MicroRNA profile in HIV-1 infection suggests differential role of Dicer dependent and independent RNAi. (A) shows the distinct structure pattern in the terminal loop of hairpin precursor of microRNA known to be up-regulated (Blue Box) and down-regulated (Red Box) in HIV-1 infection. Up-regulated miRNAs show Ago2 dependency while down-regulated show Dicer dependency. Sequences in red represents mature miRNA in hairpin precursor. (B) the left half shows Ago2 processed molecular features in TAR miRNA (short tight loop in green box), internal bulges (in red), and predicted cleavage sites by RNA endonucleases. These predictions were based on the functional parameters of Ago2 dependent processing reported in literature [35, 36, 39, 40]. The right half shows the TAR2 miRNA sequence with mature stem length of 17 to 18 (in bold) as predicted to be dominantly processed by Ago2. Total RNA was prepared form the HIV-1 infected cells and subjected to Real Time PCR to analyze the expression level of Tar1 and Tar2 miRNA. (C) shows the amplification plot for Tar1 and Tar2. Latently infected T cells (J1.1) were treated with TNF-α (10 ng/ml) and enoxacin (50 μM) for 48 hours. Total RNA was prepared and was subjected to Real Time PCR to analyze the expression level of Tar1 and Tar2 miRNA. (D) shows the quantification plot for Tar1 and Tar2. (E) shows the amplification for Tar2. (F) shows the amplification plot for miR16 (an unrelated miRNA) in enoxacin treated and untreated samples. RNU6B was used as endogenous control.