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      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.

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          Most cited references 10

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

          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

            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

              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
                iamleohwang@gmail.com
                jeongbin.park@charite.de
                limka@snu.ac.kr
                chizksh@postech.ac.kr
                muner8146@gmail.com
                kroisse@gmail.com
                stkim@ibs.re.kr
                roland.eils@charite.de
                jskim01@snu.ac.kr
                sangsubae@hanyang.ac.kr
                Journal
                BMC Bioinformatics
                BMC Bioinformatics
                BMC Bioinformatics
                BioMed Central (London )
                1471-2105
                27 December 2018
                27 December 2018
                2018
                : 19
                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
                Article
                2585
                10.1186/s12859-018-2585-4
                6307267
                30587106
                © The Author(s). 2018

                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.

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                © The Author(s) 2018

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