote HIV-1 latency. Cell Host Microbe 4, 123–133 (2008). 96. Perkins, K. J. & Proudfoot, N. J. An ungracious host for an unwelcome guest. Cell Host Microbe 4, 89–91 (2008). 97. Mazo, A., Hodgson, J. W., Petruk, S., Sedkov, Y. & Brock, H. W. Transcriptional interference: an unexpected layer of complexity in gene regulation. J. Cell Sci. 120, 2755–2761 (2007). 98. Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001). 99. Carteau, S., Hoffmann, C. & Bushman, F. D. Chromosome structure and HIV‑1 cDNA integration: centromeric alphoid repeats are a disfavored target. J. Virol. 72, 4005–4014 (1998). 100. Jordan, A., Bisgrove, D. & Verdin, E. HIV reproducibly establishes a latent infection after acute infection of T cells in vitro. EMBO J. 22, 1868–1877 (2003). 101. Zamborlini, A. et al. Centrosomal pre-integration latency of HIV‑1 in quiescent cells. Retrovirology 4, 63 (2007). 102. He, G. & Margolis, D. M. Counterregulation of chromatin deacetylation and histone deacetylase occupancy at the integrated promoter of human immunodeficiency virus type 1 (HIV-1) by the HIV-1 repressor YY1 and HIV-1 activator Tat. Mol. Cell Biol. 22, 2965–2273 (2002). This paper shows that recruitment of HDAC1 at nucleosome 1 of an integrated HIV‑1 LTR counteracts Tat activation and represses viral gene expression, whereas decreased HDAC1 occupancy by HDAC inhibitors results in LTR-dependent transcription activation. 103. Gordon, S., Akopyan, G., Garban, H. & Bonavida, B. Transcription factor YY1: structure, function, and therapeutic implications in cancer biology. Oncogene 25, 1125–1142 (2006). 104. Ylisastigui, L. et al. Polyamides reveal a role for repression in latency within resting T cells of HIVinfected donors. J. Infect. Dis. 190, 1429–1437 (2004). 105. Williams, S. A. et al. NF-κB p50 promotes HIV-1 latency through HDAC recruitment and repression of transcriptional initiation. EMBO J. 25, 139–149 (2006). This study finds that NF‑κB subunit p50 can form a complex (with HDAC1) that binds constitutively to the HIV‑1 LTR and induces repressive changes in chromatin structure that impair transcription initiation. 106. Tyagi, M. & Karn, J. CBF-1 promotes transcriptional silencing during the establishment of HIV-1 latency. EMBO J. 26, 4985–4995 (2007). 107. du Chene, I. et al. Suv39H1 and HP1γ are responsible for chromatin-mediated HIV-1 transcriptional silencing and post-integration latency. EMBO J. 26, 424–435 (2007). This work shows that the SUV39H1-mediated trimethylation of histone H3 at lysine 9 — which is necessary to form heterochromatin, as it recruits HP1γ — leads to HIV‑1 transcriptional silencing and post-integration latency that can be overcome by RNAi of HP1γ. 108. Lusic, M., Marcello, A., Cereseto, A. & Giacca, M. Regulation of HIV-1 gene expression by histone acetylation and factor recruitment at the LTR promoter. EMBO J. 22, 6550–6561 (2003). 109. Jiang, G., Espeseth, A., Hazuda, D. J. & Margolis, D. M. c-Myc and Sp1 contribute to proviral latency by recruiting histone deacetylase 1 to the human immunodeficiency virus type 1 promoter. J. Virol. 81, 10914–10923 (2007). 110. Chen, L. F., Fischle, W., Verdin, E. & Greene, W. C. Duration of nuclear NF‑κB action regulated by reversible acetylation. Science 293, 1653–1657 (2001). 111. Doetzlhofer, A. et al. Histone deacetylase 1 can repress transcription by binding to Sp1. Mol. Cell. Biol. 19, 5504–5511 (1999). 112. Ansari, K. I., Mishra, B. P. & Mandal, S. S. MLL histone methylases in gene expression, hormone signalling and cell cycle. Front. Biosci. 14, 3483–3495 (2009). 113. Grewal, S. I. & Moazed, D. Heterochromatin and epigenetic control of gene expression. Science 301, 798–802 (2003). 810 | november 2009 | Volume 7 © 2009 Macmillan Publishers Limited. All rights reserved.
  14. 14. REVIEWS 114. Marban, C. et al. Recruitment of chromatin-modifying enzymes by CTIP2 promotes HIV-1 transcriptional silencing. EMBO J. 26, 412–423 (2007). 115. Pearson, R. et al. Epigenetic silencing of HIV-1 transcription by formation of restrictive chromatin structures at the viral LTR drives the progressive entry of HIV-1 into latency. J. Virol. 82, 12291–12303 (2008). 116. Weil, R. & Israel, A. T‑cell‑receptor- and B‑cell‑receptormediated activation of NF-κB in lymphocytes. Curr. Opin. Immunol. 16, 374–381 (2004). 117. Bachelerie, F. et al. Nuclear export signal of IκBα interferes with the Rev-dependent posttranscriptional regulation of human immunodeficiency virus type I. J. Cell Sci. 110, 2883–2893 (1997). 118. Coiras, M., López-Huertas, M. R., Rullas, J., Mittelbrunn, M. & Alcamí, J. Basal shuttle of NF-κB/ IκBα in resting T lymphocytes regulates HIV-1 LTR dependent expression. Retrovirology 4, 56 (2007). This study shows that the low-level HIV‑1 replication in resting CD25– CD4+ T cells is due to the basal NF‑κB activity that is necessary for cell survival. 119. Amini, S., Saunders, M., Kelley, K., Khalili, K. & Sawaya, B. E. Interplay between HIV-1 Vpr and Sp1 modulates p21WAF1 gene expression in human astrocytes. J. Biol. Chem. 279, 46046–46056 (2004). 120. Zhang, J., Scadden, D. T. & Crumpacker, C. S. Primitive hematopoietic cells resist HIV-1 infection via p21. J. Clin. Invest. 117, 473–481 (2007). 121. Dorr, A. et al. Transcriptional synergy between Tat and PCAF is dependent on the binding of acetylated Tat to the PCAF bromodomain. EMBO J. 21, 2715–2723 (2002). 122. Col, E. et al. The histone acetyltransferase, hGCN5, interacts with and acetylates the HIV transactivator, Tat. J. Biol. Chem. 276, 28179–28184 (2001). 123. Ott, M. et al. Tat acetylation: a regulatory switch between early and late phases in HIV transcription elongation. Novartis Found. Symp. 259, 182–196 (2004). 124. Amini, S. et al. p73 interacts with human immunodeficiency virus type 1 Tat in astrocytic cells and prevents its acetylation on lysine 28. Mol. Cell. Biol. 25, 8126–8138 (2005). 125. Pagans, S. et al. SIRT1 regulates HIV transcription via Tat deacetylation. PLoS Biol. 3, e41 (2005). 126. Sabò, A., Lusic, M., Cereseto, A. & Giacca, M. Acetylation of conserved lysines in the catalytic core of cyclin-dependent kinase 9 inhibits kinase activity and regulates transcription. Mol. Cell Biol. 28, 2201–2212 (2008). 127. Boulanger, M. C. et al. Methylation of Tat by PRMT6 regulates human immunodeficiency virus type 1 gene expression. J. Virol. 79, 124–131 (2005). 128. Xie, B., Invernizzi, C. F., Richard, S. & Wainberg, M. A. Arginine methylation of the human immunodeficiency virus type 1 Tat protein by PRMT6 negatively affects Tat interactions with both cyclin T1 and the Tat transactivation region. J. Virol. 81, 4226–4234 (2007). 129. Ganesh, L. et al. The gene product Murr1 restricts HIV-1 replication in resting CD4+ lymphocytes. Nature 426, 853–857 (2003). This is the first demonstration that COMMD1 (formerly known as Murr1) inhibits HIV‑1 replication in resting CD4+ T cells by blocking NF‑κB activity, thereby contributing to viral latency. 130. Burstein, E. et al. COMMD proteins: a novel family of structural and functional homologs of MURR1. J. Biol. Chem. 280, 22222–22232 (2005). 131. Maine, G. N., Mao, X., Komarck, C. M. & Burstein, E. COMMD1 promotes the ubiquitination of NF-κB subunits through a cullin-containing ubiquitin ligase. EMBO J. 26, 436–447 (2007). 132. Mangeat, B. et al. Broad antiretroviral defence by human APOBEC3G through lethal editing of nascent reverse transcripts. Nature 424, 99–103 (2004). 133. Shirakawa, K. et al. Phosphorylation of APOBEC3G by protein kinase A regulates its interaction with HIV-1 Vif. Nature Struct. Mol. Biol. 15, 1184–1191 (2008). 134. Xu, H. et al. Stoichiometry of the antiviral protein APOBEC3G in HIV-1 virions. Virology 360, 247–256 (2007). 135. Corbeau, P. Interfering RNA and HIV: reciprocal interferences. PLoS Pathog. 4, e1000162 (2008). 136. Kim, D. H. & Rossi, J. J. Strategies for silencing human disease using RNA interference. Nature Rev. Genet. 8, 173–184 (2007). 137. Huang, J. et al. Cellular microRNAs contribute to HIV-1 latency in resting primary CD4+ T lymphocytes. Nature Med. 13, 1241–1247 (2007). This paper shows that cellular miRNAs miR‑28, miR‑125b, miR‑150, miR‑223 and miR‑382 potently inhibit HIV‑1 production in resting primary CD4+ T cells and are essential for the establishment and maintenance of viral latency. 138. Han, Y. & Siliciano, R. F. Keeping quiet: microRNAs in HIV-1 latency. Nature Med. 13, 1138–1140 (2007). 139. Omoto, S. et al. HIV-1 nef suppression by virally encoded microRNA. Retrovirology 1, 44 (2004). 140. Omoto, S. & Fujii, Y. R. Regulation of human immunodeficiency virus 1 transcription by nef microRNA. J. Gen. Virol. 86, 751–755 (2005). 141. Bennasser, Y., Le, S. Y., Yeung, M. L. & Jeang, K. T. MicroRNAs in human immunodeficiency virus-1 infection. Methods Mol. Biol. 342, 241–225 (2006). 142. Bennasser, Y., Le, S. Y., Yeung, M. L. & Jeang, K. T. HIV‑1 encoded candidate micro-RNAs and their cellular targets. Retrovirology 1, 43 (2004). 143. Couturier, J. P. & Root-Bernstein, R. S. HIV may produce inhibitory microRNAs (miRNAs) that block production of CD28, CD4 and some interleukins. J. Theor. Biol. 235, 169–184 (2005). 144. Cook, J. A., Albacker, L., August, A. & Henderson, A. J. CD28-dependent HIV‑1 transcription is associated with Vav, Rac, and NF‑κB activation. J. Biol. Chem. 278, 35812–35818 (2003). 145. Asjö, B., Cefai, D., Debré, P., Dudoit, Y. & Autran, B. A novel mode of human immunodeficiency virus type 1 (HIV‑1) activation: ligation of CD28 alone induces HIV‑1 replication in naturally infected lymphocytes. J. Virol. 67, 4395–4398 (1993). 146. Lin, J. & Cullen, B. R. Analysis of the interaction of primate retroviruses with the human RNA interference machinery. J. Virol. 81, 12218–12226 (2007). 147. Bennasser, Y., Le, S. Y., Benkirane, M. & Jeang, K. T. Evidence that HIV-1 encodes an siRNA and a Suppressor of RNA Silencing. Immunity 22, 607–619 (2005). This is the first evidence that HIV‑1 encodes siRNA precursors in its genome and that Tat hijacks Dicer to avoid the processing of pre-miRNAs. 148. Bennasser, Y. & Jeang, K. T. HIV‑1 Tat interaction with Dicer: requirement for RNA. Retrovirology 3, 95 (2006). 149. Gatignol, A., Lainé, S. & Clerzius, G. Dual role of TRBP in HIV replication and RNA interference: viral diversion of a cellular pathway or evasion from antiviral immunity? Retrovirology 2, 65 (2005). 150. Christensen, H. S. et al. Small interfering RNA against the TAR RNA binding protein TRBP, a Dicer cofactor, inhibit human immunodeficiency virus type 1 long terminal repeat expression and viral production. J. Virol. 81, 5121–5131 (2007). 151. Triboulet, R. et al. Suppression of microRNA-silencing pathway by HIV-1 during virus replication. Science 315, 1579–1582 (2007). This article shows that the cellular endonucleases Dicer and Drosha inhibit HIV‑1 replication in latently infected cells, whereas HIV‑1 suppresses the expression of miRNAs. This suppression is necessary for the efficient viral replication that is mediated by the interaction between Tat and PCAF. 152. Yeung, M. L. et al. Changes in microRNA expression profiles in HIV‑1‑transfected human cells. Retrovirology 2, 81 (2005). 153. Ouellet, D. L. et al. Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element. Nucleic Acids Res. 36, 2353–2365 (2008). 154. Kumar, A. & Jeang, K. T. Insights into cellular microRNAs and human immunodeficiency virus type 1 (HIV‑1). J. Cell Physiol. 216, 327–331 (2008). 155. Perelson, A. S., Neumann, A. U., Markowitz. M., Leonard, J. M. & Ho, D. D. HIV‑1 dynamics in vivo: virion clearance rate, infected cell life-span, and viral generation. Science 271, 1582–1586 (1996). 156. Strain, M. C. et al. Heterogeneous clearance rates of long lived lymphocytes infected with HIV‑1: intrinsic stability predicts lifelong persistence. Proc. Natl Acad. Sci. USA 100, 4819–4824 (2003). 157. Palmer, S. et al. Low-level viremia persists for at least 7 years in patients on suppressive antiretroviral therapy. Proc. Natl Acad. Sci. USA 105, 3879–3884 (2008). 158. Chun, T. W. et al. HIV-infected individuals receiving effective antiviral therapy for extended periods of time continually replenish their viral reservoir. J. Clin. Invest. 11, 3250–3255 (2005). 159. Lambotte, O. et al. The lymphocyte HIV reservoir in patients on long-term HAART is a memory of virus evolution. AIDS 18, 1147–1158 (2004). 160. Bailey, J. R. et al. Residual human immunodeficiency virus type 1 viremia in some patients on antiretroviral therapy is dominated by a small number of invariant clones rarely found in circulating CD4+ T cells. J. Virol. 80, 6441–6457 (2006). 161. Tobin, N. H. et al. Evidence that low-level viremias during effective highly active antiretroviral therapy result from two processes: expression of archival virus and replication of virus. J. Virol. 79, 9625–9634 (2005). 162. Havlir, D. V. et al. Productive infection maintains a dynamic steady state of residual viremia in human immunodeficiency virus type 1-infected persons treated with suppressive antiretroviral therapy for five years. J. Virol. 77, 11212–11219 (2003). 163. Frenkel, L. M. et al. Multiple viral genetic analyses detect low-level human immunodeficiency virus type 1 replication during effective highly active antiretroviral therapy. J. Virol. 77, 5721–5730 (2003). 164. Dinoso, J. B. et al. Treatment intensification does not reduce residual HIV‑1 viremia in patients on highly active antiretroviral therapy. Proc. Natl Acad. Sci. USA 106, 9403–9408 (2009). 165. Shen, L. et al. Dose-response curve slope sets classspecific limits on inhibitory potencial of anti-HIV drugs. Nature Med. 14, 762–766 (2008). 166. Ruiz, L. et al. Protease inhibitor-containing regimens compared with nucleoside analogues alone in the suppression of persistent HIV‑1 replication in lymphoid tissue. AIDS 13, F1–F8 (1999). 167. Guadalupe, M. et al. Viral suppression and immune restoration in the gastrointestinal mucosa of human immunodeficiency virus type 1-infected patients initiating therapy during primary or chronic infection. J. Virol. 80, 8236–8247 (2006). 168. Chun, T. W. et al. Persistence of HIV in gut-associated lymphoid tissue despite long-term antiretroviral therapy. J. Infect. Dis. 197, 714–720 (2008). 169. Poles, M. A. et al. Lack of decay of HIV‑1 in gutassociated lymphoid tissue reservoirs in maximally suppressed individuals. J. Acquir. Immune. Defic. Syndr. 43, 65–68 (2006). 170. Koelsch, K. K. et al. Dynamics of total, linear nonintegrated, and integrated HIV‑1 DNA in vivo and in vitro. J. Infect. Dis. 197, 411–419 (2008). 171. Yerly, S., Perneger, T. V., Vora, S., Hirschel, B. & Perrin, L. Decay of cell-associated HIV‑1 DNA correlates with residual replication in patients treated during acute HIV‑1 infection. AIDS 14, 2805–2812 (2000). 172. Ramratnam, B. et al. The decay of the latent reservoir of replication-competent HIV‑1 is inversely correlated with the extent of residual viral replication during prolonged anti-retroviral therapy. Nature Med. 6, 82–85 (2000). 173. Chun, T. W. et al. Decay of the HIV reservoir in patients receiving antiretroviral therapy for extended periods: implications for eradication of virus. J. Infect. Dis. 195, 1762–1764 (2007). 174. Brennan, T. P. et al. Analysis of human immunodeficiency virus type-1 viremia and provirus in resting CD4+ T cells reveals a novel source of residual viremia in patients on antiretroviral therapy. J. Virol. 83, 8470-8481 (2009). 175. Gulick, R. M. et al. Maraviroc for previously treated patients with R5 HIV‑1 infection. N. Engl. J. Med. 359, 429–441 (2008). 176. Steigbigel, R. T. et al. Raltegravir with optimized background therapy for resistant HIV‑1 infection. N. Engl. J. Med. 359, 339–354 (2008). 177. Abrams, D. I. et al. Dehydroepiandrosterone (DHEA) effects on HIV replication and host immunity: a randomized placebo-controlled study. AIDS Res. Hum. Retroviruses 23, 77–85 (2007). 178. Chapuis, A. G. et al. Effects of mycophenolic acid on human immunodeficiency virus infection in vitro and in vivo. Nature Med. 6, 762–768 (2000). 179. García, F. et al. Effect of mycophenolate mofetil on immune response and plasma and lymphatic tissue viral load during and after interruption of highly active antiretroviral therapy for patients with chronic HIV infection: a randomized pilot study. J. Acquir. Immune Defic. Syndr. 36, 823–830 (2004). 180. Rizzardi, G. P. et al. Treatment of primary HIV‑1 infection with cyclosporin A coupled with highly active antiretroviral therapy. J. Clin. Invest. 109, 681–688 (2002). nature reviews | Microbiology Volume 7 | november 2009 | 811 © 2009 Macmillan Publishers Limited. All rights reserved.