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

ABSTRACT:

Motivation

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 ex

SUBMITTER: Cazares T 

PROVIDER: S-EPMC10799297 | biostudies-literature | 2024 Jan

REPOSITORIES: biostudies-literature