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Cited by 198CRISPR and Genetic EngineeringRNA regulation and diseaseGenomics and Phylogenetic Studies

The DOI matches its Crossref record; 32 of the 33 references it cites were found in a registry or an index.

Web-based design and analysis tools for CRISPR base editing

Open access
Hwang, Gue-Ho, Park, Jeongbin, Lim, Kayeong, Kim, Sunghyun, Yu, Jihyeon, Yu, Eunchong, Kim, Sang-Tae, Eils, Roland, Kim, Jin-Soo, Bae, Sangsu·2018·BMC Bioinformatics
DOI 10.1186/s12859-018-2585-4PMC PMC6307267

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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.

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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. 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 siteCC BY · PubMed Central
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. 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 requiredCC BY · PubMed Central
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
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 manuallyCC BY · PubMed Central

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Metadata

Authors
Hwang, G.-H., Park, J., Lim, K., Kim, S., Yu, J., Yu, E., Kim, S.-T., Eils, R., Kim, J.-S., & Bae, S.
Affiliations
  • Hanyang University (KR)
  • Heidelberg University (DE)
  • Seoul National University (KR)
  • University Hospital Heidelberg (DE)
Corresponding author
Bae, Sangsu
ORCID
Venue
BMC Bioinformatics
Publisher
Springer Science and Business Media LLC
Published
2018-12
Volume
19
Issue
1
Pages
542-542
ISSN
1471-2105 (ISSN-L)
DOI
10.1186/s12859-018-2585-4
PMC
PMC6307267
OpenAlex
W2883250809
Cited by
198
References
33
Citations by year
2026: 12 · 2025: 34 · 2024: 29 · 2023: 23 · 2022: 27 · 2021: 29 · 2020: 32 · 2019: 12
FWCI
6.49
Type
journal article
Language
en
Open access
Licence
Locations
  • BMC Bioinformatics (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • heiDOK (Heidelberg University) (acceptedVersion, other-oa)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
  • Seoul National University Open Repository (Seoul National University) (submittedVersion)
Funders
  • Deutsches Krebsforschungszentrum
  • National Research Foundation (2017M3A9G8084539, 2018M3A9H3022412, HI16C1012)
  • Ministry of Trade, Industry and Energy (20000158)
  • National Research Foundation of Korea (PJ01319301, 2018M3A9H3022412, 20000158, 2017M3A9G8084539)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
CRISPR base editing, web-based design tool, off-target sites, cytidine deaminase, guanine deaminase, dCas9, next-generation sequencing data analysis, genome editing
MeSH terms
Gene Editing, Humans, Internet, Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR-Cas Systems

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