Abstract
RNA interference (RNAi) is a technique used for transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS). PTGS is an ubiquitous basic biological phenomenon involved in the regulation of transcript abundance and plants’ immune response to viruses. PTGS also mediates genomic stability by silencing of retroelements. RNAi has become an important research tool for studying gene function by strong and selective suppression of target genes. Here, we present si-Fi, a software tool for design optimization of RNAi constructs necessary for specific target gene knock-down. It offers efficiency prediction of RNAi sequences and off-target search, required for the practical application of RNAi. si-Fi is an open-source (CC BY-SA license) desktop software that works in Microsoft Windows environment and can use custom sequence databases in standard FASTA format.
Highlights
High-throughput gene silencing technologies were applied in several organisms to study gene function
RNA interference (RNAi) can be used for stable as well as for transient transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS) (Unniyampurath et al, 2016)
The results indicate that the novel version si-Fi21 provides higher sensitivity in HS-mode and better selectivity in HE-mode (RNAi design) than the previous version
Summary
High-throughput gene silencing technologies were applied in several organisms to study gene function. The novel technique of CRISPR/Cas9-directed site-specific mutagenesis is attracting wide scientific interest, RNAi still offers advantages. The RNAi-mediated silencing is quantitative (knockdown) and can be directed to tissue or developmental specificity by the utilization of the respective promoter. As this application is based on sequence similarity of the silencing trigger to the respective targets, it allows silencing of several gene family members with a unique construct. RNAi can be used for stable as well as for transient transgene-mediated gene silencing based on the mechanism of posttranscriptional gene silencing (PTGS) (Unniyampurath et al, 2016). PTGS is an essential part of plant immune response to viruses (Muhammad et al, 2019) and required for genomic stability by silencing of retroelements (Almeida and Allshire, 2005)
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