Controlling gene networks and cell fate with precision-targeted DNA-binding proteins and small-molecule-based genome readers

A Cascade of Histone Modifications Induces Chromatin Condensation in Mitosis

(2014) Bryan J. Wilkins et al.   SCIENCE

Lin28 Enhances Tissue Repair by Reprogramming Cellular Metabolism

(2013) Ng Shyh-Chang et al.   CELL

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

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

Efficient Generation of Human iPSCs by a Synthetic Self-Replicative RNA

(2013) Naohisa Yoshioka et al.   Cell Stem Cell

Small molecules, big roles - the chemical manipulation of stem cell fate and somatic cell reprogramming

(2013) Y. Zhang et al.   JOURNAL OF CELL SCIENCE

Processing-Independent CRISPR RNAs Limit Natural Transformation in Neisseria meningitidis

(2013) Yan Zhang et al.   MOLECULAR CELL

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

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Locus-specific editing of histone modifications at endogenous enhancers

(2013) Eric M Mendenhall et al.   NATURE BIOTECHNOLOGY

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

Specific elimination of mutant mitochondrial genomes in patient-derived cells by mitoTALENs

(2013) Sandra R Bacman et al.   NATURE MEDICINE

Robust, synergistic regulation of human gene expression using TALE activators

(2013) Morgan L Maeder et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

(2013) Kevin M Esvelt et al.   NATURE METHODS

Synergistic and tunable human gene activation by combinations of synthetic transcription factors

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

Advanced genetic tools for plant biotechnology

(2013) Wusheng Liu et al.   NATURE REVIEWS GENETICS

Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

De novo prediction of DNA-binding specificities for Cys2His2 zinc finger proteins

(2013) Anton V. Persikov et al.   NUCLEIC ACIDS RESEARCH

Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis

(2013) Z. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antitumor activity of a pyrrole-imidazole polyamide

(2013) F. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pluripotent Stem Cells Induced from Mouse Somatic Cells by Small-Molecule Compounds

(2013) P. Hou et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

RNA-dependent DNA endonuclease Cas9 of the CRISPR system: Holy Grail of genome editing?

(2013) Giedrius Gasiunas et al.   TRENDS IN MICROBIOLOGY

Reprogramming to Pluripotency Using Designer TALE Transcription Factors Targeting Enhancers

(2013) Xuefei Gao et al.   Stem Cell Reports

Dissecting the Roles of miR-302/367 Cluster in Cellular Reprogramming Using TALE-based Repressor and TALEN

(2013) Zhonghui Zhang et al.   Stem Cell Reports

Orthogonal control of endogenous gene expression in mammalian cells using synthetic ligands

(2012) Jing Liang et al.   BIOTECHNOLOGY AND BIOENGINEERING

A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

(2012) Ahmad S. Khalil et al.   CELL

Metabolic Plasticity in Stem Cell Homeostasis and Differentiation

(2012) Clifford D.L. Folmes et al.   Cell Stem Cell

Selective DNA demethylation by fusion of TDG with a sequence-specific DNA-binding domain

(2012) David J. Gregory et al.   Epigenetics

Gene Overexpression: Uses, Mechanisms, and Interpretation

(2012) G. Prelich   GENETICS

TAL effector RVD specificities and efficiencies

(2012) Jana Streubel et al.   NATURE BIOTECHNOLOGY

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Engineering synthetic TAL effectors with orthogonal target sites

(2012) Abhishek Garg et al.   NUCLEIC ACIDS RESEARCH

Targeted silencing of the oncogenic transcription factor SOX2 in breast cancer

(2012) Sabine Stolzenburg et al.   NUCLEIC ACIDS RESEARCH

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

Cozzarelli Prize Winner: Robust cardiomyocyte differentiation from human pluripotent stem cells via temporal modulation of canonical Wnt signaling

(2012) X. Lian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target

(2012) A. N.-S. Mak et al.   SCIENCE

Structural Basis for Sequence-Specific Recognition of DNA by TAL Effectors

(2012) D. Deng et al.   SCIENCE

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

(2012) M. Jinek et al.   SCIENCE

Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains

(2012) Le Cong et al.   Nature Communications

A synthetic small molecule for rapid induction of multiple pluripotency genes in mouse embryonic fibroblasts

(2012) Ganesh N. Pandian et al.   Scientific Reports

CRISPR-Cas Systems in Bacteria and Archaea: Versatile Small RNAs for Adaptive Defense and Regulation

(2011) Devaki Bhaya et al.   Annual Review of Genetics

HPV episome levels are potently decreased by pyrrole–imidazole polyamides

(2011) Terri G. Edwards et al.   ANTIVIRAL RESEARCH

Generation of Isogenic Pluripotent Stem Cells Differing Exclusively at Two Early Onset Parkinson Point Mutations

(2011) Frank Soldner et al.   CELL

Defining the nature of human pluripotent stem cell progeny

(2011) Michaela Patterson et al.   CELL RESEARCH

Synthetic Small Molecules for Epigenetic Activation of Pluripotency Genes in Mouse Embryonic Fibroblasts

(2011) Ganesh N. Pandian et al.   CHEMBIOCHEM

Reprogramming of mouse and human somatic cells by high-performance engineered factors

(2011) Yang Wang et al.   EMBO REPORTS

A bidirectional promoter architecture enhances lentiviral transgenesis in embryonic and extraembryonic stem cells

(2011) M C Golding et al.   GENE THERAPY

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Zinc-Finger Nucleases for Somatic Gene Therapy: The Next Frontier

(2011) Shamim H. Rahman et al.   HUMAN GENE THERAPY

Somatic coding mutations in human induced pluripotent stem cells

(2011) Athurva Gore et al.   NATURE

CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

(2011) Elitza Deltcheva et al.   NATURE

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia

(2011) Mark A. Dawson et al.   NATURE

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription

(2011) Feng Zhang et al.   NATURE BIOTECHNOLOGY

An unbiased genome-wide analysis of zinc-finger nuclease specificity

(2011) Richard Gabriel et al.   NATURE BIOTECHNOLOGY

Rapid and efficient clathrin-mediated endocytosis revealed in genome-edited mammalian cells

(2011) Jeffrey B. Doyon et al.   NATURE CELL BIOLOGY

Principles of a switch

(2011) Mark Ptashne   Nature Chemical Biology

Proteomic and phosphoproteomic comparison of human ES and iPS cells

(2011) Douglas H Phanstiel et al.   NATURE METHODS

On target? Tracing zinc-finger-nuclease specificity

(2011) Claudio Mussolino et al.   NATURE METHODS

Site-specific integration and tailoring of cassette design for sustainable gene transfer

(2011) Angelo Lombardo et al.   NATURE METHODS

Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection

(2011) Vikram Pattanayak et al.   NATURE METHODS

Turning straw into gold: directing cell fate for regenerative medicine

(2011) Dena E. Cohen et al.   NATURE REVIEWS GENETICS

Zinc-finger recombinase activities in vitro

(2011) Marko M. Prorocic et al.   NUCLEIC ACIDS RESEARCH

A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity

(2011) Claudio Mussolino et al.   NUCLEIC ACIDS RESEARCH

Enhancing the cellular uptake of Py–Im polyamides through next-generation aryl turns

(2011) Jordan L. Meier et al.   NUCLEIC ACIDS RESEARCH

Induced pluripotent stem cells: opportunities and challenges

(2011) K. Okita et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Induction of Stable Drug Resistance in Human Breast Cancer Cells Using a Combinatorial Zinc Finger Transcription Factor Library

(2011) Jeongeun Lee et al.   PLoS One

TAL Effectors: Customizable Proteins for DNA Targeting

(2011) A. J. Bogdanove et al.   SCIENCE

Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing

(2011) J. Xu et al.   SCIENCE

Concise Review: Putting a Finger on Stem Cell Biology: Zinc Finger Nuclease-Driven Targeted Genetic Editing in Human Pluripotent Stem Cells

(2011) Joseph Collin et al.   STEM CELLS

Elevated Coding Mutation Rate During the Reprogramming of Human Somatic Cells into Induced Pluripotent Stem Cells

(2011) Junfeng Ji et al.   STEM CELLS

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

The Mechanism of Double-Strand DNA Break Repair by the Nonhomologous DNA End-Joining Pathway

(2010) Michael R. Lieber   Annual Review of Biochemistry

Rewiring Cells: Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems

(2010) Caleb J. Bashor et al.   Annual Review of Biophysics

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

Small-molecule regulators that mimic transcription factors

(2010) José A. Rodríguez-Martínez et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg et al.   CELL

Reprogramming of Human Primary Somatic Cells by OCT4 and Chemical Compounds

(2010) Saiyong Zhu et al.   Cell Stem Cell

Nucleating the Assembly of Macromolecular Complexes

(2010) Kimberly J. Peterson-Kaufman et al.   CHEMBIOCHEM

A complex task? Direct modulation of transcription factors with small molecules

(2010) Angela N Koehler   CURRENT OPINION IN CHEMICAL BIOLOGY

Generation and genetic modification of induced pluripotent stem cells

(2010) Axel Schambach et al.   EXPERT OPINION ON BIOLOGICAL THERAPY

Induced pluripotency: history, mechanisms, and applications

(2010) M. Stadtfeld et al.   GENES & DEVELOPMENT

Functional genomics, proteomics, and regulatory DNA analysis in isogenic settings using zinc finger nuclease-driven transgenesis into a safe harbor locus in the human genome

(2010) R. C. DeKelver et al.   GENOME RESEARCH

Structural Basis for Cyclic Py-Im Polyamide Allosteric Inhibition of Nuclear Receptor Binding

(2010) David M. Chenoweth et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A Synthetic Coiled-Coil Interactome Provides Heterospecific Modules for Molecular Engineering

(2010) Aaron W. Reinke et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective inhibition of BET bromodomains

(2010) Panagis Filippakopoulos et al.   NATURE

Cell type of origin influences the molecular and functional properties of mouse induced pluripotent stem cells

(2010) Jose M Polo et al.   NATURE BIOTECHNOLOGY

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications in pluripotent and differentiated cells

(2010) Alexander Meissner   NATURE BIOTECHNOLOGY

Selection-free zinc-finger-nuclease engineering by context-dependent assembly (CoDA)

(2010) Jeffry D Sander et al.   NATURE METHODS

A nonviral minicircle vector for deriving human iPS cells

(2010) Fangjun Jia et al.   NATURE METHODS

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

From the editors

(2010)   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Systematic Comparison of Constitutive Promoters and the Doxycycline-Inducible Promoter

(2010) Jane Yuxia Qin et al.   PLoS One

Zinc-finger-based artificial transcription factors and their applications

(2009) Takashi Sera   ADVANCED DRUG DELIVERY REVIEWS

Restricted spacer tolerance of a zinc finger nuclease with a six amino acid linker

(2009) Yuka Shimizu et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Induced Pluripotent Stem Cells and Embryonic Stem Cells Are Distinguished by Gene Expression Signatures

(2009) Mark H. Chin et al.   Cell Stem Cell

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Forcing cells to change lineages

(2009) Thomas Graf et al.   NATURE

Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases

(2009) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Reprogramming of fibroblasts into induced pluripotent stem cells with orphan nuclear receptor Esrrb

(2009) Bo Feng et al.   NATURE CELL BIOLOGY

Without a trace? PiggyBac-ing toward pluripotency

(2009) Matthias Stadtfeld et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Positive selection of DNA-protein interactions in mammalian cells through phenotypic coupling with retrovirus production

(2009) Ulrich Tschulena et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Heterodimeric DNA methyltransferases as a platform for creating designer zinc finger methyltransferases for targeted DNA methylation in cells

(2009) Glenna E. Meister et al.   NUCLEIC ACIDS RESEARCH

ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells

(2009) Z. Ouyang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) J. Boch et al.   SCIENCE

A Simple Cipher Governs DNA Recognition by TAL Effectors

(2009) M. J. Moscou et al.   SCIENCE

Zinc finger nuclease technology heralds a new era in mammalian transgenesis

(2009) Fabienne Le Provost et al.   TRENDS IN BIOTECHNOLOGY

Targeted Chemical Wedges Reveal the Role of Allosteric DNA Modulation in Protein−DNA Assembly

(2008) Rocco Moretti et al.   ACS Chemical Biology

Targeting DNA with triplex-forming oligonucleotides to modify gene sequence

(2008) Philippe Simon et al.   BIOCHIMIE

Context-dependent DNA recognition code for C2H2 zinc-finger transcription factors

(2008) J. Liu et al.   BIOINFORMATICS

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

Stem Cells, the Molecular Circuitry of Pluripotency and Nuclear Reprogramming

(2008) Rudolf Jaenisch et al.   CELL

Modulation of drug resistance by artificial transcription factors

(2008) P. Blancafort et al.   MOLECULAR CANCER THERAPEUTICS

Reprogramming epigenetic silencing: artificial transcription factors synergize with chromatin remodeling drugs to reactivate the tumor suppressor mammary serine protease inhibitor

(2008) A. S. Beltran et al.   MOLECULAR CANCER THERAPEUTICS

Rapid “Open-Source” Engineering of Customized Zinc-Finger Nucleases for Highly Efficient Gene Modification

(2008) Morgan L. Maeder et al.   MOLECULAR CELL

Stable transgene expression in human embryonic stem cells after simple chemical transfection

(2008) Jun Liu et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Expanding or Restricting the Target Site Repertoire of Zinc-finger Nucleases: The Inter-domain Linker as a Major Determinant of Target Site Selectivity

(2008) Eva-Maria Händel et al.   MOLECULAR THERAPY

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS

Pyrrole-imidazole hairpin polyamides with high affinity at 5'-CGCG-3' DNA sequence; influence of cytosine methylation on binding

(2008) M. Minoshima et al.   NUCLEIC ACIDS RESEARCH

Growth Arrest of BCR-ABL Positive Cells with a Sequence-Specific Polyamide-Chlorambucil Conjugate

(2008) C. James Chou et al.   PLoS One

Identification and Use of Zinc Finger Transcription Factors That Increase Production of Recombinant Proteins in Yeast and Mammalian Cells

(2005) Kyung-Soon Park et al.   BIOTECHNOLOGY PROGRESS