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

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Selective Elimination of Mitochondrial Mutations in the Germline by Genome Editing

(2015) Pradeep Reddy et al.   CELL

CRISPR-Cas9-based Photoactivatable Transcription System

(2015) Yuta Nihongaki et al.   CHEMISTRY & BIOLOGY

Delivery and Specificity of CRISPR/Cas9 Genome Editing Technologies for Human Gene Therapy

(2015) Jennifer L. Gori et al.   HUMAN GENE THERAPY

Challenges in CRISPR/CAS9 Delivery: Potential Roles of Nonviral Vectors

(2015) Ling Li et al.   HUMAN GENE THERAPY

Adenovirus-Mediated Somatic Genome Editing ofPtenby CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses

(2015) Dan Wang et al.   HUMAN GENE THERAPY

TALE-mediated epigenetic suppression of CDKN2A increases replication in human fibroblasts

(2015) Diana L. Bernstein et al.   JOURNAL OF CLINICAL INVESTIGATION

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

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

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

A light-inducible CRISPR-Cas9 system for control of endogenous gene activation

(2015) Lauren R Polstein et al.   Nature Chemical Biology

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

(2015) Jing Liao et al.   NATURE GENETICS

Therapeutic genome editing: prospects and challenges

(2015) David Benjamin Turitz Cox et al.   NATURE MEDICINE

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display

(2015) David M Shechner et al.   NATURE METHODS

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation

(2015) Francesca Telese et al.   NEURON

Brains, Genes, and Primates

(2015) Juan Carlos Izpisua Belmonte et al.   NEURON

Stable oncogenic silencing in vivo by programmable and targeted de novo DNA methylation in breast cancer

(2015) S Stolzenburg et al.   ONCOGENE

Multicolor CRISPR labeling of chromosomal loci in human cells

(2015) Hanhui Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation of knock-in primary human T cells using Cas9 ribonucleoproteins

(2015) Kathrin Schumann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Production of Gene-Corrected Adult Beta Globin Protein in Human Erythrocytes Differentiated from Patient iPSCs After Genome Editing of the Sickle Point Mutation

(2015) Xiaosong Huang et al.   STEM CELLS

Quantifying on- and off-target genome editing

(2015) Ayal Hendel et al.   TRENDS IN BIOTECHNOLOGY

Efficient inversions and duplications of mammalian regulatory DNA elements and gene clusters by CRISPR/Cas9

(2015) Jinhuan Li et al.   Journal of Molecular Cell Biology

Targeted epigenome editing of an endogenous locus with chromatin modifiers is not stably maintained

(2015) Goran Kungulovski et al.   Epigenetics & Chromatin

Direct regulation of E-cadherin by targeted histone methylation of TALE-SET fusion protein in cancer cells

(2015) Hyun-Soo Cho et al.   Oncotarget

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

(2015) Tomasz P Jurkowski et al.   Clinical Epigenetics

Cloning-free CRISPR/Cas system facilitates functional cassette knock-in in mice

(2015) Tomomi Aida et al.   GENOME BIOLOGY

Improved Cell-Penetrating Zinc-Finger Nuclease Proteins for Precision Genome Engineering

(2015) Jia Liu et al.   Molecular Therapy-Nucleic Acids

Protein Delivery Using Cys2–His2 Zinc-Finger Domains

(2014) Thomas Gaj et al.   ACS Chemical Biology

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

Making designer mutants in model organisms

(2014) Y. Peng et al.   DEVELOPMENT

A CRISPR-based approach for proteomic analysis of a single genomic locus

(2014) Zachary J Waldrip et al.   Epigenetics

Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 andpiggyBac

(2014) Fei Xie et al.   GENOME RESEARCH

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9

(2014) Samuel H. Sternberg et al.   NATURE

In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9

(2014) Lukasz Swiech et al.   NATURE BIOTECHNOLOGY

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo

(2014) John A Zuris et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Locus-specific epigenetic remodeling controls addiction- and depression-related behaviors

(2014) Elizabeth A Heller et al.   NATURE NEUROSCIENCE

Efficient, Complete Deletion of Synaptic Proteins using CRISPR

(2014) Salvatore Incontro et al.   NEURON

Analysis of an artificial zinc finger epigenetic modulator: widespread binding but limited regulation

(2014) Matthew R. Grimmer et al.   NUCLEIC ACIDS RESEARCH

Comparison of TALE designer transcription factors and the CRISPR/dCas9 in regulation of gene expression by targeting enhancers

(2014) Xuefei Gao et al.   NUCLEIC ACIDS RESEARCH

Direct activation of human and mouse Oct4 genes using engineered TALE and Cas9 transcription factors

(2014) Jiabiao Hu et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Jia Liu et al.   PLoS One

Targeted Methylation of the Epithelial Cell Adhesion Molecule (EpCAM) Promoter to Silence Its Expression in Ovarian Cancer Cells

(2014) Suneetha Nunna et al.   PLoS One

sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites

(2014) Shengsong Xie et al.   PLoS One

Directed Evolution of Improved Zinc Finger Methyltransferases

(2014) Brian Chaikind et al.   PLoS One

Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

(2014) M. Jinek et al.   SCIENCE

Targeted gene suppression by inducing de novo DNA methylation in the gene promoter

(2014) Ai-Niu Ma et al.   Epigenetics & Chromatin

Expansion of the CRISPR–Cas9 genome targeting space through the use of H1 promoter-expressed guide RNAs

(2014) Vinod Ranganathan et al.   Nature Communications

Revisiting the TALE repeat

(2014) Dong Deng et al.   Protein & Cell

Concerning RNA-guided gene drives for the alteration of wild populations

(2014) Kevin M Esvelt et al.   eLife

Repeated TALEs

(2014) Thoru Pederson   Nucleus

Visualization of specific DNA sequences in living mouse embryonic stem cells with a programmable fluorescent CRISPR/Cas system

(2014) Tobias Anton et al.   Nucleus

A CRISPR/Cas9-Based System for Reprogramming Cell Lineage Specification

(2014) Syandan Chakraborty et al.   Stem Cell Reports

Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR

(2013) Toshitsugu Fujita et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Transcription activator-like effector nucleases (TALENs): A highly efficient and versatile tool for genome editing

(2013) Ning Sun et al.   BIOTECHNOLOGY AND BIOENGINEERING

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

Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System

(2013) Baohui Chen et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

Chromosomal Contact Permits Transcription between Coregulated Genes

(2013) Stephanie Fanucchi et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells

(2013) N. A. Kearns et al.   DEVELOPMENT

Clustered protocadherins

(2013) W. V. Chen et al.   DEVELOPMENT

Specific transcriptional enhancement of inducible nitric oxide synthase by targeted promoter demethylation

(2013) David J Gregory et al.   Epigenetics

TALEN or Cas9 – Rapid, Efficient and Specific Choices for Genome Modifications

(2013) Chuanxian Wei et al.   Journal of Genetics and Genomics

Towards Sustained Silencing of HER2/neu in Cancer By Epigenetic Editing

(2013) F. Falahi et al.   MOLECULAR CANCER RESEARCH

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

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

Staying on target with CRISPR-Cas

(2013) Dana Carroll   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

Efficient genome editing in zebrafish using a CRISPR-Cas system

(2013) Woong Y Hwang et al.   NATURE BIOTECHNOLOGY

RNA-guided gene activation by CRISPR-Cas9–based transcription factors

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

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

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter

(2013) Hui Chen et al.   NUCLEIC ACIDS RESEARCH

Purification of a specific native genomic locus for proteomic analysis

(2013) Stephanie D. Byrum et al.   NUCLEIC ACIDS RESEARCH

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Regulation of Endogenous Human Gene Expression by Ligand-Inducible TALE Transcription Factors

(2013) Andrew C. Mercer et al.   ACS Synthetic Biology

A CRISPR way to engineer the human genome

(2013) Sivaprakash Ramalingam et al.   GENOME BIOLOGY

Epigenetic reprogramming of cancer cells via targeted DNA methylation

(2012) Ashley G. Rivenbark et al.   Epigenetics

Targeted Methylation and Gene Silencing of VEGF-A in Human Cells by Using a Designed Dnmt3a–Dnmt3L Single-Chain Fusion Protein with Increased DNA Methylation Activity

(2012) Abu Nasar Siddique et al.   JOURNAL OF MOLECULAR BIOLOGY

Targeted gene knockout by direct delivery of zinc-finger nuclease proteins

(2012) Thomas Gaj et al.   NATURE METHODS

A transcription activator-like effector toolbox for genome engineering

(2012) Neville E Sanjana et al.   Nature Protocols

Epigenetic Editing: targeted rewriting of epigenetic marks to modulate expression of selected target genes

(2012) M. L. de Groote et al.   NUCLEIC ACIDS RESEARCH

Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers

(2012) Brian Chaikind et al.   PLoS One

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

(2012) Le Cong et al.   Nature Communications

ChAP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic Locus

(2012) Stephanie D. Byrum et al.   Cell Reports

Optogenetic Interrogation of Dopaminergic Modulation of the Multiple Phases of Reward-Seeking Behavior

(2011) A. R. Adamantidis et al.   JOURNAL OF NEUROSCIENCE

Targeting DNA Double-Strand Breaks with TAL Effector Nucleases

(2010) M. Christian et al.   GENETICS

Genome editing with engineered zinc finger nucleases

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

Regulation of selected genome loci using de novo-engineered transcription activator-like effector (TALE)-type transcription factors

(2010) R. Morbitzer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Oligomerized pool engineering (OPEN): an 'open-source' protocol for making customized zinc-finger arrays

(2009) Morgan L Maeder et al.   Nature Protocols

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

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

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

(2008) J. Liu et al.   BIOINFORMATICS

Photoexcited CRY2 Interacts with CIB1 to Regulate Transcription and Floral Initiation in Arabidopsis

(2008) H. Liu et al.   SCIENCE