CRISPR technologies for precise epigenome editing

Engineering of Effector Domains for Targeted DNA Methylation with Reduced Off-Target Effects

(2020) Daniel Hofacker et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Towards a comprehensive catalogue of validated and target-linked human enhancers

(2020) Molly Gasperini et al.   NATURE REVIEWS GENETICS

Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

(2020) Kailong Li et al.   Nature Communications

CRISPR-Cas12a: Functional overview and applications

(2020) Bijoya Paul et al.   Biomedical Journal

Development of CRISPR as an Antiviral Strategy to Combat SARS-CoV-2 and Influenza

(2020) Timothy R. Abbott et al.   CELL

An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation

(2020) Philipp Raffeiner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

Physical modeling of the heritability and maintenance of epigenetic modifications

(2020) Sarah H. Sandholtz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synthetic immunomodulation with a CRISPR super-repressor in vivo

(2020) Farzaneh Moghadam et al.   NATURE CELL BIOLOGY

RNA–protein interaction mapping via MS2- or Cas13-based APEX targeting

(2020) Shuo Han et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA N6-Methyladenosine and the Regulation of RNA Localization and Function in the Brain

(2020) Sachithrani U. Madugalle et al.   TRENDS IN NEUROSCIENCES

A gene therapy for inherited blindness using dCas9-VPR–mediated transcriptional activation

(2020) Sybille Böhm et al.   Science Advances

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

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

(2019) Muneaki Nakamura et al.   Nature Communications

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Evaluating and Enhancing Target Specificity of Gene-Editing Nucleases and Deaminases

(2019) Daesik Kim et al.   Annual Review of Biochemistry

Epigenetics in Human Obesity and Type 2 Diabetes

(2019) Charlotte Ling et al.   Cell Metabolism

Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9

(2019) S. Ali Shariati et al.   MOLECULAR CELL

An Adversarial DNA N6-Methyladenine-Sensor Network Preserves Polycomb Silencing

(2019) Soo-Mi Kweon et al.   MOLECULAR CELL

The next generation of CRISPR–Cas technologies and applications

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

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

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

Gene activation by a CRISPR-assisted trans enhancer

(2019) Xinhui Xu et al.   eLife

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

(2019) Dwi U. Kemaladewi et al.   NATURE

Advances in epigenetics link genetics to the environment and disease

(2019) Giacomo Cavalli et al.   NATURE

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

(2019) Ji Hun Kim et al.   NATURE METHODS

Chromatin-associated RNAs as facilitators of functional genomic interactions

(2019) Xiao Li et al.   NATURE REVIEWS GENETICS

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

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

The regulation, functions and clinical relevance of arginine methylation

(2019) Ernesto Guccione et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Targeted removal of epigenetic barriers during transcriptional reprogramming

(2019) Valentin Baumann et al.   Nature Communications

From molecular promise to preclinical results: HDAC inhibitors in the race for healthy aging drugs

(2019) Rebecca L McIntyre et al.   EMBO Molecular Medicine

Histone Modifications Regulate Chromatin Compartmentalization by Contributing to a Phase Separation Mechanism

(2019) Liang Wang et al.   MOLECULAR CELL

Transcription Factor-Directed Re-wiring of Chromatin Architecture for Somatic Cell Nuclear Reprogramming toward trans-Differentiation

(2019) Alessandra Dall’Agnese et al.   MOLECULAR CELL

Mechanisms of Interplay between Transcription Factors and the 3D Genome

(2019) Seungsoo Kim et al.   MOLECULAR CELL

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(2019) Daniel N. Weinberg et al.   NATURE

Programmable RNA N6-methyladenosine editing by CRISPR-Cas9 conjugates

(2019) Xiao-Min Liu et al.   Nature Chemical Biology

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

CRISPR-mediated live imaging of genome editing and transcription

(2019) Haifeng Wang et al.   SCIENCE

Functional Enhancers Shape Extrachromosomal Oncogene Amplifications

(2019) Andrew R. Morton et al.   CELL

Active and Repressed Chromatin Domains Exhibit Distinct Nucleosome Segregation during DNA Replication

(2019) Thelma M. Escobar et al.   CELL

HP1 reshapes nucleosome core to promote phase separation of heterochromatin

(2019) S. Sanulli et al.   NATURE

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs

(2019) William A. Flavahan et al.   NATURE

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

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

(2019) Pay Giesselmann et al.   NATURE BIOTECHNOLOGY

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

(2019) Charles P. Fulco et al.   NATURE GENETICS

Epigenome editing strategies for the functional annotation of CTCF insulators

(2019) Daniel R. Tarjan et al.   Nature Communications

Modes of phase separation affecting chromatin regulation

(2019) Spiros Palikyras et al.   Open Biology

The Bivalent Genome: Characterization, Structure, and Regulation

(2019) Enrique Blanco et al.   TRENDS IN GENETICS

Chemical Control of a CRISPR-Cas9 Acetyltransferase

(2018) Jonathan H. Shrimp et al.   ACS Chemical Biology

Editing the Epigenome: Reshaping the Genomic Landscape

(2018) Liad Holtzman et al.   Annual Review of Genomics and Human Genetics

CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells

(2018) Nicolas Marx et al.   Biotechnology Journal

DNA methylation of a PLPP3 MIR transposon-based enhancer promotes an osteogenic programme in calcific aortic valve disease

(2018) Ghada Mkannez et al.   CARDIOVASCULAR RESEARCH

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance

(2018) Assaf C. Bester et al.   CELL

Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene

(2018) X. Shawn Liu et al.   CELL

Dissecting the Functional Consequences of De Novo DNA Methylation Dynamics in Human Motor Neuron Differentiation and Physiology

(2018) Michael J. Ziller et al.   Cell Stem Cell

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

(2018) Peng Liu et al.   Cell Stem Cell

A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs

(2018) Christian Pflueger et al.   GENOME RESEARCH

Discovery of proteins associated with a predefined genomic locus via dCas9–APEX-mediated proximity labeling

(2018) Samuel A. Myers et al.   NATURE METHODS

An enhanced CRISPR repressor for targeted mammalian gene regulation

(2018) Nan Cher Yeo et al.   NATURE METHODS

CRISPR interference-based specific and efficient gene inactivation in the brain

(2018) Yi Zheng et al.   NATURE NEUROSCIENCE

Designer epigenome modifiers enable robust and sustained gene silencing in clinically relevant human cells

(2018) Tafadzwa Mlambo et al.   NUCLEIC ACIDS RESEARCH

dCas9-targeted locus-specific protein isolation method identifies histone gene regulators

(2018) Chiahao Tsui et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements

(2018) Bo Gu et al.   SCIENCE

Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

CRISPR-Based Targeted Epigenetic Editing Enables Gene Expression Modulation of the Silenced Beta-Galactoside Alpha-2,6-Sialyltransferase 1 in CHO Cells

(2018) Nicolas Marx et al.   Biotechnology Journal

Epigenetic Targeting of Granulin in Hepatoma Cells by Synthetic CRISPR dCas9 Epi-suppressors

(2018) Hong Wang et al.   Molecular Therapy-Nucleic Acids

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids

(2018) Anthony M. D'Ippolito et al.   Cell Systems

Temporal and Spatial Epigenome Editing Allows Precise Gene Regulation in Mammalian Cells

(2018) Cem Kuscu et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Enhancer redundancy provides phenotypic robustness in mammalian development

(2018) Marco Osterwalder et al.   NATURE

Dynamic interplay between enhancer–promoter topology and gene activity

(2018) Hongtao Chen et al.   NATURE GENETICS

High-fidelity CRISPR/Cas9- based gene-specific hydroxymethylation rescues gene expression and attenuates renal fibrosis

(2018) Xingbo Xu et al.   Nature Communications

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

Engineering Epigenetic Regulation Using Synthetic Read-Write Modules

(2018) Minhee Park et al.   CELL

Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

(2018) Ying Liu et al.   NATURE BIOTECHNOLOGY

Engineered anti-CRISPR proteins for optogenetic control of CRISPR–Cas9

(2018) Felix Bubeck et al.   NATURE METHODS

Chemically Controlled Epigenome Editing through an Inducible dCas9 System

(2017) Tingjun Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

Discovery of stimulation-responsive immune enhancers with CRISPR activation

(2017) Dimitre R. Simeonov et al.   NATURE

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

(2017) Julia Joung et al.   NATURE

CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome

(2017) Tyler S Klann et al.   NATURE BIOTECHNOLOGY

Variant-aware saturating mutagenesis using multiple Cas9 nucleases identifies regulatory elements at trait-associated loci

(2017) Matthew C Canver et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

The emerging field of epigenetics in neurodegeneration and neuroprotection

(2017) Jee-Yeon Hwang et al.   NATURE REVIEWS NEUROSCIENCE

Histone propionylation is a mark of active chromatin

(2017) Adam F Kebede et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

Predicting the impact of non-coding variants on DNA methylation

(2017) Haoyang Zeng et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Masahiro Okada et al.   Epigenetics & Chromatin

Hit-and-run epigenetic editing prevents senescence entry in primary breast cells from healthy donors

(2017) Emily A. Saunderson et al.   Nature Communications

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

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

Histone propionylation is a mark of active chromatin

(2017) Adam F Kebede et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Gene activation in human cells using CRISPR/Cpf1-p300 and CRISPR/Cpf1-SunTag systems

(2017) Xin Zhang et al.   Protein & Cell

Targeted DNA methylation in pericentromeres with genome editing-based artificial DNA methyltransferase

(2017) Taiga Yamazaki et al.   PLoS One

Targeted DNA methylation in human cells using engineered dCas9-methyltransferases

(2017) Tina Xiong et al.   Scientific Reports

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

(2016) Angelo Amabile et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson 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

Efficient sequence-specific isolation of DNA fragments and chromatin by in vitro enChIP technology using recombinant CRISPR ribonucleoproteins

(2016) Toshitsugu Fujita et al.   GENES TO CELLS

A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

(2016) Yarui Diao et al.   GENOME RESEARCH

Targeted DNA demethylation in vivo using dCas9–peptide repeat and scFv–TET1 catalytic domain fusions

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Hierarchy within the mammary STAT5-driven Wap super-enhancer

(2016) Ha Youn Shin et al.   NATURE GENETICS

Histone H3 globular domain acetylation identifies a new class of enhancers

(2016) Madapura M Pradeepa et al.   NATURE GENETICS

Complex transcriptional modulation with orthogonal and inducible dCas9 regulators

(2016) Yuchen Gao et al.   NATURE METHODS

Comparison of Cas9 activators in multiple species

(2016) Alejandro Chavez et al.   NATURE METHODS

From profiles to function in epigenomics

(2016) Stefan H. Stricker et al.   NATURE REVIEWS GENETICS

Targeting the cancer epigenome for therapy

(2016) Peter A. Jones et al.   NATURE REVIEWS GENETICS

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

(2016) Peter Stepper et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

High-resolution interrogation of functional elements in the noncoding genome

(2016) N. E. Sanjana et al.   SCIENCE

The epigenetic landscape of T cell exhaustion

(2016) D. R. Sen et al.   SCIENCE

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

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

Nucleosomes impede Cas9 access to DNA in vivo and in vitro

(2016) Max A Horlbeck et al.   eLife

Reprogrammable CRISPR/Cas9-based system for inducing site-specific DNA methylation

(2016) James I. McDonald et al.   Biology Open

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

Cas9 Functionally Opens Chromatin

(2016) Amira A. Barkal et al.   PLoS One

DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs

(2015) Estel Aparicio-Prat et al.   BMC GENOMICS

Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds

(2015) Jesse G. Zalatan et al.   CELL

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

CRISPR Inversion of CTCF Sites Alters Genome Topology and Enhancer/Promoter Function

(2015) Ya Guo et al.   CELL

Chromatin deregulation in disease

(2015) Anne C. Mirabella et al.   CHROMOSOMA

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

(2015) Lauren R. Polstein et al.   GENOME RESEARCH

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver 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

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

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Chromatin regulation at the frontier of synthetic biology

(2015) Albert J. Keung et al.   NATURE REVIEWS GENETICS

DNA methylation pathways and their crosstalk with histone methylation

(2015) Jiamu Du et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

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

Using Targeted Chromatin Regulators to Engineer Combinatorial and Spatial Transcriptional Regulation

(2014) Albert J. Keung et al.   CELL

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

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

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

(2013) Lei S. Qi et al.   CELL

Chromatin Position Effects Assayed by Thousands of Reporters Integrated in Parallel

(2013) Waseem Akhtar et al.   CELL

Dynamics and Memory of Heterochromatin in Living Cells

(2012) Nathaniel A. Hathaway et al.   CELL

Histone Ubiquitination and Deubiquitination in Transcription, DNA Damage Response, and Cancer

(2012) Jian Cao et al.   Frontiers in Oncology

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes

(2010) Gillian L. Dalgliesh et al.   NATURE