Genome-wide CRISPR off-target prediction and optimization using RNA-DNA interaction fingerprints

The CRISPR genome editing system is hindered by its off-target effects, and existing computational tools achieved limited performance in genome-wide off-target prediction due to the lack of deep understanding of the CRISPR molecular mechanism. This study proposes to incorporate molecular dynamics (MD) simulations in the computational analysis of CRISPR system, and presents CRISOT, an integrated tool suite for RNA-DNA molecular interaction fingerprint generation, genome-wide CRISPR off-target prediction, sgRNA specificity evaluation and sgRNA optimization of Cas9 system respectively. CRISOT provides an efficient and generalizable framework for genome-wide CRISPR off-target prediction, evaluation and sgRNA optimization for improved targeting specificity in CRISPR genome editing.

• 1
  CRISOT outperforms existing tools with extensive in silico validations and proof-of-concept experimental validations.
• 2
  CRISOT shows potential in accurately predicting off-target effects of the base editors and prime editors, indicating that the derived RNA-DNA molecular interaction fingerprint captures the underlying mechanisms of RNA-DNA interaction among distinct CRISPR systems.
• 3
  CRISOT provides effective sgRNA targeting specificity evaluation of Cas9 system