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pegFinder: A pegRNA designer for CRISPR prime editing

Ryan D. Chow, Jennifer S. Chen, Johanna Shen, View ORCID ProfileSidi Chen
doi: https://doi.org/10.1101/2020.05.06.081612
Ryan D. Chow
1Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
2System Biology Institute, Yale University, West Haven, Connecticut, USA
3Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
4M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
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Jennifer S. Chen
4M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
5Department of Laboratory Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
6Department of Immunobiology, Yale University School of Medicine, New Haven, Connecticut, USA
7Immunobiology Program, Yale University, New Haven, Connecticut, USA
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Johanna Shen
1Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
2System Biology Institute, Yale University, West Haven, Connecticut, USA
3Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
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Sidi Chen
1Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
2System Biology Institute, Yale University, West Haven, Connecticut, USA
3Center for Cancer Systems Biology, Yale University, West Haven, Connecticut, USA
4M.D.-Ph.D. Program, Yale University, West Haven, Connecticut, USA
7Immunobiology Program, Yale University, New Haven, Connecticut, USA
8Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, Connecticut, USA
9Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut, USA
10Department of Neurosurgery, Yale University School of Medicine, New Haven, Connecticut, USA
11Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut, USA
12Yale Liver Center, Yale University School of Medicine, New Haven, Connecticut, USA
13Yale Center for Biomedical Data Science, Yale University School of Medicine, New Haven, Connecticut, USA
14Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
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  • ORCID record for Sidi Chen
  • For correspondence: sidi.chen@yale.edu
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To the Editor

CRISPR technologies have been widely adopted as powerful tools for targeted genomic manipulation 1. Recently, a new CRISPR-based strategy for precision genome editing was developed that enables diverse genomic alterations to be directly written into target sites without requiring double-strand breaks (DSBs) or donor templates 2. Termed prime editing, this approach involves two key components: 1) a catalytically impaired Cas9 nickase fused to a reverse transcriptase (PE2), and 2) a multifunctional prime editing guide RNA (pegRNA) that specifies the target site and further acts as a template for reverse transcription (RT). pegRNAs are similar to standard single-guide RNAs (sgRNAs), but additionally have a customizable extension on the 3’ end. The 3’ extension is composed of a RT template that encodes the desired edit and a primer binding site (PBS) that anneals to the target genomic site to prime the RT reaction 2. These additional components considerably increase the complexity of pegRNA design compared to standard sgRNAs. While many tools have been developed for identifying candidate sgRNAs in a target DNA sequence 3–8, no user-friendly web application currently exists for designing pegRNAs. We therefore developed pegFinder, a streamlined web tool that rapidly designs candidate pegRNAs (Figure 1). The pegFinder web portal is freely available at http://pegfinder.sidichenlab.org/ (Supplementary Figure 1).

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 08, 2020.
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pegFinder: A pegRNA designer for CRISPR prime editing
Ryan D. Chow, Jennifer S. Chen, Johanna Shen, Sidi Chen
bioRxiv 2020.05.06.081612; doi: https://doi.org/10.1101/2020.05.06.081612
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pegFinder: A pegRNA designer for CRISPR prime editing
Ryan D. Chow, Jennifer S. Chen, Johanna Shen, Sidi Chen
bioRxiv 2020.05.06.081612; doi: https://doi.org/10.1101/2020.05.06.081612

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