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

  title={TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction},
  author={Erin L. Doyle and Nicholas J. Booher and Daniel S. Standage and Daniel F. Voytas and Volker P. Brendel and John K. VanDyk and Adam J. Bogdanove},
  journal={Nucleic Acids Research},
  pages={W117 - W122}
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… 

Computational and experimental analysis of TAL effector-DNA binding

This dissertation explores TAL effector-DNA binding through computational and experimental analyses and proposed guidelines for designing custom Tal effectors and TALeffector nucleases (TALENs) and created a software tool for TAL effects design.

Computational Predictions Provide Insights into the Biology of TAL Effector Target Sites

It is demonstrated that TALgetter successfully predicts known TAL effector target sites and often yields a greater number of predictions that are consistent with up-regulation in gene expression microarrays than an existing approach, Target Finder of the TALE-NT suite.

Site-specific gene targeting using transcription activator-like effector (TALE)-based nuclease in Brassica oleracea.

The results indicate that the TALENs bound to the target site and cleaved double-strand DNA in vitro and in vivo, whereas the effector binding elements have a 23 bp spacer.

An Improved Method for TAL Effectors DNA-Binding Sites Prediction Reveals Functional Convergence in TAL Repertoires of Xanthomonas oryzae Strains

A program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions.

E-TALEN: a web tool to design TALENs for genome engineering

E-TALEN enables the design of TALENs against a single target or a large number of target genes and guides the user through an end-to-end design process of de novo TALen pairs, which are specific to a certain sequence or genomic locus.

Targeted genome regulation and modification using transcription activator‐like effectors

The assembly of designer TALEs is described, their expanding range of current and potential future applications are described, and alternatives are briefly discussed, namely, zinc finger nucleases and clustered regularly interspaced short palindromic repeat/clustered regularly Interspaced long palindrome repeat associated protein 9.

Predicting promoters targeted by TAL effectors in plant genomes: from dream to reality

An overview of the current tools and strategies that may be applied for finding targets of TAL effectors is given and several perspectives offered by these new tools are highlighted.

TAL effectors: tools for DNA Targeting

Artificially designed TALE-DNA-binding domains fused to nuclease or activation and repressor domains provide an outstanding toolbox for targeted gene editing and gene regulation in research, biotechnology and gene therapy.

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically

The suite QueTAL was developed to offer tailored tools for comparison of TAL effector genes and will help users to rapidly analyse any TALEffector genes of interest and compare them to other available TAL genes and should improve the understanding of Tal effectors evolution.



Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors

The data demonstrate that the TALE scaffold can be tailored to target user-defined DNA sequences in whole genomes and mediates specific interaction with G nucleotides that thus far could not be targeted specifically by any known RVD type.

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

A method and reagents for efficiently assembling TALEN constructs with custom repeat arrays are presented and design guidelines based on naturally occurring TAL effectors and their binding sites are described.

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

These studies expand the realm of verified TALEN activity from cultured human cells to an intact eukaryotic organism and suggest that low-cost, highly dependable dTALENs can assume a significant role for gene modifications of value in human and animal health, agriculture and industry.

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

Wrapped DNA TAL effectors are proteins that bacterial pathogens inject into plant cells that bind to host DNA to activate expression of plant genes. The DNA-binding domain of TAL proteins is composed

Assembly of custom TALE-type DNA binding domains by modular cloning

A cloning approach that facilitates the assembly of multiple repeat-encoding DNA fragments that translate into dTALEs with pre-defined DNA binding specificity that allow rapid generation of highly specific TALE-type DNA binding domains that target binding sites of predefined length and sequence is presented.

De novo-engineered transcription activator-like effector (TALE) hybrid nuclease with novel DNA binding specificity creates double-strand breaks

The data show the feasibility of engineering TALE-based hybrid nucleases capable of generating site-specific DSBs and the great potential for site- specific genome modification in plants and eukaryotes in general.

TAL effectors are remote controls for gene activation.

Transcriptional Activators of Human Genes with Programmable DNA-Specificity

Synthetic TAL proteins with designed repeat compositions were created using a novel modular cloning strategy termed “Golden TAL Technology” and activated targeted expression of exogenous as well as endogenous genes.

TAL nucleases (TALNs): hybrid proteins composed of TAL effectors and FokI DNA-cleavage domain

The creation and initial characterization of a group of rare-cutting, site-specific DNA nucleases produced by fusion of the restriction enzyme FokI endonuclease domain (FN) with the high-specificity DNA-binding domains of AvrXa7 and PthXo1 are reported.

Heritable gene targeting in zebrafish using customized TALENs

The use of TALENs is reported to disrupt both of the two endogenous zebrafish genes the authors targeted and show that the mutations are transmitted through the germ line, confirming that TALens could induce DSBs and activate the DNA repair pathway through nonhomologous endjoining in vivo.