Web-based design and analysis tools for CRISPR base editing

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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.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2585-4) contains supplementary material, which is available to authorized users.

Related collections

Most cited references 10

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Precise base editing in rice, wheat and maize with a Cas9- cytidine deaminase fusion

Yuan Zong, Yanpeng Wang, Chao Li … (2017)

Single DNA base pairs are edited in wheat, rice and maize using a Cas9 nickase fusion protein.

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Highly efficient RNA-guided base editing in mouse embryos

Kyoungmi Kim, Seuk-Min Ryu, Sang-Tae Kim … (2017)

Mice with targeted point mutations are generated efficiently using Cas9–cytidine deaminase fusions.

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CRISPR-Mediated Base Editing Enables Efficient Disruption of Eukaryotic Genes through Induction of STOP Codons

Pierre Billon, Eric E. Bryant, Sarah A. Joseph … (2017)

Standard CRISPR-mediated gene disruption strategies rely on Cas9-induced DNA double-strand breaks (DSBs). Here, we show that CRISPR-dependent base editing efficiently inactivates genes by precisely converting four codons (CAA, CAG, CGA, and TGG) into STOP codons without DSB formation. To facilitate gene inactivation by induction of STOP codons (iSTOP), we provide access to a database of over 3.4 million single guide RNAs (sgRNAs) for iSTOP (sgSTOPs) targeting 97%-99% of genes in eight eukaryotic species, and we describe a restriction fragment length polymorphism (RFLP) assay that allows the rapid detection of iSTOP-mediated editing in cell populations and clones. To simplify the selection of sgSTOPs, our resource includes annotations for off-target propensity, percentage of isoforms targeted, prediction of nonsense-mediated decay, and restriction enzymes for RFLP analysis. Additionally, our database includes sgSTOPs that could be employed to precisely model over 32,000 cancer-associated nonsense mutations. Altogether, this work provides a comprehensive resource for DSB-free gene disruption by iSTOP.

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Author and article information

Contributors

Gue-Ho Hwang: iamleohwang@gmail.com

Jeongbin Park: jeongbin.park@charite.de

Kayeong Lim: limka@snu.ac.kr

Sunghyun Kim: chizksh@postech.ac.kr

Jihyeon Yu: muner8146@gmail.com

Eunchong Yu: kroisse@gmail.com

Sang-Tae Kim: stkim@ibs.re.kr

Roland Eils: roland.eils@charite.de

Jin-Soo Kim: jskim01@snu.ac.kr

Sangsu Bae:

ORCID: http://orcid.org/0000-0003-3615-8566

sangsubae@hanyang.ac.kr

Journal

Journal ID (nlm-ta): BMC Bioinformatics

Journal ID (iso-abbrev): BMC Bioinformatics

Title: BMC Bioinformatics

Publisher: BioMed Central (London )

ISSN (Electronic): 1471-2105

Publication date (Electronic): 27 December 2018

Publication date PMC-release: 27 December 2018

Publication date Collection: 2018

Volume: 19

Electronic Location Identifier: 542

Affiliations

[1 ]ISNI 0000 0001 1364 9317, GRID grid.49606.3d, Department of Chemistry, , Hanyang University, ; Seoul, South Korea

[2 ]ISNI 0000 0001 2218 4662, GRID grid.6363.0, Center for Digital Health, Berlin Institute of Health and Charité Universitätsmedizin Berlin, ; Berlin, Germany

[3 ]ISNI 0000 0001 2190 4373, GRID grid.7700.0, Faculty of Biosciences, Heidelberg University, ; Heidelberg, Germany

[4 ]ISNI 0000 0004 0470 5905, GRID grid.31501.36, Department of Chemistry, , Seoul National University, ; Seoul, South Korea

[5 ]ISNI 0000 0004 1784 4496, GRID grid.410720.0, Center for Genome Engineering, , Institute for Basic Science, ; Seoul, South Korea

[6 ]ISNI 0000 0001 1364 9317, GRID grid.49606.3d, Research Institute for Convergence of Basic Sciences, , Hanyang University, ; Seoul, South Korea

[7 ]ISNI 0000 0004 1784 4496, GRID grid.410720.0, Center for Genome Engineering, Institute for Basic Science, ; Daejeon, South Korea

[8 ]ISNI 0000 0001 0328 4908, GRID grid.5253.1, Health Data Science Unit, Heidelberg University Hospital, ; Heidelberg, Germany

Author information

Sangsu Bae http://orcid.org/0000-0003-3615-8566

Article

Publisher ID: 2585

DOI: 10.1186/s12859-018-2585-4

PMC ID: 6307267

PubMed ID: 30587106

SO-VID: f151878a-f2f4-48db-b2e2-9032932f4565

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.