School of Biological and Health Systems Engineering, Arizona State University, Tempe, Arizona, USA; University of Connecticut Health Center, Farmington, Connecticut, USA.
The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA; University of Connecticut Health Center, Farmington, Connecticut, USA.
CRISPR J. 2022 Aug;5(4):618-628. doi: 10.1089/crispr.2022.0042. Epub 2022 Jul 12.
Zinc finger protein-, transcription activator like effector-, and CRISPR-based methods for genome and epigenome editing and imaging have provided powerful tools to investigate functions of genomes. Targeting sequence design is vital to the success of these experiments. Although existing design software mainly focus on designing target sequence for specific elements, we report here the implementation of Jackie and Albert's Comprehensive K-mer Instances Enumerator (JACKIE), a suite of software for enumerating all single- and multicopy sites in the genome that can be incorporated for genome-scale designs as well as loaded onto genome browsers alongside other tracks for convenient web-based graphic-user-interface-enabled design. We also implement fast algorithms to identify sequence neighborhoods or off-target counts of targeting sequences so that designs with low probability of off-target can be identified among millions of design sequences in reasonable time. We demonstrate the application of JACKIE-designed CRISPR site clusters for genome imaging.
锌指蛋白、转录激活因子样效应物和基于 CRISPR 的基因组和表观基因组编辑和成像方法为研究基因组功能提供了强大的工具。靶向序列设计对于这些实验的成功至关重要。虽然现有的设计软件主要专注于为特定元件设计目标序列，但我们在这里报告了 Jackie 和 Albert 的 Comprehensive K-mer Instances Enumerator (JACKIE)的实现，这是一套用于枚举基因组中所有单拷贝和多拷贝位点的软件，可以用于基因组规模的设计，也可以与其他跟踪器一起加载到基因组浏览器中，以便在方便的基于网络的图形用户界面启用的设计中使用。我们还实现了快速算法来识别靶向序列的序列邻域或脱靶计数，以便在合理的时间内从数百万个设计序列中识别出脱靶概率低的设计。我们展示了 JACKIE 设计的 CRISPR 位点簇在基因组成像中的应用。
