Web-based design and analysis tools for CRISPR base editing

Abstract

Background: As a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.

Results: We present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (< 1 GB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/be-designer/ and http://www.rgenome.net/be-analyzer /, respectively.

Conclusion: We develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.

Keywords: Base editing; CRISPR; Genome editing; NGS analysis; Web-based tool.

Fig. 1

Overview of BE-Designer. a BE-Designer allows analysis of potential target sequences for base editors based on WT and variant forms of CRISPR-Cas9/-Cpf1 endonucleases, which recognize a variety of PAM sequences. The application supports 319 reference genomes from a variety of organisms including vertebrates, insects, plants, and bacteria. Furthermore, users can select base editing windows for different CRISPR base editors. b After a user clicks on the submit button, BE-Designer rapidly displays the results page showing all possible target sequences and associated useful information: target nucleotides, colored red in the base editing window, and their relative position and GC content. Possible off-target sequences from throughout the selected genome, which differ by up to 2 nucleotides from the on-target sequences, are supplied. In addition, BE-Designer offers a link to the corresponding Ensembl genome browser for each off-target site

Fig. 2

BE-Analyzer input panels. a BE-Analyzer allows various types of NGS data files: single-end reads, paired-end reads, or merged sequencing data. Moreover, BE-Analyzer optionally accepts data from CRISPR-untreated control samples. b BE-Analyzer requires basic information: a full WT sequence for reference, the type of base editor, the desired base editing window, and the target DNA sequence. Additionally, analysis parameters for flanking windows on each side of the target and a minimum frequency are required

Fig. 3

Overview of the BE-Analyzer results page. a The results are summarized in a table that includes the number of sequence reads with WT or different mutation patterns. Ultimately, the ratio of intended substitutions induced by CRISPR base editors is calculated. b For query sequences classified as substitutions, the substitution table shows the percentages of each of the 4 nucleotides at each position in the target window. For users’ convenience, expected amino acid sequences are provided. c Graphic plots show the substitution efficiencies (left) and the C to D transition patterns in the targeting region, with the ratio of types of nucleotide changes shown as C to T (red), C to G (black), and C to A (green) at each position (right). d All filtered sequences from the input data are aligned to the reference sequence. Users can confirm the mutated sequences manually