The role of unintegrated DNA in HIV infection.
Sloan RD, Wainberg MA.


Abstract

Integration of the reverse transcribed viral genome into host chromatin is the hallmark of retroviral replication. Yet, during natural HIV infection, various unintegrated viral DNA forms exist in abundance. Though linear viral cDNA is the precursor to an integrated provirus, increasing evidence suggests that transcription and translation of unintegrated DNAs prior to integration may aid productive infection through the expression of early viral genes. Additionally, unintegrated DNA has the capacity to result in preintegration latency, or to be rescued and yield productive infection and so unintegrated DNA, in some circumstances, may be considered to be a viral reservoir. Recently, there has been interest in further defining the role and function of unintegrated viral DNAs, in part because the use of anti-HIV integrase inhibitors leads to an abundance of unintegrated DNA, but also because of the potential use of non-integrating lentiviral vectors in gene therapy and vaccines. There is now increased understanding that unintegrated viral DNA can either arise from, or be degraded through, interactions with host DNA repair enzymes that may represent a form of host antiviral defence. This review focuses on the role of unintegrated DNA in HIV infection and additionally considers the potential implications for antiviral therapy.


The various forms of unintegrated HIV cDNA. Linear cDNA, the product of reverse transcription, is susceptible to a number of fates other than integration into host chromatin as proviral DNA. Autointegration may lead to the formation of truncated or internally rearranged circular forms. Although recombination may yield 1-LTR circles, host factors may also contribute their presence. Host factors, such as those involved in the non-homologous end joining pathway, participate in the formation of 2-LTR circles. Various DNA repair factors and restriction factors may also result in direct degradation of linear cDNA. Collectively, these processes help to explain patterns of unintegrated viral DNA present in infected cells.

Transcription from preintegrated or unintegrated DNA. Prior to integration, or if integration is blocked, transcription from unintegrated cDNA may still occur, the template for which is unknown. Virally imported Vpr is important in the initial stages of viral gene transcription. Translation of multiply-spliced RNA (msRNA) transcripts leads to expression of Tat, Nef and Rev. Levels of Rev are insufficient to lead to the export of singly spliced and unspliced transcripts. Rev is thought to later interfere with the integration process and to thereby inhibit superinfection. Tat and Nef collectively lead to increased cellular activation in resting T-cells. Newly synthesized Tat will also promote viral gene transcription. Nef downregulates cell surface CD4, CXCR4, CCR5 and MHC-I (HLA Class I), thereby limiting superinfection, signal transduction and likely resulting evasion from cytotoxic T-lymphocytes. Preintegration transcription of viral genes has also been linked to altered cytokine secretion in both resting T-cells and macrophages.

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