Comprehensive computational analysis of epigenetic descriptors affecting CRISPR-Cas9 off-target activity

Abstract

Abstract Background A common issue in CRISPR-Cas9 genome editing is off-target activity, which prevents the widespread use of CRISPR-Cas9 in medical applications. Among other factors, primary chromatin structure and epigenetics may influence off-target activity. Methods In this work, we utilize crisprSQL, an off-target database, to analyze the effect of 19 epigenetic descriptors on CRISPR-Cas9 off-target activity. Termed as 19 epigenetic features/scores, they consist of 6 experimental epigenetic and 13 computed nucleosome organization-related features. In terms of novel features, 15 of the epigenetic scores are newly considered. The 15 newly considered scores consist of 13 freshly computed nucleosome occupancy/positioning scores and 2 experimental features (MNase and DRIP). The other 4 existing scores are experimental features (CTCF, DNase I, H3K4me3, RRBS) commonly used in deep learning models for off-target activity prediction. For data curation, MNase was aggregated from existing experimental nucleosome occupancy data. Based on the sequence context information available in crisprSQL, we also computed nucleosome occupancy/positioning scores for off-target sites. Results To investigate the relationship between the 19 epigenetic features and off-target activity, we first conducted Spearman and Pearson correlation analysis. Such analysis shows that some computed scores derived from training-based models and training-free algorithms outperform all experimental epigenetic features. Next, we evaluated the contribution of all epigenetic features in two successful machine/deep learning models which predict off-target activity. We found that some computed scores, unlike all 6 experimental features, significantly contribute to the predictions of both models. As a practical research contribution, we make the off-target dataset containing all 19 epigenetic features available to the research community. Conclusions Our comprehensive computational analysis helps the CRISPR-Cas9 community better understand the relationship between epigenetic features and CRISPR-Cas9 off-target activity.