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

EL Doyle, NJ Booher, DS Standage… - Nucleic acids …, 2012 - academic.oup.com
Nucleic acids research, 2012academic.oup.com
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 …
Abstract
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.
Oxford University Press