Human cellular microRNA hsa-miR-29a interferes with viral nef protein expression and HIV-1 replication

We find that the human miRNAs hsa-miR-29a and 29b are expressed in human peripheral blood mononuclear cells. Expression of a luciferase reporter bearing the nef miR-29a target site was decreased compared to the luciferase construct without the target site. Locked nucleic acid modified anti-miRNAs targeted against hsa-miR-29a and 29b specifically reversed the inhibitory effect mediated by cellular miRNAs on the target site. Ectopic expression of the miRNA results in repression of the target Nef protein and reduction of virus levels.Our results show that the cellular miRNA hsa-miR29a downregulates the expression of Nef protein and interferes with HIV-1 replication.MicroRNAs (miRNAs) are naturally occurring small RNA molecules that modulate gene expression by binding to partially complementary target sites usually located in the 3'UTR of protein coding transcripts[1]. They have been implicated in biological functions like tissue differentiation, establishment of cell fate during development, apoptosis and oncogenesis [2-5]. The cellular miRNA, hsa-miR-32 has been shown to directly interfere with the replication of primate foamy virus in HeLa cells and to reduce viral RNA levels[6]. Another cellular miRNA, miR-122a, involved in cellular stress response and modulated by interferon beta, can also influence the susceptibility to Hepatitis C virus [7-9]. Earlier, we had predicted sites in the HIV-1 genome that can be potentially targeted by human encoded miRNAs using consensus target prediction, and we had proposed the possibility that the cellular levels of these miRNAs may determine disease progression following HIV-1 infection[10]. Here we experimentally confirmed our computational predictions by demonstrating that the expression of specific cellular miRNAs can reduce target protein expression and HIV-1 replication in cultured human cells.We used a consensus approach to predict targets in the HIV-1 genome for all human miRNAs. Five miRNAs (hsa-miR-29a, 29b, 149, 324–5p a