Using CRISPR/Cas in three dimensions: towards synthetic plant genomes, transcriptomes and epigenomes

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Functional Correction of Large Factor VIII Gene Chromosomal Inversions in Hemophilia A Patient-Derived iPSCs Using CRISPR-Cas9

(2015) Chul-Yong Park et al.   Cell Stem Cell

Editing plant genomes with CRISPR/Cas9

(2015) Khaoula Belhaj et al.   CURRENT OPINION IN BIOTECHNOLOGY

DNA methylation epigenetically silences crossover hot spots and controls chromosomal domains of meiotic recombination inArabidopsis

(2015) Nataliya E. Yelina et al.   GENES & DEVELOPMENT

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

CRISPR, the disruptor

(2015) Heidi Ledford   NATURE

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

In vivo genome editing using Staphylococcus aureus Cas9

(2015) F. Ann Ran et al.   NATURE

DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins

(2015) Je Wook Woo et al.   NATURE BIOTECHNOLOGY

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease

(2015) James E Dahlman et al.   NATURE BIOTECHNOLOGY

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

Plant artificial chromosome technology and its potential application in genetic engineering

(2015) Weichang Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

Targeted gene exchange in plant cells mediated by a zinc finger nuclease double cut

(2015) Katja Schneider et al.   PLANT BIOTECHNOLOGY JOURNAL

Designed nucleases for targeted genome editing

(2015) Junwon Lee et al.   PLANT BIOTECHNOLOGY JOURNAL

Use of designer nucleases for targeted gene and genome editing in plants

(2015) Donald P. Weeks et al.   PLANT BIOTECHNOLOGY JOURNAL

Gene stacking by recombinases

(2015) Vibha Srivastava et al.   PLANT BIOTECHNOLOGY JOURNAL

Chromatin and development: a special issue

(2015) Crisanto Gutierrez et al.   PLANT JOURNAL

Highly efficient heritable plant genome engineering using Cas9 orthologues fromStreptococcus thermophilusandStaphylococcus aureus

(2015) Jeannette Steinert et al.   PLANT JOURNAL

A CRISPR/Cas9 Toolbox for Multiplexed Plant Genome Editing and Transcriptional Regulation

(2015) Levi G. Lowder et al.   PLANT PHYSIOLOGY

Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

(2015) Sergei Svitashev et al.   PLANT PHYSIOLOGY

CRISPR/Cas9-mediated genome editing and gene replacement in plants: Transitioning from lab to field

(2015) Scott M. Schaeffer et al.   PLANT SCIENCE

Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system

(2015) Kabin Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of an inversion in the Ty-2 region between S. lycopersicum and S. habrochaites by a combination of de novo genome assembly and BAC cloning

(2015) Anne-Marie A. Wolters et al.   THEORETICAL AND APPLIED GENETICS

Promises and pitfalls of synthetic chromosomes in plants

(2015) James A. Birchler   TRENDS IN BIOTECHNOLOGY

Enabling plant synthetic biology through genome engineering

(2015) Nicholas J. Baltes et al.   TRENDS IN BIOTECHNOLOGY

Plant synthetic biology

(2015) Wusheng Liu et al.   TRENDS IN PLANT SCIENCE

Strategies for precision modulation of gene expression by epigenome editing: an overview

(2015) Benjamin I. Laufer et al.   Epigenetics & Chromatin

Targeted mutagenesis in soybean using the CRISPR-Cas9 system

(2015) Xianjun Sun et al.   Scientific Reports

Synthetic epigenetics—towards intelligent control of epigenetic states and cell identity

(2015) Tomasz P Jurkowski et al.   Clinical Epigenetics

Rewriting the blueprint of life by synthetic genomics and genome engineering

(2015) Narayana Annaluru et al.   GENOME BIOLOGY

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

DNA recombination in somatic plant cells: mechanisms and evolutionary consequences

(2014) Alexander Knoll et al.   CHROMOSOME RESEARCH

The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria

(2014) R. Louwen et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Regulation of RNA polymerase II activation by histone acetylation in single living cells

(2014) Timothy J. Stasevich et al.   NATURE

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

CRISPR transcriptional repression devices and layered circuits in mammalian cells

(2014) Samira Kiani et al.   NATURE METHODS

Large chromosomal deletions and heritable small genetic changes induced by CRISPR/Cas9 in rice

(2014) Huanbin Zhou et al.   NUCLEIC ACIDS RESEARCH

Multigene Knockout Utilizing Off-Target Mutations of the CRISPR/Cas9 System in Rice

(2014) Masaki Endo et al.   PLANT AND CELL PHYSIOLOGY

RNA-guided transcriptional regulationin plantavia synthetic dCas9-based transcription factors

(2014) Agnieszka Piatek et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome engineering via TALENs and CRISPR/Cas9 systems: challenges and perspectives

(2014) Magdy M. Mahfouz et al.   PLANT BIOTECHNOLOGY JOURNAL

Improved soybean oil quality by targeted mutagenesis of the fatty acid desaturase 2 gene family

(2014) William Haun et al.   PLANT BIOTECHNOLOGY JOURNAL

DNA Replicons for Plant Genome Engineering

(2014) N. J. Baltes et al.   PLANT CELL

Emerging tools for synthetic biology in plants

(2014) Ian Small et al.   PLANT JOURNAL

The CRISPR/Cas system can be used as nuclease forin plantagene targeting and as paired nickases for directed mutagenesis in Arabidopsis resulting in heritable progeny

(2014) Simon Schiml et al.   PLANT JOURNAL

Both CRISPR/Cas-based nucleases and nickases can be used efficiently for genome engineering inArabidopsis thaliana

(2014) Friedrich Fauser et al.   PLANT JOURNAL

Comparative assessments of CRISPR-Cas nucleases’ cleavage efficiency in planta

(2014) Ross A. Johnson et al.   PLANT MOLECULAR BIOLOGY

Artificial transcription factor-mediated regulation of gene expression

(2014) Niels van Tol et al.   PLANT SCIENCE

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Genome Elimination: Translating Basic Research into a Future Tool for Plant Breeding

(2014) Luca Comai   PLOS BIOLOGY

Plant Genome Engineering with Sequence-Specific Nucleases

(2013) Daniel F. Voytas   Annual Review of Plant Biology

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

In vivo modification of a maize engineered minichromosome

(2013) Robert T. Gaeta et al.   CHROMOSOMA

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases

(2013) S. W. Cho et al.   GENOME RESEARCH

Gene targeting in plants: 25 years later

(2013) Holger Puchta et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL BIOLOGY

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

(2013) Prashant Mali et al.   NATURE BIOTECHNOLOGY

Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems

(2013) Ines Fonfara et al.   NUCLEIC ACIDS RESEARCH

Zinc finger artificial transcription factor-based nearest inactive analogue/nearest active analogue strategy used for the identification of plant genes controlling homologous recombination

(2013) Qi Jia et al.   PLANT BIOTECHNOLOGY JOURNAL

Synthetic biology in plastids

(2013) Lars B. Scharff et al.   PLANT JOURNAL

Synthetic nucleases for genome engineering in plants: prospects for a bright future

(2013) Holger Puchta et al.   PLANT JOURNAL

Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU

(2013) Frank Hartung et al.   PLANT JOURNAL

Nonhomologous End Joining-Mediated Gene Replacement in Plant Cells

(2013) D. M. Weinthal et al.   PLANT PHYSIOLOGY

Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases

(2013) Yiping Qi et al.   G3-Genes Genomes Genetics

Epigenetic reprogramming of cancer cells via targeted DNA methylation

(2012) Ashley G. Rivenbark et al.   Epigenetics

Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer

(2012) Sabine Stolzenburg et al.   NUCLEIC ACIDS RESEARCH

Transcriptional activation ofBrassica napusβ-ketoacyl-ACP synthase II with an engineered zinc finger protein transcription factor

(2012) Manju Gupta et al.   PLANT BIOTECHNOLOGY JOURNAL

Construction of rice mini-chromosomes by telomere-mediated chromosomal truncation

(2012) Chunhui Xu et al.   PLANT JOURNAL

Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria

(2012) G. Gasiunas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In planta gene targeting

(2012) F. Fauser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Telomere-mediated truncation of barley chromosomes

(2011) Eszter Kapusi et al.   CHROMOSOMA

Parameters Affecting Telomere-Mediated Chromosomal Truncation inArabidopsis

(2011) Andrew D. Nelson et al.   PLANT CELL

Induction of telomere-mediated chromosomal truncation and stability of truncated chromosomes inArabidopsis thaliana

(2011) Chee How Teo et al.   PLANT JOURNAL

Creating Designed Zinc-Finger Nucleases with Minimal Cytotoxicity

(2010) Sivaprakash Ramalingam et al.   JOURNAL OF MOLECULAR BIOLOGY

Zinc finger nuclease-mediated transgene deletion

(2010) Joseph F. Petolino et al.   PLANT MOLECULAR BIOLOGY

Progress of chromosome engineering mediated by asymmetric somatic hybridization

(2009) Guangmin Xia   Journal of Genetics and Genomics

High-frequency modification of plant genes using engineered zinc-finger nucleases

(2009) Jeffrey A. Townsend et al.   NATURE

Precise genome modification in the crop species Zea mays using zinc-finger nucleases

(2009) Vipula K. Shukla et al.   NATURE

Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors

(2009) J. Boch et al.   SCIENCE

Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome

(2008) D. G. Gibson et al.   SCIENCE