PE-Designer and PE-Analyzer: web-based design and analysis tools for CRISPR prime editing

Area of Science:

• Molecular Biology
• Genetics
• Bioinformatics

Background:

• Prime editing is an advanced gene editing technology capable of precise DNA insertions, deletions, and base conversions.
• Designing prime editing guide RNAs (pegRNAs) and analyzing prime editor (PE) outcomes present unique challenges compared to other gene editing systems.

Purpose of the Study:

• To develop user-friendly, web-based computational tools to facilitate prime editing workflows.
• To address the complexities in pegRNA design and high-throughput sequencing data analysis for prime editing applications.

Main Methods:

• Introduction of PE-Designer for selecting pegRNA sequences, including target sites, extension sequences, and nicking guide RNAs.
• Development of PE-Analyzer for analyzing high-throughput sequencing data from PE experiments, summarizing mutations, and generating interactive graphs.
• Implementation of PE-Analyzer using JavaScript for efficient, secure, and local analysis of large sequencing datasets.

Main Results:

• PE-Designer provides comprehensive information for pegRNA design, visualized interactively.
• PE-Analyzer efficiently processes sequencing data, presenting mutation analysis in tables and graphs.
• Both tools are freely accessible online without requiring user registration.

Conclusions:

• PE-Designer and PE-Analyzer significantly streamline the design and analysis phases of prime editing experiments.
• These tools enhance the accessibility and efficiency of prime editing technology for researchers.
• The developed web tools contribute to the advancement of precise genome engineering.