Abstract
Small interfering RNAs (siRNAs) are widely used to repress gene expression by targeting mRNAs. Some reports reveal that siRNAs can also activate or inhibit gene expression through targeting the gene promoters. Our group has found that microRNAs (miRNAs) could activate gene transcription via interaction with the TATA-box motif in gene promoters. To investigate whether siRNA targeting the same region could upregulate the promoter activity, we test the activating efficiency of siRNAs targeting the TATA-box motif of 16 genes and perform a systematic analysis to identify the common features of the functional siRNAs for effective activation of gene promoters. Further, we try various modifications to improve the activating efficiency of siRNAs and find that it is quite useful to design the promoter-targeting activating siRNA by following several rules such as (a) complementary to the TATA-box-centered region; (b) UA usage at the first two bases of the antisense strand; (c) twenty-three nucleotides (nts) in length; (d) 2′-O-Methyl (2′-OMe) modification at the 3′ terminus of the antisense strand; (e) avoiding mismatches at the 3′ end of the antisense strand. The optimized activating siRNAs potently enhance the expression of interleukin-2 (IL-2) gene in human and mouse primary CD4+ T cells with a long-time effect. Taken together, our study provides a guideline for rational design the promoter-targeting siRNA to sequence-specifically enhance gene expression.
Highlights
SiRNAs are widely used to repress genes expression by targeting mRNAs [1,2,3,4,5,6]
We found that almost all the siRNAs centered position (CEN) activated the target gene promoter activity (14 out of 16), certain siRNA UP or DN was more efficient in some cases (Fig. 1B–Q)
Gene expression is regulated by the activation or deactivation of transcription factors after receiving signals from pathways triggered by ligand-receptor interactions [56,57,58]
Summary
SiRNAs are widely used to repress genes expression by targeting mRNAs [1,2,3,4,5,6]. so far, there is not an easy-to-use method to upregulate gene expression . It has been reported that cellular miRNAs and synthetic siRNAs could inhibit or induce gene expression through targeting gene promoters. MiR-423-5p causes transcriptional silencing of progesterone receptor (PR) by targeting a highly conserved region in the promoter [8]. It was reported that a short hairpin RNA (shRNA), shPromA, induced highly specific transcriptional gene silencing of HIV-1 through targeting the NFkB binding sequences of the HIV-1 promoter [9,10]. MiR-744 and miR-1186 induce Ccnb expression and manipulate mouse cell proliferation with putative binding site in the gene promoter [11]. Previous studies have not yet identified any unique feature of the binding site(s) for these activating small RNAs. it is difficult to predict whether a siRNA targeting a sequence in the promoter will have either upor down- regulatory effects
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