TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction.
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.
Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA 50011, USA.
Erin L
EL
Doyle
Nicholas J
NJ
Booher
Daniel S
DS
Standage
Daniel F
DF
Voytas
Volker P
VP
Brendel
John K
JK
Vandyk
Adam J
AJ
Bogdanove
D000465:Algorithms; D001665:Binding Sites; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism*; D020407:Internet; D015202:Protein Engineering; D020449:Repetitive Sequences, Amino Acid; D017422:Sequence Analysis, DNA; D012984:Software; D015534:Trans-Activators / Q000737:chemistry* / Q000378:metabolism*; D014584:User-Computer Interface
D004268:DNA-Binding Proteins; D015534:Trans-Activators; D004247:DNA