SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing

Area of Science:

• Genetics
• Molecular Biology
• Bioinformatics

Background:

• Saturation genome editing (SGE) is crucial for functional genomics, enabling the study of disease-associated genes and variants.
• Prime editing is a powerful tool for inducing single nucleotide variants (SNVs), but designing efficient prime editing guide RNAs (pegRNAs) is complex.

Purpose of the Study:

• To introduce SynDesign, a user-friendly webtool for designing, evaluating, and constructing precision pegRNA libraries for SGE.
• To streamline the process of generating all feasible pegRNA designs for targeted genes or variants.

Main Methods:

• SynDesign automates pegRNA library design for SGE, incorporating synonymous mutation markers.
• It utilizes predictive models to assess prime editing efficiencies across different editors and cell types.
• Synonymous mutation markers are employed to enhance pegRNA efficiency and facilitate downstream sequencing analysis.

Main Results:

• SynDesign provides an automated and efficient workflow for pegRNA design.
• The tool integrates predictive models and synonymous mutation markers to optimize pegRNA performance.
• It facilitates the creation of comprehensive pegRNA libraries for SGE applications.

Conclusions:

• SynDesign simplifies and accelerates the design of pegRNA libraries for saturation genome editing.
• The tool is expected to significantly aid research into disease-associated genes and variants.
• SynDesign is freely accessible, promoting wider adoption in the scientific community.