WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat
WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat
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DOI：
10.1186/s12870-019-2097-z
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发表时间：
2019-11-06
影响因子：
5.3
通讯作者：
Kagale, Sateesh
中科院分区：
文献类型：
--
作者：
Cram, Dustin;Kulkarni, Manoj;Kagale, Sateesh
背景CRISPR/Cas9基因编辑已成为作物改良的一项革命性技术，因为它可以在不保留最终植株系中转基因成分的情况下，促进快速而有效的遗传变化。目前缺乏强大的生物信息学工具来促进小麦高度特异的功能引导RNA(GRNAs)的设计和非靶点位置的预测，这是CRISPR技术在小麦改良中有效应用的障碍。我们已经开发了一个基于网络的生物信息学工具来设计特定的gRNAs，用于基因组编辑和小麦基因表达的转录调控。布罗德研究所和微软研究所之间的一项合作研究使用大规模经验证据来设计算法(Doech等人，2016，自然生物技术34,184-191)，以预测CRISPR/SpCas9(化脓链球菌Cas9)的靶上活性和脱靶潜力。我们应用这些预测模型来确定针对小麦基因组中特定基因座的单个gRNA的靶上特异性和潜在的非靶标活性。全基因组gRNA映射和相应的预测靶上和靶外活动的道奇分数被用来创建一个gRNA数据库，该数据库被用作名为WheatCRISPR的网络应用的数据源。结论WheatCRISPR工具允许研究人员浏览所有可能针对感兴趣的基因或序列的gRNA，并根据其预测的高靶上和低靶外活性分数以及其他特征(如在靶基因中的位置)选择有效的gRNA。它在https://crispr.bioinfo.nrc.ca/WheatCrispr/.上公开可用
Background CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. Description We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184-191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. Conclusion The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/.