Identification of functional microRNAs released through asymmetrical processing of HIV-1 TAR element

TLDR

HIV‑1’s trans‑activation responsive (TAR) RNA, essential for viral transcription and Tat‑mediated transactivation, engages complex interactions with host RNA‑silencing pathways. Using primer‑extension and RNase‑protection assays, the authors mapped both strands of the TAR‑derived miRNA duplex, identifying miR‑TAR‑5p and miR‑TAR‑3p. The study shows that TAR RNA is processed asymmetrically by Dicer to release functional miR‑TAR‑5p and miR‑TAR‑3p, which down‑regulate target activity—miR‑TAR‑3p being more potent—providing new insights into viral miRNA biogenesis.

Abstract

The interaction between human immunodeficiency virus type 1 (HIV-1) and RNA silencing pathways is complex and multifaceted. Essential for efficient viral transcription and supporting Tat-mediated transactivation of viral gene expression, the trans-activation responsive (TAR) element is a structured RNA located at the 5′ end of all transcripts derived from HIV-1. Here, we report that this element is a source of microRNAs (miRNAs) in cultured HIV-1-infected cell lines and in HIV-1-infected human CD4+ T lymphocytes. Using primer extension and ribonuclease (RNase) protection assays, we delineated both strands of the TAR miRNA duplex deriving from a model HIV-1 transcript, namely miR-TAR-5p and miR-TAR-3p. In vitro RNase assays indicate that the lack of a free 3′ extremity at the base of TAR may contribute to its low processing reactivity in vivo . Both miR-TAR-5p and miR-TAR-3p down-regulated TAR miRNA sensor activity in a process that required an integral miRNA-guided RNA silencing machinery. miR-TAR-3p exerted superior gene downregulatory effects, probably due to its preferential release from HIV-1 TAR RNA by the RNase III Dicer. Our study suggests that the TAR element of HIV-1 transcripts releases functionally competent miRNAs upon asymmetrical processing by Dicer, thereby providing novel insights into viral miRNA biogenesis.