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      • Record: found
      • Abstract: found
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      OffScan: a universal and fast CRISPR off-target sites detection tool

      research-article
      Author(s): 1 , 1 , 2 , 3 , 1 , 1 , , 1
      Publication date (Electronic):
      Journal: BMC Genomics
      Publisher: BioMed Central
      Conference name: 14th International Symposium on Bioinformatics Research and Applications (ISBRA'18) (ISBRA 2018)
      Conference date: 8-11 June 2018
      Keywords: CRISPR/Cas, sgRNA, Off-target, FM-index

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          Abstract

          Background

          The Type II clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas) is a powerful genome editing technology, which is more and more popular in gene function analysis. In CRISPR/Cas, RNA guides Cas nuclease to the target site to perform DNA modification.

          Results

          The performance of CRISPR/Cas depends on well-designed single guide RNA (sgRNA). However, the off-target effect of sgRNA leads to undesired mutations in genome and limits the use of CRISPR/Cas. Here, we present OffScan, a universal and fast CRISPR off-target detection tool.

          Conclusions

          OffScan is not limited by the number of mismatches and allows custom protospacer-adjacent motif (PAM), which is the target site by Cas protein. Besides, OffScan adopts the FM-index, which efficiently improves query speed and reduce memory consumption.

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          Most cited references9

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          CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences

          Yanni Lin, Thomas J. Cradick, Matthew Brown … (2014)
          CRISPR/Cas9 systems are a versatile tool for genome editing due to the highly efficient targeting of DNA sequences complementary to their RNA guide strands. However, it has been shown that RNA-guided Cas9 nuclease cleaves genomic DNA sequences containing mismatches to the guide strand. A better understanding of the CRISPR/Cas9 specificity is needed to minimize off-target cleavage in large mammalian genomes. Here we show that genomic sites could be cleaved by CRISPR/Cas9 systems when DNA sequences contain insertions (‘DNA bulge’) or deletions (‘RNA bulge’) compared to the RNA guide strand, and Cas9 nickases used for paired nicking can also tolerate bulges in one of the guide strands. Variants of single-guide RNAs (sgRNAs) for four endogenous loci were used as model systems, and their cleavage activities were quantified at different positions with 1- to 5-bp bulges. We further investigated 114 putative genomic off-target loci of 27 different sgRNAs and confirmed 15 off-target sites, each harboring a single-base bulge and one to three mismatches to the guide strand. Our results strongly indicate the need to perform comprehensive off-target analysis related to DNA and sgRNA bulges in addition to base mismatches, and suggest specific guidelines for reducing potential off-target cleavage.
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            CasOT: a genome-wide Cas9/gRNA off-target searching tool.

            Bo Zhang, Shuo Lin, Johnathan Cheng … (2014)
            The CRISPR/Cas or Cas9/guide RNA system is a newly developed, easily engineered and highly effective tool for gene targeting; it has considerable off-target effects in cultured human cells and in several organisms. However, the Cas9/guide RNA target site is too short for existing alignment tools to exhaustively and effectively identify potential off-target sites. CasOT is a local tool designed to find potential off-target sites in any given genome or user-provided sequence, with user-specified types of protospacer adjacent motif, and number of mismatches allowed in the seed and non-seed regions. http://eendb.zfgenetics.org/casot/ CONTACT: zfgenetics@gmail.com or bzhang@pku.edu.cn SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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              GuideScan software for improved single and paired CRISPR guide RNA design

              Alexendar R. Perez, Yuri Pritykin, Joana Vidigal … (2017)
              We present GuideScan software for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of gRNAs for single- and paired-gRNA genome-wide screens. We also show that by using a trie data structure GuideScan designs gRNAs that are more specific than those designed by existing tools.
              Article 0 comments Cited 112 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Yingbo Cui: yingbocui@nudt.edu.cn
                Xiangke Liao: xkliao@nudt.edu.cn
                Shaoliang Peng: pengshaoliang@nudt.edu.cn
                Tao Tang: taotang84@nudt.edu.cn
                Chun Huang:
                ORCID: http://orcid.org/0000-0002-0317-8192
                chunhuang@nudt.edu.cn
                Canqun Yang: canqun@nudt.edu.cn
                Conference
                Journal ID (nlm-ta): BMC Genomics
                Journal ID (iso-abbrev): BMC Genomics
                Title: BMC Genomics
                Publisher: BioMed Central (London )
                ISSN (Electronic): 1471-2164
                Publication date (Electronic): 5 March 2020
                Publication date PMC-release: 5 March 2020
                Publication date Collection: 2020
                Volume: 21
                Issue : Suppl 1 Issue sponsor : Publication of this supplement has not been supported by sponsorship. Information about the source of funding for publication charges can be found in the individual articles. The articles have undergone the journal's standard peer review process for supplements. The Supplement Editors declare that they have no competing interests.
                Electronic Location Identifier: 872
                Affiliations
                [1 ]ISNI 0000 0000 9548 2110, GRID grid.412110.7, School of Computer, , National University of Defense Technology, ; Changsha,, 410073 China
                [2 ]National Supercomputing Center, Changsha, 410082 China
                [3 ]GRID grid.67293.39, College of Information Science and Engineering, , Hunan University, ; Changsha, 410006 China
                Author information
                http://orcid.org/0000-0002-0317-8192
                Article
                Publisher ID: 6241
                DOI: 10.1186/s12864-019-6241-9
                PMC ID: 7057453
                PubMed ID: 32138651
                SO-VID: 37e718ff-7490-46fd-83a4-7509dc637c7f
                Copyright © © The Author(s). 2020
                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.

                Conference name: 14th International Symposium on Bioinformatics Research and Applications (ISBRA'18)
                Conference acronym: ISBRA 2018
                Conference location: Beijing, China
                Conference date: 8-11 June 2018
                History
                Date received : 26 October 2019
                Date accepted : 29 October 2019
                Funding
                Funded by: National Key R&D Program of China
                Award ID: 2017YFB0202003
                Award ID: 2017YFB0202602
                Award ID: 2017YFC1311003
                Award ID: 2016YFC1302500
                Award ID: 2016YFB0200400
                Award Recipient :
                Categories
                Subject: Research
                Custom metadata
                issue-copyright-statement © The Author(s) 2020

                ScienceOpen disciplines: Genetics
                Keywords: crispr/cas,sgrna,off-target,fm-index
                Data availability:
                ScienceOpen disciplines: Genetics
                Keywords: crispr/cas, sgrna, off-target, fm-index

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