CRISPR-Cas“非靶”位点抑制靶位切割率。

CRISPR-Cas "Non-Target" Sites Inhibit On-Target Cutting Rates.

机构信息

Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA.

出版信息

CRISPR J. 2020 Dec;3(6):550-561. doi: 10.1089/crispr.2020.0065.

Abstract

CRISPR-Cas systems have become ubiquitous for genome editing in eukaryotic as well as bacterial systems. Cas9 forms a complex with a guide RNA (gRNA) and searches DNA for a matching sequence (target site) next to a protospacer adjacent motif (PAM). Once found, Cas9 cuts the DNA. Cas9 is revolutionary for the ability to change the RNA sequence and target a new site easily. However, while algorithms have been developed to predict gRNA-specific Cas9 activity, a fundamental biological understanding of gRNA-specific activity is lacking. The number of PAM sites in the genome is effectively a large pool of inhibitory substrates, competing with the target site for the Cas9/gRNA complex. We demonstrate that increasing the number of non-target sites for a given gRNA reduces on-target activity in a dose-dependent manner. Furthermore, we show that the use of Cas9 mutants with increased PAM specificity toward a smaller subset of PAMs (or smaller pool of competitive substrates) improves cutting rates, while increased PAM promiscuity decreases cutting rates. Decreasing the potential search space by increasing PAM specificity provides a path toward improving on-target activity for slower high-fidelity Cas9 variants. Engineering improved PAM specificity to reduce the competitive search space offers an alternative strategy to engineer Cas9 variants with increased specificity and maintained on-target activity.

摘要

CRISPR-Cas 系统已成为真核生物和细菌系统基因组编辑的通用工具。Cas9 与向导 RNA(gRNA)形成复合物,并在紧邻原间隔序列邻近基序(PAM)的位置搜索与靶序列匹配的序列(靶标位点)。一旦找到,Cas9 就会切割 DNA。Cas9 能够改变 RNA 序列并轻松靶向新位点,这具有革命性意义。然而,尽管已经开发出用于预测 gRNA 特异性 Cas9 活性的算法,但对 gRNA 特异性活性的基本生物学理解仍存在不足。基因组中的 PAM 位点数量实际上是一个大量的抑制性底物库,与靶标位点竞争 Cas9/gRNA 复合物。我们证明,给定 gRNA 的非靶标位点数量的增加以剂量依赖的方式降低了靶标活性。此外,我们表明,使用对较小 PAM 子集(或较小的竞争底物库)具有更高 PAM 特异性的 Cas9 突变体可提高切割率,而增加 PAM 的广谱性则会降低切割率。通过增加 PAM 特异性来减小潜在搜索空间为提高较慢的高保真 Cas9 变体的靶标活性提供了一条途径。工程化提高 PAM 特异性以减少竞争搜索空间为工程化具有更高特异性和保持靶标活性的 Cas9 变体提供了一种替代策略。

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