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      ULtiMATE System for Rapid Assembly of Customized TAL Effectors

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          Abstract

          Engineered TAL-effector nucleases (TALENs) and TALE-based constructs have become powerful tools for eukaryotic genome editing. Although many methods have been reported, it remains a challenge for the assembly of designer-based TALE repeats in a fast, precise and cost-effective manner. We present an ULtiMATE ( USER-based Liga tion Mediated Assembly of TAL Effector) system for speedy and accurate assembly of customized TALE constructs. This method takes advantage of uracil-specific excision reagent (USER) to create multiple distinct sticky ends between any neighboring DNA fragments for specific ligation. With pre-assembled templates, multiple TALE DNA-binding domains could be efficiently assembled in order within hours with minimal manual operation. This system has been demonstrated to produce both functional TALENs for effective gene knockout and TALE-mediated gene-specific transcription activation (TALE-TA). The feature of both ease-of-operation and high efficiency of ULtiMATE system makes it not only an ideal method for biologic labs, but also an approach well suited for large-scale assembly of TALENs and any other TALE-based constructions.

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          Most cited references14

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

          TALENs are important new tools for genome engineering. Fusions of transcription activator-like (TAL) effectors of plant pathogenic Xanthomonas spp. to the FokI nuclease, TALENs bind and cleave DNA in pairs. Binding specificity is determined by customizable arrays of polymorphic amino acid repeats in the TAL effectors. We present a method and reagents for efficiently assembling TALEN constructs with custom repeat arrays. We also describe design guidelines based on naturally occurring TAL effectors and their binding sites. Using software that applies these guidelines, in nine genes from plants, animals and protists, we found candidate cleavage sites on average every 35 bp. Each of 15 sites selected from this set was cleaved in a yeast-based assay with TALEN pairs constructed with our reagents. We used two of the TALEN pairs to mutate HPRT1 in human cells and ADH1 in Arabidopsis thaliana protoplasts. Our reagents include a plasmid construct for making custom TAL effectors and one for TAL effector fusions to additional proteins of interest. Using the former, we constructed de novo a functional analog of AvrHah1 of Xanthomonas gardneri. The complete plasmid set is available through the non-profit repository AddGene and a web-based version of our software is freely accessible online.
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            A TALE nuclease architecture for efficient genome editing.

            Nucleases that cleave unique genomic sequences in living cells can be used for targeted gene editing and mutagenesis. Here we develop a strategy for generating such reagents based on transcription activator-like effector (TALE) proteins from Xanthomonas. We identify TALE truncation variants that efficiently cleave DNA when linked to the catalytic domain of FokI and use these nucleases to generate discrete edits or small deletions within endogenous human NTF3 and CCR5 genes at efficiencies of up to 25%. We further show that designed TALEs can regulate endogenous mammalian genes. These studies demonstrate the effective application of designed TALE transcription factors and nucleases for the targeted regulation and modification of endogenous genes.
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              Targeting DNA double-strand breaks with TAL effector nucleases.

              Engineered nucleases that cleave specific DNA sequences in vivo are valuable reagents for targeted mutagenesis. Here we report a new class of sequence-specific nucleases created by fusing transcription activator-like effectors (TALEs) to the catalytic domain of the FokI endonuclease. Both native and custom TALE-nuclease fusions direct DNA double-strand breaks to specific, targeted sites.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2013
                27 September 2013
                1 November 2013
                : 8
                : 9
                : e75649
                Affiliations
                [1 ]State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing, China
                [2 ]Department of Electronics, School of Electronics Engineering and Computer Science, Peking University, Beijing, China
                IGBMC/ICS, France
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: WW JY PY YS. Performed the experiments: JY PY DW YS SZ YY. Analyzed the data: WW JY PY. Contributed reagents/materials/analysis tools: XG. Wrote the manuscript: WW JY PY.

                [¤a]

                Current address: Department of Bioengineering, Rice University, Houston, Texas, United States of America

                [¤b]

                Current address: Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America

                Article
                PONE-D-13-08150
                10.1371/journal.pone.0075649
                3815405
                24228087
                b9b8c029-0f4f-4f5a-a338-619c9578c6a3
                Copyright @ 2013

                This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 22 February 2013
                : 16 August 2013
                Funding
                This work was supported in part by the Major State Basic Research Development Program of China (grant number 2010CB911800), the National Science Foundation of China (grant numbers NSFC31070115, NSFC31170126), and a grant of the 985 Project of Peking University and Peking-Tsinghua Center for Life Sciences. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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