CRISPR/Cas-Based Epigenome Editing: Advances, Applications, and Clinical Utility

Heat-Triggered Remote Control of CRISPR-dCas9 for Tunable Transcriptional Modulation

(2020) Lena Gamboa et al.   ACS Chemical Biology

Multiple Input Sensing and Signal Integration Using a Split Cas12a System

(2020) Hannah R. Kempton et al.   MOLECULAR CELL

Titrating gene expression using libraries of systematically attenuated CRISPR guide RNAs

(2020) Marco Jost et al.   NATURE BIOTECHNOLOGY

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Multiplexed CRISPR technologies for gene editing and transcriptional regulation

(2020) Nicholas S. McCarty et al.   Nature Communications

The delivery challenge: fulfilling the promise of therapeutic genome editing

(2020) Joost van Haasteren et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas9 Circular Permutants as Programmable Scaffolds for Genome Modification

(2019) Benjamin L. Oakes et al.   CELL

Anti-CRISPR-mediated control of gene editing and synthetic circuits in eukaryotic cells

(2019) Muneaki Nakamura et al.   Nature Communications

Engineering of CRISPR-Cas12b for human genome editing

(2019) Jonathan Strecker et al.   Nature Communications

Genome-Scale CRISPRa Screen Identifies Novel Factors for Cellular Reprogramming

(2019) Jian Yang et al.   Stem Cell Reports

Improving CRISPR Genome Editing by Engineering Guide RNAs

(2019) Su Bin Moon et al.   TRENDS IN BIOTECHNOLOGY

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

(2019) Benjamin P. Kleinstiver et al.   NATURE BIOTECHNOLOGY

CasX enzymes comprise a distinct family of RNA-guided genome editors

(2019) Jun-Jie Liu et al.   NATURE

A High-Throughput Platform to Identify Small-Molecule Inhibitors of CRISPR-Cas9

(2019) Basudeb Maji et al.   CELL

Increasing the specificity of CRISPR systems with engineered RNA secondary structures

(2019) D. Dewran Kocak et al.   NATURE BIOTECHNOLOGY

Long-range enhancer–promoter contacts in gene expression control

(2019) Stefan Schoenfelder et al.   NATURE REVIEWS GENETICS

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Live-Animal Epigenome Editing: Convergence of Novel Techniques

(2019) J. Antonio Gomez et al.   TRENDS IN GENETICS

Ezh2-dCas9 and KRAB-dCas9 enable engineering of epigenetic memory in a context-dependent manner

(2019) Henriette O’Geen et al.   Epigenetics & Chromatin

A mutation-independent approach for muscular dystrophy via upregulation of a modifier gene

(2019) Dwi U. Kemaladewi et al.   NATURE

Allele-selective transcriptional repression of mutant HTT for the treatment of Huntington’s disease

(2019) Bryan Zeitler et al.   NATURE MEDICINE

LADL: light-activated dynamic looping for endogenous gene expression control

(2019) Ji Hun Kim et al.   NATURE METHODS

Combinatorial mutagenesis en masse optimizes the genome editing activities of SpCas9

(2019) Gigi C. G. Choi et al.   NATURE METHODS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis

(2019) Joseph Yusup Shin et al.   Science Translational Medicine

Targeted removal of epigenetic barriers during transcriptional reprogramming

(2019) Valentin Baumann et al.   Nature Communications

Controlling CRISPR-Cas9 with ligand-activated and ligand-deactivated sgRNAs

(2019) Kale Kundert et al.   Nature Communications

dCas9-based Scn1a gene activation restores inhibitory interneuron excitability and attenuates seizures in Dravet syndrome mice

(2019) Gaia Colasante et al.   MOLECULAR THERAPY

Targeted transcriptional modulation with type I CRISPR–Cas systems in human cells

(2019) Adrian Pickar-Oliver et al.   NATURE BIOTECHNOLOGY

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

CRISPR-Edited Stem Cells in a Patient with HIV and Acute Lymphocytic Leukemia

(2019) Lei Xu et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dose-dependent activation of gene expression is achieved using CRISPR and small molecules that recruit endogenous chromatin machinery

(2019) Anna M. Chiarella et al.   NATURE BIOTECHNOLOGY

Histone hyperacetylation disrupts core gene regulatory architecture in rhabdomyosarcoma

(2019) Berkley E. Gryder et al.   NATURE GENETICS

Engineered materials for in vivo delivery of genome-editing machinery

(2019) Sheng Tong et al.   Nature Reviews Materials

Recent advances in neuroepigenetic editing

(2019) Song-Jun Xu et al.   CURRENT OPINION IN NEUROBIOLOGY

Probing and engineering liquid-phase organelles

(2019) Dan Bracha et al.   NATURE BIOTECHNOLOGY

Engineering strategies to overcome the current roadblocks in CAR T cell therapy

(2019) Sarwish Rafiq et al.   Nature Reviews Clinical Oncology

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers

(2018) Jian Yan et al.   CELL RESEARCH

CRISPR-Based Chromatin Remodeling of the Endogenous Oct4 or Sox2 Locus Enables Reprogramming to Pluripotency

(2018) Peng Liu et al.   Cell Stem Cell

Combinatorial genetics in liver repopulation and carcinogenesis with a novel in vivo CRISPR activation platform

(2018) Kirk J. Wangensteen et al.   HEPATOLOGY

In Situ Gene Therapy via AAV-CRISPR-Cas9-Mediated Targeted Gene Regulation

(2018) Ana M. Moreno et al.   MOLECULAR THERAPY

An enhanced CRISPR repressor for targeted mammalian gene regulation

(2018) Nan Cher Yeo et al.   NATURE METHODS

In vivo simultaneous transcriptional activation of multiple genes in the brain using CRISPR–dCas9-activator transgenic mice

(2018) Haibo Zhou et al.   NATURE NEUROSCIENCE

Human pluripotent reprogramming with CRISPR activators

(2018) Jere Weltner et al.   Nature Communications

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

RNA-guided transcriptional silencing in vivo with S. aureus CRISPR-Cas9 repressors

(2018) Pratiksha I. Thakore et al.   Nature Communications

Downregulation of SNCA Expression by Targeted Editing of DNA Methylation: A Potential Strategy for Precision Therapy in PD

(2018) Boris Kantor et al.   MOLECULAR THERAPY

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Non-Viral Delivery To Enable Genome Editing

(2018) Yuan Rui et al.   TRENDS IN BIOTECHNOLOGY

Liquid Nuclear Condensates Mechanically Sense and Restructure the Genome

(2018) Yongdae Shin et al.   CELL

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

CRISPR Activation Screens Systematically Identify Factors that Drive Neuronal Fate and Reprogramming

(2018) Yanxia Liu et al.   Cell Stem Cell

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution

(2018) Efrat Shema et al.   NATURE GENETICS

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Functionally diverse type V CRISPR-Cas systems

(2018) Winston X. Yan et al.   SCIENCE

CRISPR-mediated activation of a promoter or enhancer rescues obesity caused by haploinsufficiency

(2018) Navneet Matharu et al.   SCIENCE

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Enhanced proofreading governs CRISPR–Cas9 targeting accuracy

(2017) Janice S. Chen et al.   NATURE

CRISPR–Cas9-based photoactivatable transcription systems to induce neuronal differentiation

(2017) Yuta Nihongaki et al.   NATURE METHODS

Inducible and multiplex gene regulation using CRISPR–Cpf1-based transcription factors

(2017) Y Esther Tak et al.   NATURE METHODS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Autologous Induced Stem-Cell–Derived Retinal Cells for Macular Degeneration

(2017) Michiko Mandai et al.   NEW ENGLAND JOURNAL OF MEDICINE

dCas9-based epigenome editing suggests acquisition of histone methylation is not sufficient for target gene repression

(2017) Henriette O’Geen et al.   NUCLEIC ACIDS RESEARCH

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Stabilization of Foxp3 expression by CRISPR-dCas9-based epigenome editing in mouse primary T cells

(2017) Masahiro Okada et al.   Epigenetics & Chromatin

Rapid and reversible epigenome editing by endogenous chromatin regulators

(2017) Simon M. G. Braun et al.   Nature Communications

Targeted DNA methylation in vivo using an engineered dCas9-MQ1 fusion protein

(2017) Yong Lei et al.   Nature Communications

In vivo genome editing with a small Cas9 orthologue derived from Campylobacter jejuni

(2017) Eunji Kim et al.   Nature Communications

Locus-specific histone deacetylation using a synthetic CRISPR-Cas9-based HDAC

(2017) Deborah Y. Kwon et al.   Nature Communications

Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping

(2017) Stefanie L. Morgan et al.   Nature Communications

Identification and characterization of a FOXA2-regulated transcriptional enhancer at a type 2 diabetes intronic locus that controls GCKR expression in liver cells

(2017) Maykel López Rodríguez et al.   Genome Medicine

Evaluating Synthetic Activation and Repression of Neuropsychiatric-Related Genes in hiPSC-Derived NPCs, Neurons, and Astrocytes

(2017) Seok-Man Ho et al.   Stem Cell Reports

Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing

(2016) Angelo Amabile et al.   CELL

Editing DNA Methylation in the Mammalian Genome

(2016) X. Shawn Liu et al.   CELL

Casilio: a versatile CRISPR-Cas9-Pumilio hybrid for gene regulation and genomic labeling

(2016) Albert W Cheng et al.   CELL RESEARCH

Targeted Epigenetic Remodeling of Endogenous Loci by CRISPR/Cas9-Based Transcriptional Activators Directly Converts Fibroblasts to Neuronal Cells

(2016) Joshua B. Black et al.   Cell Stem Cell

Genome-editing Technologies for Gene and Cell Therapy

(2016) Morgan L Maeder et al.   MOLECULAR THERAPY

High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects

(2016) Benjamin P. Kleinstiver et al.   NATURE

Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch

(2016) Benjamin L Oakes et al.   NATURE BIOTECHNOLOGY

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

The molecular hallmarks of epigenetic control

(2016) C. David Allis et al.   NATURE REVIEWS GENETICS

Efficient targeted DNA methylation with chimeric dCas9–Dnmt3a–Dnmt3L methyltransferase

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

Optimizing sgRNA position markedly improves the efficiency of CRISPR/dCas9-mediated transcriptional repression

(2016) Aliaksandra Radzisheuskaya et al.   NUCLEIC ACIDS RESEARCH

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Repair Pathway Choices and Consequences at the Double-Strand Break

(2016) Raphael Ceccaldi et al.   TRENDS IN CELL BIOLOGY

Writing of H3K4Me3 overcomes epigenetic silencing in a sustained but context-dependent manner

(2016) David Cano-Rodriguez et al.   Nature Communications

CRISPR-dCas9 mediated TET1 targeting for selective DNA demethylation at BRCA1 promoter

(2016) Samrat Roy Choudhury et al.   Oncotarget

Conversion of embryonic stem cells into extraembryonic lineages by CRISPR-mediated activators

(2016) Shu Wei et al.   Scientific Reports

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Silvana Konermann 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

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

Highly efficient Cas9-mediated transcriptional programming

(2015) Alejandro Chavez et al.   NATURE METHODS

Cooperation between SMYD3 and PC4 drives a distinct transcriptional program in cancer cells

(2015) Jin-Man Kim et al.   NUCLEIC ACIDS RESEARCH

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy

(2015) C. E. Nelson et al.   SCIENCE

Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond

(2015) Achim Breiling et al.   Epigenetics & Chromatin

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

(2014) Carolin Anders et al.   NATURE

A comparison of non-integrating reprogramming methods

(2014) Thorsten M Schlaeger et al.   NATURE BIOTECHNOLOGY

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

(2014) Syandan Chakraborty et al.   Stem Cell Reports

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

Optical control of mammalian endogenous transcription and epigenetic states

(2013) Silvana Konermann et al.   NATURE

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Extensive Methylation of Promoter Sequences Silences Lentiviral Transgene Expression During Stem Cell Differentiation In Vivo

(2012) Friederike Herbst et al.   MOLECULAR THERAPY

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

(2012) M. Jinek et al.   SCIENCE