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Pervasive off-target activity in CRISPR-interference (CRISPRi) system [RNA-seq]

ABSTRACT: CRISPR/Cas system and its dCas derivatives have been widely and effectively used to alter the intended genomic target. However, the presence of off-targets due to unintended binding of sgRNAs to sequences that closely resemble the target sequence, is still a major challenge. Here, we utilized a genome-wide sgRNA library for the dCas9-KRAB CRISPRi system to investigate the presence of off-target activity and its effects on gene expression. Our study provides strong evidence that CRISPRi off-targets affect the transcriptome of a cell extensively. We also highlight that mis-matches to the target DNA are tolerated while sgRNA binding and the length of the contiguous matches in the PAM-proximal region is one of the most predictive features of binding, along with open chromatin and the DNA-RNA hybrid energy. Additionally, we provide a curated random forest model that can be used to predict the off-target activity in the dCas systems.

ORGANISM(S): Homo sapiens

PROVIDER: GSE252977 | GEO | 2024/10/11

REPOSITORIES: GEO

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Pervasive off-target activity in CRISPR-interference (CRISPRi) system [ChIP-seq]

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