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Table of Contents: Synthetic Biology Collection: Genome Editing

COVER

Image Credit: Ivan Morozov (Virginia Bioinformatics Institute) / PLOS
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Synthetic Biology is an emerging, trans-disciplinary field at the intersection between many engineering and scientific disciplines such as biology, chemical engineering, chemistry, electrical engineering, and computer science.

This section of the Synthetic Biology Collection details papers related to Genome Editing.

Articles in the Synthetic Biology Collection are presented in order of publication date and new articles will be added as they are published. PLOS welcome submissions in this field.

PLOS Collections: www.ploscollections.org/syntheticbiology

Research Articles

AAV-Mediated Delivery of Zinc Finger Nucleases Targeting Hepatitis B Virus Inhibits Active Replication

Nicholas D. Weber, Daniel Stone, Ruth Hall Sedlak, Harshana S. De Silva Feelixge, Pavitra Roychoudhury, Joshua T. Schiffer, Martine Aubert, Keith R. Jerome

Efficient Generation of Myostatin (MSTN) Biallelic Mutations in Cattle Using Zinc Finger Nucleases

Junjie Luo, Zhiyuan Song, Shengli Yu, Dan Cui, Benli Wang, Fangrong Ding, Song Li, Yunping Dai, Ning Li

A Novel Genetic System Based on Zinc Finger Nucleases for the Identification of Interactions between Proteins In Vivo

Ling Wang, Kun Xu, Juan Lin, Simin Shao, Tingting Zhang, Huarong Xu, Zehui Wei, Zhiying Zhang

Functional Analysis of a Breast Cancer-Associated FGFR2 Single Nucleotide Polymorphism Using Zinc Finger Mediated Genome Editing

Luisa J. Robbez-Masson, Csaba Bödör, J. Louise Jones, Helen C. Hurst, Jude Fitzgibbon, Ian R. Hart, Richard P. Grose

An Over Expression APP Model for Anti-Alzheimer Disease Drug Screening Created by Zinc Finger Nuclease Technology

Xiaojing Zhang, Hui Li, Yiqing Mao, Zhixin Li, Rong Wang, Tingting Guo, Ling Jin, Rongjing Song, Wei Xu, Na Zhou, Yizhuang Zhang, Ruobi Hu, Xi Wang, Huakang Huang, Zhen Lei, Gang Niu, David M. Irwin, Huanran Tan

Efficient Knockin Mouse Generation by ssDNA Oligonucleotides and Zinc-Finger Nuclease Assisted Homologous Recombination in Zygotes

Bin Shen, Xin Zhang, Yinan Du, Jianying Wang, Jun Gong, Xiaodong Zhang, Peri H. Tate, Hongliang Li, Xingxu Huang, Wensheng Zhang

Generation of Interleukin-2 Receptor Gamma Gene Knockout Pigs from Somatic Cells Genetically Modified by Zinc Finger Nuclease-Encoding mRNA

Masahito Watanabe, Kazuaki Nakano, Hitomi Matsunari, Taisuke Matsuda, Miki Maehara, Takahiro Kanai, Mirina Kobayashi, Yukina Matsumura, Rieko Sakai, Momoko Kuramoto, Gota Hayashida, Yoshinori Asano, Shuko Takayanagi, Yoshikazu Arai, Kazuhiro Umeyama, Masaki Nagaya, Yutaka Hanazono, Hiroshi Nagashima

Zinc Finger Nuclease Mediated Knockout of ADP-Dependent Glucokinase in Cancer Cell Lines: Effects on Cell Survival and Mitochondrial Oxidative Metabolism

Susan Richter, Shona Morrison, Tim Connor, Jiechuang Su, Cristin G. Print, Ron S. Ronimus, Sean L. McGee, William R. Wilson

Simultaneous Screening and Validation of Effective Zinc Finger Nucleases in Yeast

Ling Wang, Juan Lin, Tingting Zhang, Kun Xu, Chonghua Ren, Zhiying Zhang

Efficient Methods for Targeted Mutagenesis in Zebrafish Using Zinc-Finger Nucleases: Data from Targeting of Nine Genes Using CompoZr or CoDA ZFNs

Raman Sood, Blake Carrington, Kevin Bishop, MaryPat Jones, Alberto Rissone, Fabio Candotti, Settara C. Chandrasekharappa, Paul Liu

Magnetic Separation and Antibiotics Selection Enable Enrichment of Cells with ZFN/TALEN-Induced Mutations

Hyojin Kim, Myung-Sun Kim, Gabbine Wee, Choong-il Lee, Hyongbum Kim, Jin-Soo Kim

Targeted Genomic Integration of a Selectable Floxed Dual Fluorescence Reporter in Human Embryonic Stem Cells

Jay A. Gantz, Nathan J. Palpant, Robert E. Welikson, Stephen D. Hauschka, Charles E. Murry, Michael A. Laflamme

Rescue the Failed Half-ZFN by a Sensitive Mammalian Cell-Based Luciferase Reporter System

Weifeng Zhang, Yuanxu Guo, Chen Zhang, Haiyan Ji, Wenpeng Meng, Dongyang Wang, Xing Li, Qinwen Mao, Haibin Xia

Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse Embryos

Mario Hermann, Morgan L. Maeder, Kyle Rector, Joseph Ruiz, Burkhard Becher, Kurt Bürki, Cyd Khayter, Adriano Aguzzi, J. Keith Joung, Thorsten Buch, Pawel Pelczar

Zebrafish foxP2 Zinc Finger Nuclease Mutant Has Normal Axon Pathfinding

Lingyan Xing, Kazuyuki Hoshijima, David J. Grunwald, Esther Fujimoto, Tyler S. Quist, Jacob Sneddon, Chi-Bin Chien, Tamara J. Stevenson, Joshua L. Bonkowsky

Selection-Independent Generation of Gene Knockout Mouse Embryonic Stem Cells Using Zinc-Finger Nucleases

Anna Osiak, Frank Radecke, Eva Guhl, Sarah Radecke, Nadine Dannemann, Fabienne Lütge, Silke Glage, Cornelia Rudolph, Tobias Cantz, Klaus Schwarz, Regine Heilbronn, Toni Cathomen

Heritable Targeted Inactivation of Myostatin Gene in Yellow Catfish (Pelteobagrus fulvidraco) Using Engineered Zinc Finger Nucleases

Zhangji Dong, Jiachun Ge, Kui Li, Zhiqiang Xu, Dong Liang, Jingyun Li, Junbo Li, Wenshuang Jia, Yuehua Li, Xiaohua Dong, Shasha Cao, Xiaoxiao Wang, Jianlin Pan, Qingshun Zhao

Efficient Immunoglobulin Gene Disruption and Targeted Replacement in Rabbit Using Zinc Finger Nucleases

Tatiana Flisikowska, Irmgard S. Thorey, Sonja Offner, Francesca Ros, Valeria Lifke, Bryan Zeitler, Oswald Rottmann, Anna Vincent, Lei Zhang, Shirin Jenkins, Helmut Niersbach, Alexander J. Kind, Philip D. Gregory, Angelika E. Schnieke, Josef Platzer

p53 Gene Repair with Zinc Finger Nucleases Optimised by Yeast 1-Hybrid and Validated by Solexa Sequencing

Frank Herrmann, Mireia Garriga-Canut, Rebecca Baumstark, Emmanuel Fajardo-Sanchez, James Cotterell, André Minoche, Heinz Himmelbauer, Mark Isalan

Dissection of Splicing Regulation at an Endogenous Locus by Zinc-Finger Nuclease-Mediated Gene Editing

Sandra Cristea, Philip D. Gregory, Fyodor D. Urnov, Gregory J. Cost

Generation of Knockout Rats with X-Linked Severe Combined Immunodeficiency (X-SCID) Using Zinc-Finger Nucleases

Tomoji Mashimo, Akiko Takizawa, Birger Voigt, Kazuto Yoshimi, Hiroshi Hiai, Takashi Kuramoto, Tadao Serikawa

Rapid Mutation of Endogenous Zebrafish Genes Using Zinc Finger Nucleases Made by Oligomerized Pool ENgineering (OPEN)

Jonathan E. Foley, Jing-Ruey J. Yeh, Morgan L. Maeder, Deepak Reyon, Jeffry D. Sander, Randall T. Peterson, J. Keith Joung

Simple and Efficient Methods for Enrichment and Isolation of Endonuclease Modified Cells

Branden S. Moriarity, Eric P. Rahrmann, Dominic A. Beckmann, Caitlin B. Conboy, Adrienne L. Watson, Daniel F. Carlson, Erik R. Olson, Kendra A. Hyland, Scott C. Fahrenkrug, R. Scott McIvor, David A. Largaespada

Highly Specific Contractions of a Single CAG/CTG Trinucleotide Repeat by TALEN in Yeast

Guy-Franck Richard, David Viterbo, Varun Khanna, Valentine Mosbach, Lauriane Castelain, Bernard Dujon

Precise Gene Modification Mediated by TALEN and Single-Stranded Oligodeoxynucleotides in Human Cells

Xiaoling Wang, Yingjia Wang, He Huang, Buyuan Chen, Xinji Chen, Jianda Hu, Tammy Chang, Ren-Jang Lin, Jiing-Kuan Yee

True-Breeding Targeted Gene Knock-Out in Barley Using Designer TALE-Nuclease in Haploid Cells

Maia Gurushidze, Goetz Hensel, Stefan Hiekel, Sindy Schedel, Vladimir Valkov, Jochen Kumlehn

Bacterial Delivery of TALEN Proteins for Human Genome Editing

Jingyue Jia, Yongxin Jin, Ting Bian, Donghai Wu, Lijun Yang, Naohiro Terada, Weihui Wu, Shouguang Jin

Generation of TALEN-Mediated GRdim Knock-In Rats by Homologous Recombination

Verónica Ponce de León, Anne-Marie Mérillat, Laurent Tesson, Ignacio Anegón, Edith Hummler

Cell-Penetrating Peptide-Mediated Delivery of TALEN Proteins via Bioconjugation for Genome Engineering

Jia Liu, Thomas Gaj, James T. Patterson, Shannon J. Sirk, Carlos F. Barbas III

A Modified TALEN-Based Strategy for Rapidly and Efficiently Generating Knockout Mice for Kidney Development Studies

Yunhong Liu, Xiaoyan Lv, Ruizhi Tan, Tianming Liu, Tielin Chen, Mi Li, Yuhang Liu, Fang Nie, Xiaoyan Wang, Puhui Zhou, Mianzhi Chen, Qin Zhou

Highly Efficient Generation of GGTA1 Biallelic Knockout Inbred Mini-Pigs with TALENs

Jige Xin, Huaqiang Yang, Nana Fan, Bentian Zhao, Zhen Ouyang, Zhaoming Liu, Yu Zhao, Xiaoping Li, Jun Song, Yi Yang, Qingjian Zou, Quanmei Yan, Yangzhi Zeng, Liangxue Lai

TALE-PvuII Fusion Proteins – Novel Tools for Gene Targeting

Mert Yanik, Jamal Alzubi, Thomas Lahaye, Toni Cathomen, Alfred Pingoud, Wolfgang Wende

Targeted Gene Therapy of Xeroderma Pigmentosum Cells Using Meganuclease and TALEN™

Aurélie Dupuy, Julien Valton, Sophie Leduc, Jacques Armier, Roman Galetto, Agnès Gouble, Céline Lebuhotel, Anne Stary, Frédéric Pâques, Philippe Duchateau, Alain Sarasin, Fayza Daboussi

Rapid Assembly of Customized TALENs into Multiple Delivery Systems

Zhengxing Zhang, Siliang Zhang, Xin Huang, Kyle E. Orwig, Yi Sheng

Targeted Gene Deletion of miRNAs in Mice by TALEN System

Shuji Takada, Tempei Sato, Yoshiaki Ito, Satoshi Yamashita, Tomoko Kato, Miyuri Kawasumi, Masami Kanai-Azuma, Arisa Igarashi, Tomomi Kato, Moe Tamano, Hiroshi Asahara

Inheritable and Precise Large Genomic Deletions of Non-Coding RNA Genes in Zebrafish Using TALENs

Yun Liu, Daji Luo, Hui Zhao, Zuoyan Zhu, Wei Hu, Christopher H. K. Cheng

Molecular Dynamics Simulations of DNA-Free and DNA-Bound TAL Effectors

Hua Wan, Jian-ping Hu, Kang-shun Li, Xu-hong Tian, Shan Chang

Efficient TALEN Construction for Bombyx mori Gene Targeting

Yoko Takasu, Suresh Sajwan, Takaaki Daimon, Mizuko Osanai-Futahashi, Keiro Uchino, Hideki Sezutsu, Toshiki Tamura, Michal Zurovec

Targeted Mutagenesis in the Malaria Mosquito Using TALE Nucleases

Andrea L. Smidler, Olivier Terenzi, Julien Soichot, Elena A. Levashina, Eric Marois

A Simple and Efficient Method for Assembling TALE Protein Based on Plasmid Library

Zhiqiang Zhang, Duo Li, Huarong Xu, Ying Xin, Tingting Zhang, Lixia Ma, Xin Wang, Zhilong Chen, Zhiying Zhang

High Efficiency In Vivo Genome Engineering with a Simplified 15-RVD GoldyTALEN Design

Alvin C. Ma, Han B. Lee, Karl J. Clark, Stephen C. Ekker

Targeting Human MicroRNA Genes Using Engineered Tal-Effector Nucleases (TALENs)

Ruozhen Hu, Jared Wallace, Timothy J. Dahlem, David Jonah Grunwald, Ryan M. O'Connell

Site Specific Mutation of the Zic2 Locus by Microinjection of TALEN mRNA in Mouse CD1, C3H and C57BL/6J Oocytes

Benjamin Davies, Graham Davies, Christopher Preece, Rathi Puliyadi, Dorota Szumska, Shoumo Bhattacharya

TALEN-Based Gene Disruption in the Dengue Vector Aedes aegypti

Azadeh Aryan, Michelle A. E. Anderson, Kevin M. Myles, Zach N. Adelman

Targeting G with TAL Effectors: A Comparison of Activities of TALENs Constructed with NN and NK Repeat Variable Di-Residues

Michelle L. Christian, Zachary L. Demorest, Colby G. Starker, Mark J. Osborn, Michael D. Nyquist, Yong Zhang, Daniel F. Carlson, Philip Bradley, Adam J. Bogdanove, Daniel F. Voytas

Highly Efficient and Specific Genome Editing in Silkworm Using Custom TALENs

Sanyuan Ma, Shengling Zhang, Feng Wang, Yong Liu, Yuanyuan Liu, Hanfu Xu, Chun Liu, Ying Lin, Ping Zhao, Qingyou Xia

Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs)

Finola E. Moore, Deepak Reyon, Jeffry D. Sander, Sarah A. Martinez, Jessica S. Blackburn, Cyd Khayter, Cherie L. Ramirez, J. Keith Joung, David M. Langenau

Epigenetic Alterations at Genomic Loci Modified by Gene Targeting in Arabidopsis thaliana

Michal Lieberman-Lazarovich, Cathy Melamed-Bessudo, Sylvia de Pater, Avraham A. Levy

The Design and In Vivo Evaluation of Engineered I-OnuI-Based Enzymes for HEG Gene Drive

Yuk-Sang Chan, Ryo Takeuchi, Jordan Jarjour, David S. Huen, Barry L. Stoddard, Steven Russell

A Universal Vector for High-Efficiency Multi-Fragment Recombineering of BACs and Knock-In Constructs

Karamjit Singh Dolt, Melanie L. Lawrence, Eve Miller-Hodges, Joan Slight, Anna Thornburn, Paul S. Devenney, Peter Hohenstein

p53 Gene Targeting by Homologous Recombination in Fish ES Cells

Yan Yan, Ni Hong, Tiansheng Chen, Mingyou Li, Tiansu Wang, Guijun Guan, Yongkang Qiao, Songlin Chen, Manfred Schartl, Chang-Ming Li, Yunhan Hong

High Frequency Targeted Mutagenesis Using Engineered Endonucleases and DNA-End Processing Enzymes

Fabien Delacôte, Christophe Perez, Valérie Guyot, Marianne Duhamel, Christelle Rochon, Nathalie Ollivier, Rachel Macmaster, George H. Silva, Frédéric Pâques, Fayza Daboussi, Philippe Duchateau

Engineering HIV-1-Resistant T-Cells from Short-Hairpin RNA-Expressing Hematopoietic Stem/Progenitor Cells in Humanized BLT Mice

Gene-Errol E. Ringpis, Saki Shimizu, Hubert Arokium, Joanna Camba-Colón, Maria V. Carroll, Ruth Cortado, Yiming Xie, Patrick Y. Kim, Anna Sahakyan, Emily L. Lowe, Munetoshi Narukawa, Fadi N. Kandarian, Bryan P. Burke, Geoff P. Symonds, Dong Sung An, Irvin S. Y. Chen, Masakazu Kamata

Simple Monitoring of Gene Targeting Efficiency in Human Somatic Cell Lines Using the PIGA Gene

Sivasundaram Karnan, Yuko Konishi, Akinobu Ota, Miyuki Takahashi, Lkhagvasuren Damdindorj, Yoshitaka Hosokawa, Hiroyuki Konishi

I-SceI-Mediated Double-Strand Break Does Not Increase the Frequency of Homologous Recombination at the Dct Locus in Mouse Embryonic Stem Cells

Myriam Fenina, Dominique Simon-Chazottes, Sandrine Vandormael-Pournin, Jihane Soueid, Francina Langa, Michel Cohen-Tannoudji, Bruno A. Bernard, Jean-Jacques Panthier

Targeting of the Human Coagulation Factor IX Gene at rDNA Locus of Human Embryonic Stem Cells

Xionghao Liu, Yong Wu, Zhuo Li, Junlin Yang, Jinfeng Xue, Youjin Hu, Mai Feng, Wenbin Niu, Qiurui Yang, Ming Lei, Jiahui Xia, Lingqian Wu, Desheng Liang

Stable Gene Targeting in Human Cells Using Single-Strand Oligonucleotides with Modified Bases

Xavier Rios, Adrian W. Briggs, Danos Christodoulou, Josh M. Gorham, Jonathan G. Seidman, George M. Church

A Rapid FACS-Based Strategy to Isolate Human Gene Knockin and Knockout Clones

João F. Mata, Telma Lopes, Rui Gardner, Lars E. T. Jansen

Inducible Gene Manipulations in Brain Serotonergic Neurons of Transgenic Rats

Tillmann Weber, Kai Schönig, Björn Tews, Dusan Bartsch

Assembly of Designer TAL Effectors by Golden Gate Cloning

Ernst Weber, Ramona Gruetzner, Stefan Werner, Carola Engler, Sylvestre Marillonnet

Transcriptional Activators of Human Genes with Programmable DNA-Specificity

René Geiβler, Heidi Scholze, Simone Hahn, Jana Streubel, Ulla Bonas, Sven-Erik Behrens, Jens Boch

Zinc Finger Recombinases with Adaptable DNA Sequence Specificity

Chris Proudfoot, Arlene L. McPherson, Andreas F. Kolb, W. Marshall Stark

Successful Targeting and Disruption of an Integrated Reporter Lentivirus Using the Engineered Homing Endonuclease Y2 I-AniI

Martine Aubert, Byoung Y. Ryu, Lindsey Banks, David J. Rawlings, Andrew M. Scharenberg, Keith R. Jerome

Temporally-Controlled Site-Specific Recombination in Zebrafish

Stefan Hans, Jan Kaslin, Dorian Freudenreich, Michael Brand

Group II Intron-Based Gene Targeting Reactions in Eukaryotes

Marta Mastroianni, Kazuo Watanabe, Travis B. White, Fanglei Zhuang, Jamie Vernon, Manabu Matsuura, John Wallingford, Alan M. Lambowitz

Heritable Multiplex Genetic Engineering in Rats Using CRISPR/Cas9

Yuanwu Ma, Bin Shen, Xu Zhang, Yingdong Lu, Wei Chen, Jing Ma, Xingxu Huang, Lianfeng Zhang

Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System

Woong Y. Hwang, Yanfang Fu, Deepak Reyon, Morgan L. Maeder, Prakriti Kaini, Jeffry D. Sander, J. Keith Joung, Randall T. Peterson, Jing-Ruey Joanna Yeh