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Nucleic Acids Res., Apr 29 2024, gkae304 | https://doi.org/10.1093/nar/gkae304 SynDesign: web-based prime editing guide RNA design and evaluation tool for saturation genome editing

Jinman Park^1,2, Goosang Yu^1,2, Sang-Yeon Seo^1,2, Jinyeong Yang^1,2 and Hyongbum Henry Kim^{1,2,3,4,5,6,7,8,*}

¹Department of Pharmacology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

²Graduate School of Medical Science, Brain Korea 21 Plus Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

³Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

⁴Center for Nanomedicine, Institute for Basic Science (IBS), Seoul 03722, Republic of Korea

⁵Yonsei-IBS Institute, Yonsei University, Seoul 03722, Republic of Korea

⁶Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

⁷Woo Choo Lee Institute for Precision Drug Development, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

⁸Won-Sang Lee Institute for Hearing Loss, Yonsei University College of Medicine, Seoul 03722, Republic of Korea

^*To whom correspondence should be addressed. : Hyongbum Henry Kim

Abstract

Saturation genome editing (SGE) enables in-depth functional evaluation of disease-associated genes and variants by generating all possible single nucleotide variants (SNVs) within a given coding region. Although prime editing can be employed for inducing these SNVs, designing efficient prime editing guide RNAs (pegRNAs) can be challenging and time-consuming. Here, we present SynDesign, an easy-to-use webtool for the design, evaluation, and construction precision pegRNA libraries for SGE with synonymous mutation markers. SynDesign offers a simple yet powerful interface that automates the generation of all feasible pegRNA designs for a target gene or variant of interest. The pegRNAs are selected using the state-of-the-art models to predict prime editing efficiencies for various prime editors and cell types. Top-scoring pegRNA designs are further enhanced using synonymous mutation markers which improve pegRNA efficiency by diffusing the cellular mismatch repair mechanism and serve as sequence markers for improved identification of intended edits following deep sequencing. SynDesign is expected to facilitate future research using SGE to investigate genes or variants of interest associated with human diseases. SynDesign is freely available at https://deepcrispr.info/SynDesign without a login process.

논문정보

형식Research article
게재일2024년 04월 (BRIC 등록일 2024-05-03)
연구진국내 연구진
분야 의약학 > 유전 및 유전체의학

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