Rabinowitz Roy, Almog Shiri, Darnell Roy, Offen Daniel
Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
Felsenstein Medical Research Center, Tel Aviv University, Tel Aviv, Israel.
Front Genet. 2020 Aug 18;11:851. doi: 10.3389/fgene.2020.00851. eCollection 2020.
Clustered regularly interspaced short palindromic repeats (CRISPR) is a promising novel technology that holds the potential of treating genetic diseases. Safety and specificity of the treatment are to be further studied and developed prior to implementation of the technology into the clinic. The guide-RNA (gRNA) allows precise position-specific DNA targeting, although it may tolerate small changes such as point mutations. The permissive nature of the CRISPR-Cas system makes allele-specific targeting a challenging goal. Hence, an allele-specific targeting approach is in need for future treatments of heterozygous patients suffering from diseases caused by dominant negative mutations. The single-nucleotide polymorphism (SNP)-derived protospacer adjacent motif (PAM) approach allows highly allele-specific DNA cleavage due to the existence of a novel PAM sequence only at the target allele. Here, we present CrisPam, a computational tool that detects PAMs within the variant allele for allele-specific targeting by CRISPR-Cas systems. The algorithm scans the sequences and attempts to identify the generation of multiple PAMs for a given reference sequence and its variations. A successful result is such that at least a single PAM is generated by the variation nucleotide. Since the PAM is present within the variant allele only, the Cas enzyme will bind the variant allele exclusively. Analyzing a dataset of human pathogenic point mutations revealed that 90% of the analyzed mutations generated at least a single PAM. Thus, the SNP-derived PAM approach is ideal for targeting most of the point mutations in an allele-specific manner. CrisPam simplifies the gRNAs design process to specifically target the allele of interest and scans a wide range of 26 unique PAMs derived from 23 Cas enzymes. CrisPam is freely available at https://www.danioffenlab.com/crispam.
成簇规律间隔短回文重复序列（CRISPR）是一项很有前景的新技术，具有治疗遗传疾病的潜力。在将该技术应用于临床之前，其治疗的安全性和特异性还有待进一步研究和开发。引导RNA（gRNA）允许对特定位置的DNA进行精确靶向，尽管它可能容忍一些小的变化，如点突变。CRISPR-Cas系统的宽容性使得等位基因特异性靶向成为一个具有挑战性的目标。因此，对于未来治疗由显性负性突变引起疾病的杂合患者，需要一种等位基因特异性靶向方法。单核苷酸多态性（SNP）衍生的原间隔相邻基序（PAM）方法由于仅在目标等位基因处存在新的PAM序列，从而允许高度等位基因特异性的DNA切割。在此，我们展示了CrisPam，这是一种计算工具，可检测变异等位基因内的PAM，用于CRISPR-Cas系统的等位基因特异性靶向。该算法扫描序列，并尝试为给定的参考序列及其变体识别多个PAM的产生。成功的结果是变异核苷酸至少产生一个PAM。由于PAM仅存在于变异等位基因中，Cas酶将仅结合变异等位基因。对人类致病点突变数据集的分析表明，90%的分析突变至少产生一个PAM。因此，SNP衍生的PAM方法是以等位基因特异性方式靶向大多数点突变的理想方法。CrisPam简化了gRNA的设计过程，以特异性靶向感兴趣的等位基因，并扫描来自23种Cas酶的26种独特PAM的广泛范围。CrisPam可在https://www.danioffenlab.com/crispam免费获取。
