TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction

By Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove. Nucleic Acids Res., 2012

589 citations recorded by the source corpus.

Transcription activator-like (TAL) effectors are repeat-containing proteins used by plant pathogenic bacteria to manipulate host gene expression. Repeats are polymorphic and individually specify single nucleotides in the DNA target, with some degeneracy. A TAL effector-nucleotide binding code that links repeat type to specified nucleotide enables prediction of genomic binding sites for TAL effectors and customization of TAL effectors for use in DNA targeting, in particular as custom transcription factors for engineered gene regulation and as site-specific nucleases for genome editing. We have developed a suite of web-based tools called TAL Effector-Nucleotide Targeter 2.0 (TALE-NT 2.0; https://boglab.plp.iastate.edu/) that enables design of custom TAL effector repeat arrays for desired targets and prediction of TAL effector binding sites, ranked by likelihood, in a genome, promoterome or other sequence of interest. Search parameters can be set by the user to work with any TAL effector or TAL effector nuclease architecture. Applications range from designing highly specific DNA targeting tools and identifying potential off-target sites to predicting effector targets important in plant disease.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/58e6551dbe4f5b0e1afb521d3d353157ed36d78f

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Citations in the corpus

The CRISPR/Cas9 system for plant genome editing and beyond. (2015, background): “TALEN targets are limited by the need for a thymidine residue at the first position (Doyle et al., 2012), but not all TALENs work efficiently in vivo and some pairs therefore fail to generate the anticipated mutations, which means that each TALEN pair must be experimentally validated (Hwang et al.”
A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation1[OPEN] (2015, background): “Compared to ZFNs, TALENs possess a broader targeting range and 109 are less difficult to engineer (Bogdanove and Voytas, 2011; Doyle et al., 2012).”
CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing (2014, methodology): “CHOPCHOP has a number of features that separate it from the other CRISPR/Cas9 or TALEN tools currently available (Supplementary Table S1) (25,28-34).”
TALENs: a widely applicable technology for targeted genome editing (2012, unknown): “In addition, it has been suggested that users should apply computationally derived design guidelines (originally proposed for dimeric TALENs 15 ) to monomeric TALE-based transcription factors 100 but no published experimental support yet exists for this recommendation.”