TALENs: Methods and Protocols

278 Pages·2016·8.718 MB·English

by  Ralf Kühn, Wolfgang Wurst, Benedikt Wefers (eds.)

Methods in
Molecular Biology 1338
Ralf Kühn
Wolfgang Wurst
Benedikt Wefers Editors
TALENs
Methods and Protocols
M M B
ETHODS IN OLECULAR IOLOGY
Series Editor
John M. Walker
School of Life and Medical Sciences
University of Hertfordshire
Hatfield, Hertfordshire , AL10 9AB, UK
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TALENs
Methods and Protocols
Edited by
Ralf Kühn
Max-Delbrück-Center for Molecular Medicine, Berlin, Germany;
Berlin Institute of Health, Berlin, Germany
Wolfgang Wurst
Institute of Developmental Genetics, Helmholtz Zentrum München,
German Research Center for Environmental Health, Neuherberg, Germany;
Technische Universität München, Freising-Weihenstephan, Germany;
Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE), Munich, Germany;
Munich Cluster for Systems Neurology (SyNergy),
Ludwig-Maximilians-Universität München, Munich, Germany
Benedikt Wefers
Institute of Developmental Genetics, Helmholtz Zentrum München,
German Research Center for Environmental Health, Neuherberg, Germany;
Deutsches Zentrum für Neurodegenerative Erkrankungen e. V. (DZNE),
Munich, Germany
Editors
Ralf K ühn Wolfgang W urst
Max-Delbrück-Center for Molecular Medicine Institute of Developmental Genetics
Berlin, Germany Helmholtz Zentrum München
German Research Center for
Berlin Institute of Health, Berlin, Germany
Environmental Health
Neuherberg, Germany
Benedikt W efers
Institute of Developmental Genetics Technische Universität München
Helmholtz Zentrum München Freising-Weihenstephan, Germany
German Research Center for Environmental Health
Deutsches Zentrum für Neurodegenerative
Neuherberg, Germany
Erkrankungen e. V. (DZNE)
Deutsches Zentrum für Neurodegenerative Munich, Germany
Erkrankungen e. V. (DZNE)
Munich Cluster for Systems Neurology (SyNergy)
Munich, Germany
Ludwig-Maximilians-Universität München
Munich, Germany
ISSN 1064-3745 ISSN 1940-6029 (electronic)
Methods in Molecular Biology
ISBN 978-1-4939-2931-3 ISBN 978-1-4939-2932-0 (eBook)
DOI 10.1007/978-1-4939-2932-0
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Prefa ce
Genetic engineering to create targeted mutations in cells and organisms is a key technology
for biomedical research and biotechnology. The wide use of mice as mammalian genetic
model is based on gene targeting in embryonic stem cells that undergo spontaneous homol-
ogous recombination with externally provided gene targeting vectors. Besides mouse stem
cells, most other cell lines and organisms were for a long time refractory to HR and the
available tools enabled mainly random genome integrations. These limitations are over-
come with the generation of designer nucleases. The fi rst generation of sequence-specifi c
nucleases, the zinc-fi nger nucleases (ZFN), provided proof-of-principle that the induction
of targeted double-strand breaks is a powerful tool for gene editing by the stimulation of
DNA repair. Nevertheless, this system was not convenient since ZFNs cannot be easily
programmed for the recognition of new target sequences. In 2009 a novel, modular DNA
recognition code from the transcription activator-like (TAL) proteins of Xanthomonas was
discovered and, based on the extensive experience with ZFNs, could be rapidly adapted for
use as sequence-specifi c TAL effector nucleases (TALEN) by fusion with the FokI nuclease
domain. Within the last years TAL proteins and TALENs were further characterized and
successfully applied in various species which were previously inaccessible for gene editing.
In line with the successful format of Methods in Molecular Biology, this volume provides a
comprehensive collection of step-by-step protocols to support the use of this new technol-
ogy across various model organisms. While most of the chapters describe species-specifi c
methods to generate new mutants, the content is completed by chapters on natural TAL
effectors, TAL element DNA binding principles, TALEN target site prediction, and meth-
ods for the effi cient construction of TALEN coding regions. In addition to the application
of TALEN as sequence-specifi c nucleases, this volume includes a chapter on TAL-based
gene activators or inhibitors and the visualization of chromatin dynamics in live cells. More
recently a new generation of nuclease technology was provided by the clustered, regularly
interspaced, short palindromic repeat (CRISPR)/Cas bacterial defense system, using short
RNAs for DNA sequence recognition. We expect that in future both TALEN and CRISPR/
Cas will be successfully used for genetic engineering in a wide range of cell and animal
model systems. For this purpose we also included one chapter on CRISPR/Cas mutagen-
esis in mammalian cells.
Berlin, Germany R alf K ühn
Munich, Germany Wolfgang Wurst
Munich, Germany Benedikt Wefers
v

Contents
Preface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . v
Contributors. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . i x
1 Xanthomonas and the TAL Effectors: Nature’s Molecular Biologist. . . . . . . . . 1
Frank W hite
2 TAL Effector DNA-Binding Principles and Specificity. . . . . . . . . . . . . . . . . . . 9
Annekatrin Richter , Jana S treubel , and Jens B och
3 T he Development of TALE Nucleases for Biotechnology . . . . . . . . . . . . . . . . 2 7
David G . O usterout and Charles A. G ersbach
4 O nline Tools for TALEN Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3
Adam J . Bogdanove and N icholas J . B ooher
5 A ssembly of Customized TAL Effectors Through Advanced
ULtiMATE System. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
Junjiao Y ang , S hengjie Guo , Pengfei Y uan , and Wensheng Wei
6 E ngineering Customized TALENs Using the Platinum Gate TALEN Kit . . . . 6 1
Tetsushi S akuma and Takashi Y amamoto
7 D esign, Assembly, and Characterization of TALE-Based
Transcriptional Activators and Repressors . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 1
Pratiksha I. Thakore and Charles A . G ersbach
8 A New Approach to Dissect Nuclear Organization: TALE-M ediated
Genome Visualization (TGV) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 9
Yusuke Miyanari
9 T ALEN-Induced Translocations in Human Cells . . . . . . . . . . . . . . . . . . . . . . 9 9
Marion Piganeau , B enjamin Renouf , H ind G hezraoui ,
and Erika Brunet
10 Mutagenesis in Newts: Protocol for Iberian Ribbed Newts . . . . . . . . . . . . . . . 1 19
Toshinori H ayashi and T akashi T akeuchi
11 T argeted Mutagenesis in Bombyx mori Using TALENs . . . . . . . . . . . . . . . . . . 1 27
Yoko T akasu , Toshiki T amura , M arian G oldsmith , and Michal Z urovec
12 GeneKnockout by Targeted Mutagenesis in a Hemimetabolous Insect,
the Two-Spotted Cricket Gryllus bimaculatus, using TALENs. . . . . . . . . . . . . 143
Takahito Watanabe , Sumihare Noji , and T aro M ito
13 M ethods for TALEN Evaluation, Use, and Mutation Detection
in the Mosquito Aedes aegypti. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 157
Sanjay Basu , A zadeh A ryan , M ary Etna H aac , K evin M. M yles ,
and Zach N . Adelman
14 M ethods for TALEN-Mediated Genomic Manipulations in Drosophila . . . . . . 1 79
Jiyong Liu , Yawen G uo , C hangqing L i , Yixu C hen , and Renjie Jiao
vii
viii Contents
15 Targeted Mutagenesis in Zebrafish by TALENs. . . . . . . . . . . . . . . . . . . . . . . . 1 91
Peng H uang , An X iao , Xiangjun Tong , Shuo L in , and Bo Zhang
16 Mutagenesis in Xenopus and Zebrafish using TALENs . . . . . . . . . . . . . . . . . . 2 07
Yun Liu , Hui Z hao , and Christopher H . K. Cheng
17 Genome Editing in Mice Using TALE Nucleases . . . . . . . . . . . . . . . . . . . . . . 2 29
Benedikt Wefers , Christina B randl , Oskar Ortiz , W olfgang W urst ,
and Ralf Kühn
18 Genome Editing in Rats Using TALE Nucleases. . . . . . . . . . . . . . . . . . . . . . . 245
Laurent Tesson , Séverine Remy , Séverine Ménoret , Claire U sal ,
R eynald Thinard , Chloé S avignard , Anne D e Cian , Carine G iovannangeli ,
Jean-Paul C oncordet , and Ignacio Anegon
19 D esigner Nuclease-Mediated Generation of Knockout THP1 Cells. . . . . . . . . 2 61
Tobias S chmidt , J onathan L. Schmid-Burgk , T homas S . E bert ,
Moritz M. G aidt , and Veit H ornung
Index. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 273
Contributors

ZACH N. A DELMAN • 305 Fralin Life Science Institute, V irginia Tech , B lacksburg, V A,
USA ; D epartment of Entomology, Virginia Tech , Blacksburg, V A, USA
IGNACIO A NEGON • Transgenic Rats Nantes IBiSA-Centre National de Recherche
Scientifi que, N antes , France ; I TUN, CHU Nantes , N antes , F rance ; I NSERM UMR
1064 , C enter for Research in Transplantation and Immunology , N antes, France
AZADEH ARYAN • 305 Fralin Life Science Institute, Virginia Tech , B lacksburg, VA, U SA ;
Department of Entomology, Virginia Tech , Blacksburg, V A , U SA
SANJAY B ASU • 305 Fralin Life Science Institute, V irginia Tech , Blacksburg, V A, USA ;
Department of Entomology, Virginia Tech , Blacksburg, V A , U SA
JENS B OCH • Department of Genetics, M artin Luther University Halle-Wittenberg ,
Halle (Saale), G ermany
ADAM J. B OGDANOVE • Plant Pathology and Plant-Microbe Biology Section, School of
Integrative Plant Science, Cornell University , I thaca , N Y , U SA
NICHOLAS J. BOOHER • Plant Pathology and Plant-Microbe Biology Section, School of
Integrative Plant Science, Cornell University , Ithaca , N Y , U SA
CHRISTINA B RANDL • Institute of Developmental Genetics, Helmholtz Zentrum München,
German Research Center for Environmental Health , Neuherberg, Germany ;
Technische Universität München , F reising-Weihenstephan, G ermany
ERIKA BRUNET • Museum National d’Histoire Naturelle , P aris, France ;
CNRS, UMR7196 , P aris , F rance ; Inserm, U1154 , P aris, France
YIXU CHEN • State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics,
Chinese Academy of Sciences , B eijing, China
CHRISTOPHER H. K. CHENG • School of Biomedical Sciences, T he Chinese University of
Hong Kong , H ong Kong, C hina ; S chool of Biomedical Sciences Core Laboratory ,
Shenzhen Research Institute, The Chinese University of Hong Kong , S henzhen, C hina
ANNE DE C IAN • INSERM U1154, CNRS UMR7196, Museum National d’Histoire
Naturelle , P aris , F rance
JEAN-PAUL CONCORDET • INSERM U1154, CNRS UMR7196, Museum National
d’Histoire Naturelle , Paris, France
THOMAS S. EBERT • Institute of Molecular Medicine, University Hospital,
University of Bonn , B onn , G ermany
MORITZ M . G AIDT • Institute of Molecular Medicine, University Hospital,
University of Bonn , Bonn, Germany
CHARLES A. GERSBACH • Department of Biomedical Engineering, D uke University ,
Durham , N C, U SA ; C enter for Genomic and Computational Biology, Duke University ,
Durham, N C, USA ; Department of Orthopaedic Surgery , Duke University
Medical Center , D urham, NC, USA
HIND G HEZRAOUI • Museum National d’Histoire Naturelle , P aris, F rance ;
CNRS, UMR7196 , Paris, France ; I nserm, U1154 , P aris , F rance
CARINE G IOVANNANGELI • INSERM U1154, CNRS UMR7196, Museum National
d’Histoire Naturelle , Paris, France
MARIAN GOLDSMITH • Department of Biological Sciences, U niversity of Rhode Island ,
Kingston, R I, U SA
ix