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

Erin L. Doyle, Nicholas J. Booher, Daniel S. Standage, Daniel F. Voytas, Volker P. Brendel, John K. VanDyk, Adam J. Bogdanove
2012 Nucleic Acids Research  
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  ...  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  ...  Kokulapalan and the Iowa State University Bioinformatics and Computational Biology Laboratory for assistance creating the web site and members of the Bogdanove and Voytas laboratories for beta-testing  ... 
doi:10.1093/nar/gks608 pmid:22693217 pmcid:PMC3394250 fatcat:wqho65z4bvffta3if25epqqnxm

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

Laurent D. Noël, Nicolas Denancé, Boris Szurek
2013 Frontiers in Plant Science  
Pérez-Quintero for providing us with the predicted targets of Hax4 obtained with Talvez and Storyteller and E. Doyle for providing us with Hax4 targets with Target Finder.  ...  This work was in part supported by the LABEX TULIP (ANR-10-LABX-41) and a Jeunes Chercheurs grant from the Agence Nationale de la Recherche (Xopaque ANR-10-JCJC-1703-01) to Laurent D. Noël.  ...  "100" and position correction "19") and Target Finder (TALE-NT 2.0, default parameters).  ... 
doi:10.3389/fpls.2013.00333 pmid:24027573 pmcid:PMC3759964 fatcat:gzfdqsp5arao7agotvwylfgimi

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

Jan Grau, Annett Wolf, Maik Reschke, Ulla Bonas, Stefan Posch, Jens Boch, Achim Tresch
2013 PLoS Computational Biology  
than an existing approach, Target Finder of the TALE-NT suite.  ...  Hence, these predicted TAL effector virulence targets are promising candidates for studying the virulence function of TAL effectors.  ...  Acknowledgments We thank Heidi Scholze for preparing samples for the hax2 microarray experiment. We thank Ivo Grosse for valuable discussions. Author Contributions  ... 
doi:10.1371/journal.pcbi.1002962 pmid:23526890 pmcid:PMC3597551 fatcat:dbrzffwtgfez7fszb4dxn22haq

Transcription Activator-like Effectors: A Toolkit for Synthetic Biology

Richard Moore, Anita Chandrahas, Leonidas Bleris
2014 ACS Synthetic Biology  
Recent results show that TALE proteins consist of a central repeat domain, which determines the DNA targeting specificity and can be rapidly synthesized de novo.  ...  Transcription activator-like effectors (TALEs) are proteins secreted by Xanthomonas bacteria to aid the infection of plant species.  ...  TALE-NT 2.0 ranks target sites for key characteristics including off-target effects (using Target Finder for TALEs or Paired Target Finder for TALENs) . 26 The off-target predictions are based off  ... 
doi:10.1021/sb400137b pmid:24933470 pmcid:PMC4210167 fatcat:3k6w4t5a5jd3fppqn42bahao2i

TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors

Katherine E. Wilkins, Nicholas J. Booher, Li Wang, Adam J. Bogdanove
2015 Frontiers in Plant Science  
Citation: Wilkins KE, Booher NJ, Wang L and Bogdanove AJ (2015) TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv.  ...  oryzicola while strict conservation suggests universal importance of five TAL effectors.  ...  For the retained TAL effectors, EBEs were predicted using the TALE-NT 2.0 Target Finder tool .  ... 
doi:10.3389/fpls.2015.00536 pmid:26257749 pmcid:PMC4508525 fatcat:2n574bfadrc2zdzcmlupwhp23q

Rapid and Efficient Gene Modification in Rice and Brachypodium Using TALENs

Qiwei Shan, Yanpeng Wang, Kunling Chen, Zhen Liang, Jun Li, Yi Zhang, Kang Zhang, Jinxing Liu, Daniel F. Voytas, Xuelian Zheng, Yong Zhang, Caixia Gao
2013 Molecular Plant  
Supplementary (S) information Materials and methods TALEN design and plasmid construction All TALEN target sites were identified using the TAL effector-Nucleotide Targeter 2.0 (TALE-NT) program (https:  ...  //tale-nt.cac.cornell.edu/) (Doyle et al., 2012).  ...  ., and Bogdanove, A.J. (2012). TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction. Nucleic Acids Research 40:W117-W122.  ... 
doi:10.1093/mp/sss162 pmid:23288864 pmcid:PMC3968307 fatcat:dcnongdn5veopcbjvxcfmneho4

Identification of putative TAL effector targets of the citrus canker pathogens shows functional convergence underlying disease development and defense response

Andre LA Pereira, Marcelo F Carazzolle, Valeria Y Abe, Maria LP de Oliveira, Mariane N Domingues, Jaqueline C Silva, Raul A Cernadas, Celso E Benedetti
2014 BMC Genomics  
We also present evidence indicating that the TAL effectors act as transcriptional repressors and that the best scoring predicted DNA targets of PthA"s" and PthC"s" in citrus promoters predominantly overlap  ...  Biologically relevant targets of TAL effectors, i.e. host genes whose induction is vital to establish a compatible interaction, have been reported for xanthomonads that colonize rice and pepper; however  ...  In order to test the performance of our computational matrix analysis, we used the target finder function of the TAL Effector-Nucleotide Targeter 2.0 (TALE-NT) tools [48] to search for PthA"s" and PthC"s  ... 
doi:10.1186/1471-2164-15-157 pmid:24564253 pmcid:PMC4028880 fatcat:ah2getpza5bkbawj6lykvxyfmi

Context influences on TALE–DNA binding revealed by quantitative profiling

Julia M. Rogers, Luis A. Barrera, Deepak Reyon, Jeffry D. Sander, Manolis Kellis, J Keith Joung, Martha L. Bulyk
2015 Nature Communications  
We provide SIFTED as a publicly available web tool that predicts potential genomic off-target sites for improved TALE design.  ...  We used the PBM data to develop a computational model, Specificity Inference For TAL-Effector Design (SIFTED), to predict the DNA-binding specificity of any TALE.  ...  We thank Alexandre Palagi and Kian Hong Kock for helpful discussion.  ... 
doi:10.1038/ncomms8440 pmid:26067805 pmcid:PMC4467457 fatcat:p3raht76wjfxnki77ihflmb7qu

Precision genetic modifications: a new era in molecular biology and crop improvement

Franziska Fichtner, Reynel Urrea Castellanos, Bekir Ülker
2014 Planta  
single nucleotide changes.  ...  has produced unprecedented advances in gene targeting and genome editing in prokaryotes and eukaryotes.  ...  Waidmann and Tobias Berson for reading the manuscript, contributions to the literature survey and for many helpful discussions.  ... 
doi:10.1007/s00425-014-2029-y pmid:24510124 fatcat:ofwexpfyfzdsta7qhpxxamn6hq

TAL Effectors Drive Transcription Bidirectionally in Plants

Li Wang, Fabio C. Rinaldi, Pallavi Singh, Erin L. Doyle, Zoe E. Dubrow, Tuan Tu Tran, Alvaro L. Pérez-Quintero, Boris Szurek, Adam J. Bogdanove
2017 Molecular Plant  
The modularity of DNA recognition by TAL effectors makes them important also as tools for gene targeting and genome editing.  ...  Our results reveal new modes of action for TAL effectors, suggesting the possibility of yet unrecognized targets important in plant disease, expanding the search space for off-targets of custom TAL effectors  ...  Chakravarthy for providing N. benthamiana plants, R.A. Cernadas and K.E. Wilkins for technical assistance, A. Eggenberger, W.A. Miller, and S. Whitham for plasmids used in constructing pPS1, and H.  ... 
doi:10.1016/j.molp.2016.12.002 pmid:27965000 fatcat:bdzidtxepbhxrjhy4rx3avhv5e

Dissection of TALE-dependent gene activation reveals that they induce transcription cooperatively and in both orientations

Jana Streubel, Heidi Baum, Jan Grau, Johannes Stuttman, Jens Boch, Richard A Wilson
2017 PLoS ONE  
Our results implicate that TALEs function like classical enhancer-binding proteins and initiate transcription in both orientations which has consequences for in planta target gene prediction and design  ...  Plant-pathogenic Xanthomonas bacteria inject transcription activator-like effector proteins (TALEs) into host cells to specifically induce transcription of plant genes and enhance susceptibility.  ...  Acknowledgments We thank Ulla Bonas for support, and the 2013 MSc course "Plant Genetics" at the Martin Luther University for demonstrating that reverse binding TALEs can activate gene expression.  ... 
doi:10.1371/journal.pone.0173580 pmid:28301511 pmcid:PMC5354296 fatcat:3mbpoxj7d5ginfr3kfc5vtbxc4

A Strain of an Emerging Indian Xanthomonas oryzae pv. oryzae Pathotype Defeats the Rice Bacterial Blight Resistance Gene xa13 Without Inducing a Clade III SWEET Gene and Is Nearly Identical to a Recent Thai Isolate

Sara C. D. Carpenter, Prashant Mishra, Chandrika Ghoshal, Prasanta K. Dash, Li Wang, Samriti Midha, Gouri S. Laha, Jagjeet S. Lore, Wichai Kositratana, Nagendra K. Singh, Kuldeep Singh, Prabhu B. Patil (+4 others)
2018 Frontiers in Microbiology  
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host "susceptibility" (S) genes important for disease  ...  The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed.  ...  Sundaram and R. Sonti for helpful comments and discussion.  ... 
doi:10.3389/fmicb.2018.02703 pmid:30483230 pmcid:PMC6243107 fatcat:gaforloefveb3cg6l5d2o5tcve

The Scope for Thalassemia Gene Therapy by Disruption of Aberrant Regulatory Elements

Petros Patsali, Claudio Mussolino, Petros Ladas, Argyro Floga, Annita Kolnagou, Soteroula Christou, Maria Sitarou, Michael N. Antoniou, Toni Cathomen, Carsten Werner Lederer, Marina Kleanthous
2019 Journal of Clinical Medicine  
The high efficiency of DARE and unexpected freedom of target design render the approach potentially suitable for 14 known thalassemia mutations besides IVSI-110(G>A) and put it forward for several prominent  ...  short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9, Cas12a, and transcription activator-like effector nuclease (TALEN) platforms.  ...  Part of the present study was awarded the George Stamatoyiannopoulos Prize 2018 of the Hellenic Society of Gene Therapy and Regenerative Medicine.  ... 
doi:10.3390/jcm8111959 pmid:31766235 pmcid:PMC6912506 fatcat:kiaoqsptungfvmsuxdl5j324uq

A strain of an emerging Indian pathotype of Xanthomonas oryzae pv. oryzae defeats the rice bacterial blight resistance gene xa13 without inducing a clade III SWEET gene and is nearly identical to a recent Thai isolate [article]

Sara Carpenter, Prashant Mishra, Chandrika Ghoshal, Prasanta Dash, Li Wang, Samriti Midha, Gouri Shankar Laha, Jagjeet Lore, Wichai Kositratana, Nagendra Singh, Kuldeep Singh, Prabhu Patil (+4 others)
2018 bioRxiv   pre-print
The rice bacterial blight pathogen Xanthomonas oryzae pv. oryzae (Xoo) injects transcription activator-like effectors (TALEs) that bind and activate host susceptibility (S) genes important for disease.  ...  The resistance genes xa5, which reduces TALE activity generally, and xa13, a SWEET11 allele not recognized by the cognate TALE, have been effectively deployed.  ...  The results from the two tools were consistent. Targets of IX-280 and SK2-3 TALEs of interest were predicted using the TALE-NT 2.0 Target Finder tool 35 and TalGetter 36 .  ... 
doi:10.1101/384289 fatcat:kqojeqxvpjawfiyzwzw5bhqf4a

TALE-induced bHLH transcription factors that activate a pectate lyase contribute to water soaking in bacterial spot of tomato

Allison R. Schwartz, Robert Morbitzer, Thomas Lahaye, Brian J. Staskawicz
2017 Proceedings of the National Academy of Sciences of the United States of America  
Designer TALEs (dTALEs) for the bHLH transcription factors and the pectate lyase, but not for the pectinesterase, complement water soaking when delivered by XgΔavrHah1.  ...  AvrHah1 [avirulence (avr) gene homologous to avrBs3 and hax2, no. 1] is a transcription activator-like (TAL) effector (TALE) in Xanthomonas gardneri that induces water-soaked disease lesions on fruits  ...  We thank Megan Cohn for reading and critical review of the manuscript. A.R.S. was supported by the National Science Foundation Graduate Research Fellowship Program.  ... 
doi:10.1073/pnas.1620407114 pmid:28100489 pmcid:PMC5293091 fatcat:f26l6bqpknglxcouovfhmki6x4
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