Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing

CRISPR technologies for precise epigenome editing

(2021) Muneaki Nakamura et al.   NATURE CELL BIOLOGY

A unique bipartite Polycomb signature regulates stimulus-response transcription during development

(2021) Taro Kitazawa et al.   NATURE GENETICS

Stable DNMT3L overexpression in SH-SY5Y neurons recreates a facet of the genome-wide Down syndrome DNA methylation signature

(2021) Benjamin I. Laufer et al.   Epigenetics & Chromatin

Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing

(2021) James K. Nuñez et al.   CELL

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

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

An atlas of dynamic chromatin landscapes in mouse fetal development

(2020) David U. Gorkin et al.   NATURE

Distinct contributions of DNA methylation and histone acetylation to the genomic occupancy of transcription factors

(2020) Martin Cusack et al.   GENOME RESEARCH

Epigenome engineering: new technologies for precision medicine

(2020) Agustin Sgro et al.   NUCLEIC ACIDS RESEARCH

Genome-wide investigation of the dynamic changes of epigenome modifications after global DNA methylation editing

(2020) Julian Broche et al.   NUCLEIC ACIDS RESEARCH

Chromatin accessibility and the regulatory epigenome

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

CG dinucleotides enhance promoter activity independent of DNA methylation

(2019) Dominik Hartl et al.   GENOME RESEARCH

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

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

Experience-dependent neuroplasticity of the developing hypothalamus: integrative epigenomic approaches

(2018) Annie Vogel Ciernia et al.   Epigenetics

A CRISPR–dCas Toolbox for Genetic Engineering and Synthetic Biology

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

Distinct Stimulatory Mechanisms Regulate the Catalytic Activity of Polycomb Repressive Complex 2

(2018) Chul-Hwan Lee et al.   MOLECULAR CELL

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

(2018) Tafadzwa Mlambo et al.   NUCLEIC ACIDS RESEARCH

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells

(2017) Nipun Verma et al.   NATURE GENETICS

Chromatin-state discovery and genome annotation with ChromHMM

(2017) Jason Ernst et al.   Nature Protocols

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

Nucleosome Positioning and NDR Structure at RNA Polymerase III Promoters

(2017) Alexandra Søgaard Helbo et al.   Scientific Reports

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

(2016) Angelo Amabile et al.   CELL

Editing the epigenome: technologies for programmable transcription and epigenetic modulation

(2016) Pratiksha I Thakore et al.   NATURE METHODS

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Epigenetics and Human Disease

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

Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation

(2016) Max A Horlbeck et al.   eLife

Changes of bivalent chromatin coincide with increased expression of developmental genes in cancer

(2016) Stephan H. Bernhart et al.   Scientific Reports

How specific is CRISPR/Cas9 really?

(2015) Henriette O’Geen et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Pratiksha I Thakore et al.   NATURE METHODS

DNA methylation pathways and their crosstalk with histone methylation

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

A genome-wide analysis of Cas9 binding specificity using ChIP-seq and targeted sequence capture

(2015) Henriette O'Geen et al.   NUCLEIC ACIDS RESEARCH

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

(2014) Allison M. Cotton et al.   HUMAN MOLECULAR GENETICS

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

(2013) Lei S. Qi et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Epigenetic mechanisms in neurological disease

(2012) Mira Jakovcevski et al.   NATURE MEDICINE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Epigenetics and the environment: emerging patterns and implications

(2012) Robert Feil et al.   NATURE REVIEWS GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(2011) Hao Wu et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

GC-Rich Sequence Elements Recruit PRC2 in Mammalian ES Cells

(2010) Eric M. Mendenhall et al.   PLoS Genetics

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

A model for transmission of the H3K27me3 epigenetic mark

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