SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments

• Published in: Bioinformatics (Oxford, England) Vol. 40; no. 1
• Main Authors: Cazares, Tareian, Higgs, Richard E, Wang, Jibo, Ozer, Hatice Gulcin
• Format: Journal Article
• Language: English
• Published: England 02.01.2024
• Subjects: 3' Untranslated Regions; MicroRNAs - metabolism; Nucleotides; RNA Interference; RNA, Messenger - metabolism; RNA, Small Interfering - genetics; RNA-Seq
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btae011

On-target gene knockdown, using siRNA, ideally results from binding fully complementary regions in mRNA transcripts to induce direct cleavage. Off-target siRNA gene knockdown can occur through several modes, one being a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated off-target effects occur when the ∼8 nucleotides at the 5' end of the guide strand, called a seed region, bind the 3' untranslated regions of mRNA, causing reduced translation. Experiments using siRNA knockdown paired with RNA-seq can be used to detect siRNA sequences with off-target effects driven by the seed region. However, there are limited computational tools designed specifically for detecting siRNA off-target effects mediated by the seed region in differential gene expression experiments. SeedMatchR is an R package developed to provide users a single, unified resource for detecting and visualizing seed-mediated off-target effects of siRNA using RNA-seq experiments. SeedMatchR is designed to extend current differential expression analysis tools, such as DESeq2, by annotating results with predicted seed matches. Using publicly available data, we demonstrate the ability of SeedMatchR to detect cumulative changes in differential gene expression attributed to siRNA seed region activity. SeedMatchR is available on CRAN. Documentation and example workflows are available through the SeedMatchR GitHub page at https://github.com/tacazares/SeedMatchR.