Epigenetic editing: Dissecting chromatin function in context

Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells

(2020) Donnchadh S. Dunican et al.   BMC BIOLOGY

Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase

(2020) Sandra Catania et al.   CELL

X chromosome inactivation in human development

(2020) Catherine Patrat et al.   DEVELOPMENT

Robustness of catalytically-dead Cas9 activators in human pluripotent and mesenchymal stem cells

(2020) Paolo Petazzi et al.   Molecular Therapy-Nucleic Acids

Enhanced CRISPR-Cas9 correction of Duchenne muscular dystrophy in mice by a self-complementary AAV delivery system

(2020) Yu Zhang et al.   Science Advances

Synthetic multi-layer nanoparticles for CRISPR-Cas9 genome editing

(2020) Hao Tang et al.   ADVANCED DRUG DELIVERY REVIEWS

Lipid Nanoparticles for Cell-Specific in Vivo Targeted Delivery of Nucleic Acids

(2020) Ikramy A. Khalil et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors

(2020) Dan Wang et al.   CELL

Nanoparticles Modified with Cell-Penetrating Peptides: Conjugation Mechanisms, Physicochemical Properties, and Application in Cancer Diagnosis and Therapy

(2020) Isabel Gessner et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DNA methylation disruption reshapes the hematopoietic differentiation landscape

(2020) Franco Izzo et al.   NATURE GENETICS

Multiplexed CRISPR technologies for gene editing and transcriptional regulation

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

Epigenetic regulator function through mouse gastrulation

(2020) Stefanie Grosswendt et al.   NATURE

Perspectives on ENCODE

(2020) Michael P. Snyder et al.   NATURE

Programmable m6A modification of cellular RNAs with a Cas13-directed methyltransferase

(2020) Christopher Wilson et al.   NATURE BIOTECHNOLOGY

Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development

(2020) Kristjan H. Gretarsson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters

(2020) Mathieu Boulard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR artificial splicing factors

(2020) Menghan Du et al.   Nature Communications

Advancements and Obstacles of CRISPR-Cas9 technology in Translational Research

(2019) Liting You et al.   Molecular Therapy-Methods & Clinical Development

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

(2019) Ashot Papikian et al.   Nature Communications

Cancer therapy with a CRISPR-assisted telomerase-activating gene expression system

(2019) Wei Dai et al.   ONCOGENE

A New Class of Medicines through DNA Editing

(2019) Matthew H. Porteus   NEW ENGLAND JOURNAL OF MEDICINE

Adeno-associated virus vector as a platform for gene therapy delivery

(2019) Dan Wang et al.   NATURE REVIEWS DRUG DISCOVERY

DNA (de)methylation in embryonic stem cells controls CTCF-dependent chromatin boundaries

(2019) Laura Wiehle et al.   GENOME RESEARCH

Lentiviral CRISPR Epigenome Editing of Inflammatory Receptors as a Gene Therapy Strategy for Disc Degeneration

(2019) Niloofar Farhang et al.   HUMAN GENE THERAPY

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

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

Extracellular vesicles: a new communication paradigm?

(2019) Graça Raposo et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs

(2019) Yuelin Song et al.   MOLECULAR CELL

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

(2019) Gaia Colasante et al.   MOLECULAR THERAPY

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

(2019) Daniel N. Weinberg et al.   NATURE

Epigenome editing strategies for the functional annotation of CTCF insulators

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

In vivo epigenetic editing of Sema6a promoter reverses transcallosal dysconnectivity caused by C11orf46/Arl14ep risk gene

(2019) Cyril J. Peter et al.   Nature Communications

A Comprehensive Haplotype-Targeting Strategy for Allele-Specific HTT Suppression in Huntington Disease

(2019) Chris Kay et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A computational method to predict topologically associating domain boundaries combining histone Marks and sequence information

(2019) Wei Gan et al.   BMC GENOMICS

Dynamic Imaging of RNA in Living Cells by CRISPR-Cas13 Systems

(2019) Liang-Zhong Yang et al.   MOLECULAR CELL

Multi-omics profiling of mouse gastrulation at single-cell resolution

(2019) Ricard Argelaguet et al.   NATURE

Gene activation by dCas9-CBP and the SAM system differ in target preference

(2019) Suresh Sajwan et al.   Scientific Reports

A ligand-based system for receptor-specific delivery of proteins

(2019) Mariano Maffei et al.   Scientific Reports

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

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

A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology

(2018) Xiaoshu Xu et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2018) Haibo Zhou et al.   NATURE NEUROSCIENCE

Shedding light on the cell biology of extracellular vesicles

(2018) Guillaume van Niel et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Rett syndrome: insights into genetic, molecular and circuit mechanisms

(2018) Jacque P. K. Ip et al.   NATURE REVIEWS NEUROSCIENCE

The CRISPR tool kit for genome editing and beyond

(2018) Mazhar Adli   Nature Communications

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

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

Development of an integrated CRISPRi targeting ΔNp63 for treatment of squamous cell carcinoma

(2018) Masakazu Yoshida et al.   Oncotarget

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

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

Molecular and Synaptic Bases of CDKL5 Disorder

(2018) Yong-Chuan Zhu et al.   Developmental Neurobiology

Nano based drug delivery systems: recent developments and future prospects

(2018) Jayanta Kumar Patra et al.   JOURNAL OF NANOBIOTECHNOLOGY

CRISPR-Mediated Programmable 3D Genome Positioning and Nuclear Organization

(2018) Haifeng Wang et al.   CELL

Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance

(2018) Anastasiya Kazachenka et al.   CELL

Probing the Function of Metazoan Histones with a Systematic Library of H3 and H4 Mutants

(2018) Weimin Zhang et al.   DEVELOPMENTAL CELL

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

(2018) Navneet Matharu et al.   SCIENCE

Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells

(2018) Jiangping He et al.   Nature Communications

Tracing the transitions from pluripotency to germ cell fate with CRISPR screening

(2018) Jamie A. Hackett et al.   Nature Communications

Activating PTEN Tumor Suppressor Expression with the CRISPR/dCas9 System

(2018) Colette Moses et al.   Molecular Therapy-Nucleic Acids

Beyond histones - the expanding roles of protein lysine methylation

(2017) Zhouran Wu et al.   FEBS Journal

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

ISWI chromatin remodellers sense nucleosome modifications to determine substrate preference

(2017) Geoffrey P. Dann 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

Associating cellular epigenetic models with human phenotypes

(2017) Tuuli Lappalainen et al.   NATURE REVIEWS GENETICS

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

Impact of cytosine methylation on DNA binding specificities of human transcription factors

(2017) Yimeng Yin et al.   SCIENCE

Rapid and reversible epigenome editing by endogenous chromatin regulators

(2017) Simon M. G. Braun 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

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

Epigenetics, cellular memory and gene regulation

(2016) Steven Henikoff et al.   CURRENT BIOLOGY

CRISPR gene-editing tested in a person for the first time

(2016) David Cyranoski   NATURE

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

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

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

The molecular hallmarks of epigenetic control

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

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Neural circuits for pain: Recent advances and current views

(2016) C. Peirs 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

Lateral Thinking: How Histone Modifications Regulate Gene Expression

(2016) Moyra Lawrence et al.   TRENDS IN GENETICS

Epigenetics and Human Disease

(2016) Huda Y. Zoghbi et al.   Cold Spring Harbor Perspectives in 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

Epigenome-wide Association Studies and the Interpretation of Disease -Omics

(2016) Ewan Birney et al.   PLoS Genetics

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

(2016) Marius Walter 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

Histone demethylases in chromatin biology and beyond

(2015) E. Dimitrova et al.   EMBO REPORTS

Chromatin remodeling and bivalent histone modifications in embryonic stem cells

(2015) A. Harikumar et al.   EMBO REPORTS

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

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

Transcriptional regulators form diverse groups with context-dependent regulatory functions

(2015) Gerald Stampfel et al.   NATURE

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke 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

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

Olmsted syndrome: clinical, molecular and therapeutic aspects

(2015) Sabine Duchatelet et al.   Orphanet Journal of Rare Diseases

Cytosine DNA Methylation Is Found in Drosophila melanogaster but Absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Other Yeast Species

(2014) Floriana Capuano et al.   ANALYTICAL CHEMISTRY

Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases

(2014) S. Bae et al.   BIOINFORMATICS

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

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Histones: At the Crossroads of Peptide and Protein Chemistry

(2014) Manuel M. Müller et al.   CHEMICAL REVIEWS

Suv39h-Dependent H3K9me3 Marks Intact Retrotransposons and Silences LINE Elements in Mouse Embryonic Stem Cells

(2014) Aydan Bulut-Karslioglu et al.   MOLECULAR CELL

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

What are memories made of? How Polycomb and Trithorax proteins mediate epigenetic memory

(2014) Philipp A. Steffen et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Epigenetic inheritance uncoupled from sequence-specific recruitment

(2014) K. Ragunathan et al.   SCIENCE

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity

(2014) S. Saeed et al.   SCIENCE

Mechanisms of epigenetic memory

(2014) Agustina D’Urso et al.   TRENDS IN GENETICS

Gene Therapy for Skin Diseases

(2014) E. Gorell et al.   Cold Spring Harbor Perspectives in Medicine

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

(2014) Syandan Chakraborty et al.   Stem Cell Reports

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

(2013) Luke A. Gilbert 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

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

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

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

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

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

TALE: A tale of genome editing

(2013) Mingjie Zhang et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

A Histone Mutant Reproduces the Phenotype Caused by Loss of Histone-Modifying Factor Polycomb

(2013) A. R. Pengelly et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

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

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

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Reprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling

(2011) Richard P. Koche et al.   Cell Stem Cell

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

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

(2010) Aaron Klug   Annual Review of Biochemistry

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Aberrant Epigenetic Landscape in Cancer: How Cellular Identity Goes Awry

(2010) María Berdasco et al.   DEVELOPMENTAL CELL

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New insight into mechanisms of pruritus from molecular studies on familial primary localized cutaneous amyloidosis

(2009) A. Tanaka et al.   BRITISH JOURNAL OF DERMATOLOGY

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Identification of human haploinsufficient genes and their genomic proximity to segmental duplications

(2008) Vinh T Dang et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Histone Modifications and Nuclear Architecture: A Review

(2008) Eva Bártová et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

A model for transmission of the H3K27me3 epigenetic mark

(2008) Klaus H. Hansen et al.   NATURE CELL BIOLOGY