CrisprGE: a central hub of CRISPR/Cas-based genome editing

Kaur, Karambir; Tandon, Himani; Gupta, Amit; Kumar, Manoj

doi:10.1093/database/bav055

Cited by 33 publications

(16 citation statements)

References 50 publications

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“…Notably, shortening the guide further to 14-nt or 15-nt creates a ‘dead guide’ that can mediate efficient wild-type Cas9 binding without nuclease activation, enabling multiplexed applications of DNA cleavage and targeted effector activity (Dahlman et al, 2015; Kiani et al, 2015). This engineered guide approach benefited from insight into the mechanism of Cas9 cleavage, which has been shown to require near-complete strand invasion and complementarity (Figure 1).…”

Section: Modified Guidesmentioning

confidence: 99%

“…The research community could begin to report guide RNA on- and off-target activity to shared databases, like EENdb (Xiao et al, 2013) or CrisprGE (Kaur et al, 2015). Such standardized information, in combination with continued progress in off-target detection methods and Cas9 optimization, could greatly improve guide selection, enable fair comparison and benchmarking across publications while ultimately enabling precise and safe genome-editing.…”

Section: The Need For Standardizationmentioning

confidence: 99%

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Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

2016

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Summary Advances in the development of delivery, repair, and specificity strategies for the CRISPR-Cas9 genome engineering toolbox are helping researchers understand gene function with unprecedented precision and sensitivity. CRISPR-Cas9 also holds enormous therapeutic potential for the treatment of genetic disorders by directly correcting disease-causing mutations. Although the Cas9 protein has been shown to bind and cleave DNA at off-target sites, the field of Cas9 specificity is rapidly progressing with marked improvements in guide RNA selection, protein and guide engineering, novel enzymes, and off-target detection methods. We review important challenges and breakthroughs in the field as a comprehensive practical guide to interested users of genome editing technologies, highlighting key tools and strategies for optimizing specificity. The genome editing community should now strive to standardize such methods for measuring and reporting off-target activity, while keeping in mind that the goal for specificity should be continued improvement and vigilance.

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Section: Modified Guidesmentioning

confidence: 99%

Section: The Need For Standardizationmentioning

confidence: 99%

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

2016

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“…CRISPR screening derived from publications or by directed submission is integrated with data from various sources (14,17,18). Screening data is then visualized characteristics of CRISPR reagents and screens.…”

Section: Data Accessmentioning

confidence: 99%

“…Several resources have been established to address this need. These include CRISPRz (12), a database of sgRNAs validated in zebrafish, WGE (13), a data resource that contains information about sgRNAs that can be used to target genes of interest and CrisprGE (14), a platform that provides knowledge about sequence mutations caused by sgRNAs previously used in various experimental settings. Nevertheless, a database that allows to compare screening results, such as perturbation phenotypes or sgRNA efficiency, of many different experiments on a genome-wide scale has so far not been available.…”

Section: Introductionmentioning

confidence: 99%

GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens

et al. 2016

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Over the past years, CRISPR/Cas9 mediated genome editing has developed into a powerful tool for modifying genomes in various organisms. In high-throughput screens, CRISPR/Cas9 mediated gene perturbations can be used for the systematic functional analysis of whole genomes. Discoveries from such screens provide a wealth of knowledge about gene to phenotype relationships in various biological model systems. However, a database resource to query results efficiently has been lacking. To this end, we developed GenomeCRISPR (http://genomecrispr.org), a database for genome-scale CRISPR/Cas9 screens. Currently, GenomeCRISPR contains data on more than 550 000 single guide RNAs (sgRNA) derived from 84 different experiments performed in 48 different human cell lines, comprising all screens in human cells using CRISPR/Cas published to date. GenomeCRISPR provides data mining options and tools, such as gene or genomic region search. Phenotypic and genome track views allow users to investigate and compare the results of different screens, or the impact of different sgRNAs on the gene of interest. An Application Programming Interface (API) allows for automated data access and batch download. As more screening data will become available, we also aim at extending the database to include functional genomic data from other organisms and enable cross-species comparisons.

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“…Online resources, such as CRISPR-PLANT (Xie et al, 2014), CRISPR-P 2.0 (Liu et al, 2017), Cas-Database (Park et al, 2016), CRISPR-GE (Xie et al, 2017), and Cpf1-Database (Park and Bae, 2018) allow researchers to design gRNAs with minimal off-target potential; however, these tools and databases are not designed to manage data or search for CRISPR-generated plant mutants. The database CrisprGE (Kaur et al, 2015) contains information about CRISPRmediated mutants that have been reported from both plants and other organisms, but currently provides little information about the transformation experiment, the variety used, the progeny derived, or seed availability. It is therefore needed to establish a database that will serve as a central repository to efficiently manage plant mutant data and to provide a platform for sharing the data and mutants with the research community, thereby saving time and making more efficient use of resources.…”

mentioning

confidence: 99%

Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants

et al. 2019

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Recent advances in genome editing technologies, particularly CRISPR/Cas, enable the alteration of DNA sequences to produce deletions, insertions, and substitutions in genes (Jaganathan et al., 2018), as well as large or entire chromosome deletions in the genomes of plants and animals (Zhou et al., 2014; Adikusuma et al., 2017). Theoretically, CRISPR/Cas can target any DNA sequence in a genome that is preceded by a protospacer adjacent motif (PAM). Such genome editing by CRISPR/Cas is easy to implement and requires that just two components be integrated into a plasmid vector: a 20-nucleotide (nt) guide RNA (gRNA) targeting a specific genomic region and a gene encoding a Cas nuclease (e.g., Cas9 or Cpf1) which generates a doublestranded DNA break near the target region (Xie and Yang, 2013). Alternatively, catalytically inactive Cas variants (e.g., dCas9 or dCpf1) have been used to tether diverse functional domains to specific DNA sequences for various applications, including transcriptional regulation, epigenetic modification, and precise single-base changes or substitutions (base editing) (Eid et al., 2018), holding great promise for trait improvement in crops. As a user-friendly and efficient system for genome editing, CRISPR/ Cas is being widely used to modify genes in model and economically important plant species, and an increasing number of plant lines are becoming available that have mutations in a wide array of genes, including those with key roles in growth, development, and biotic and abiotic stresses (

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CrisprGE: a central hub of CRISPR/Cas-based genome editing

Cited by 33 publications

References 50 publications

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

GenomeCRISPR - a database for high-throughput CRISPR/Cas9 screens

Plant Genome Editing Database (PGED): A Call for Submission of Information about Genome-Edited Plant Mutants

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