EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering

Xiao, An; Wu, Yingnian; Yang, Zhenbiao; Hu, Yingying; Wang, Wei‐Ye; Zhang, Yutian; Kong, Lei; Gao, Ge; Zhu, Zuoyan; Lin, Shuo; Zhang, Bo

doi:10.1093/nar/gks1144

Cited by 48 publications

(29 citation statements)

References 83 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The database and knowledge base of EENdb (http://eendb.zfgenetics.org) was built to collect information of all reported ZFNs and TALENs tested in different species and the related information, uses and resources for EEN engineering (1). With the development of the new gene-targeting technology based on the CRISPR/Cas system and the predictable rapid increasing of Cas9/gRNA target sites, we have started to collect the information of Cas9/gRNA in EENdb.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

Xiao

Wang²,

Hu³

et al. 2013

Nucleic Acids Research

Self Cite

359

254

View full text Add to dashboard Cite

Customized TALENs and Cas9/gRNAs have been used for targeted mutagenesis in zebrafish to induce indels into protein-coding genes. However, indels are usually not sufficient to disrupt the function of non-coding genes, gene clusters or regulatory sequences, whereas large genomic deletions or inversions are more desirable for this purpose. By injecting two pairs of TALEN mRNAs or two gRNAs together with Cas9 mRNA targeting distal DNA sites of the same chromosome, we obtained predictable genomic deletions or inversions with sizes ranging from several hundred bases to nearly 1 Mb. We have successfully achieved this type of modifications for 11 chromosomal loci by TALENs and 2 by Cas9/gRNAs with different combinations of gRNA pairs, including clusters of miRNA and protein-coding genes. Seven of eight TALEN-targeted lines transmitted the deletions and one transmitted the inversion through germ line. Our findings indicate that both TALENs and Cas9/gRNAs can be used as an efficient tool to engineer genomes to achieve large deletions or inversions, including fragments covering multiple genes and non-coding sequences. To facilitate the analyses and application of existing ZFN, TALEN and CRISPR/Cas data, we have updated our EENdb database to provide a chromosomal view of all reported engineered endonucleases targeting human and zebrafish genomes.

show abstract

Section: Resultsmentioning

confidence: 99%

“…Web pages of chromosomal view of human and zebrafish, the two species that are targeted by most of the reported EENs, were developed with PHP script. EENdb is running on a public server and more information for this database was described previously (1). …”

Section: Methodsmentioning

confidence: 99%

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

Xiao

Wang²,

Hu³

et al. 2013

Nucleic Acids Research

Self Cite

359

254

View full text Add to dashboard Cite

show abstract

“…Large-scale guide RNA efficiency datasets have been used to create increasingly accurate computational models that predict the knockout efficiency of new guide RNAs (Doench et al, 2014; Chari et al, 2015; Xu et al, 2015). Most recently, a pooled screen analysis of 9,914 guide RNA variants covering all single mismatch and single RNA indels for 65 DNA targets was used to derive a cutting frequency determination (CFD) score capable of predicting the likelihood of off-target activity (Doench et al, 2016).…”

Section: Computational Guide Rna Selection and Predictive Modelsmentioning

confidence: 99%

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

2016

View full text Add to dashboard Cite

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.

show abstract

“…They include links to tools, references, and protocols. Although their CRISPR/Cas information is currently limited, their TALEN and ZFN databases are well designed [79]. …”

Section: Designing and Engineering Talens And Crispr Reagentsmentioning

confidence: 99%

Targeted genome engineering techniques in Drosophila

Beumer

Carroll

2014

Methods

View full text Add to dashboard Cite

For a century, Drosophila has been a favored organism for genetic research. However, the array of materials and methods available to the Drosophila worker has expanded dramatically in the last decade. The most common gene targeting tools, zinc finger nucleases, TALENs, and RNA-guided CRISPR/Cas9, have all been adapted for use in Drosophila, both for simple mutagenesis and for gene editing via homologous recombination. For each tool, there exist a number of web sites, design applications, and delivery methods. The successful application of any of these tools also requires an understanding of methods for detecting successful genome modifications. This article provides an overview of the available gene targeting tools and their application in Drosophila. In lieu of simply providing a protocol for gene targeting, we direct the researcher to resources that will allow access to the latest research in this rapidly evolving field.

show abstract

EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering

Cited by 48 publications

References 83 publications

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish

Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity

Targeted genome engineering techniques in Drosophila

Contact Info

Product

Resources

About