1. Introduction
Nearly half of the known pathogenic genetic variants are induced by single-nucleotide variants (SNVs) and most of the observed SNVs are lacking clinical interpretations. Recently, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) system has been used as a powerful tool to generate genetic alterations to investigate the relationship between genetic variations and human diseases. Actually, in the pioneer version of CRISPR/Cas system, Cas9 from Streptococcus pyogenes (SpCas9) is often used as nuclease to generate double strand breaks (DSBs) on DNA templates, which can lead to unintended chromosomal alterations or elicit an unwanted DNA damage response. Subsequently, DSBs are repaired through either non-homologous end joining (NHEJ) or homology-directed recombination (HDR), resulting in small insertions/deletions (indels) or substitutions at the target region, respectively (Jinek et al., 2012). However, the most common genetic alterations induced by CRISPR/Cas9 were deletions or insertions but not precise nucleotide substitutions (Feng et al., 2014).
Fortunately, base editing (BE) systems based on CRISPR/Cas technology have been developed rapidly, and various elements are being exploited and modified to increase the efficiency and precision. To avoid creating DSBs, diverse modified Cas proteins have been employed in CRISPR BE systems including nuclease-dead Cas9 (dCas9) and Cas9 nickase (nCas9), and other modified nucleases such as d/nCas12a, d/nCas12b, d/nCasX and d/nCas13 (Liang et al., 2019). Growing number of studies have indicated that CRISPR/Cas BE system is a powerful tool to manipulate genetic base editing in vitro and in vivo. To maximize the editing efficiency, BE systems with various deaminases have been developed and utilized in many organisms and cell lines. For instance, the cytidine deaminases include rAPOBEC1 (rat cytidine deaminase) (Kim et al., 2017), A3A (human APOBEC3A) (Gehrke et al., 2018) and AID (activation-induced cytidine deaminase) (Nishimasu et al., 2018) are employed in cytosine base editors (CBEs). And TadA (tRNA adenosine deaminase) is often used as adenosine deaminase in adenine base editors (ABEs). Consequently, the CRISPR/Cas BE data is increasing rapidly, being a challenge for researchers to access all related information of base editing outcomes. Moreover, the off-target effect remains uncertain and the on-target efficiency differs among various BE systems. Hence, an integrated resource and analysis platform is urgently needed for comprehensive annotation and comparative analysis of the off-target effect and the on-target efficiency among various CRISPR-mediated BE systems.
Herein, we developed the CRISPRbase, a novel platform that integrated comprehensive information for 1 252 935 records of base editing outcomes in 17 species, covering more than 54 cell types. CRISPRbase provides putative editing precision of different BE systems by incorporating multiple annotations including “organisms”, “genomebuild”, “chromosome”, “position”, “sgRNA sequences”, “PAM sequences”, “strand direction”, “mutant”, “editing systems”, “cell/tissue name”, “CRISPR type”, “Cas variant” and “mutation frequency”. Moreover, we annotated the functional effect of all single-nucleotide mutations induced by BE systems with ANNOVAR software and consequently evaluate the outcome of off-targeting. Further, CRISPRbase provides the fold change of gene expression before and after base editing induced by CRISPR-mediated BE systems. Most importantly, users could search their own sgRNA sequence by blasting the deposited sgRNA sequences to infer base editing ability with similar BE systems. CRISPRbase is a powerful and convenient tool to study the efficiency of different base editors and recommend appropriate BE system for researchers. We are dedicated to maintaining CRISPRbase and keeping the resource updated in the future.
2. Web interface of CRISPRbase
2.1 How to search CRISPRbase?
Users can search sgRNA through two ways including 'quick Search' and 'batch Search' as shown below.
2.2 Search Result
Search resul including 'primary' and 'detail' sections as shown below.
