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

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity

(2020) Paul Adrian Ginno et al.   Nature Communications

CRISPR/Cas9-based epigenome editing: An overview of dCas9-based tools with special emphasis on off-target activity

(2019) Vanja Tadić et al.   METHODS

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

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

A DNMT3A PWWP mutation leads to methylation of bivalent chromatin and growth retardation in mice

(2019) Gintarė Sendžikaitė et al.   Nature Communications

MBD-seq - realities of a misunderstood method for high-quality methylome-wide association studies

(2019) Karolina A. Aberg et al.   Epigenetics

Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions

(2019) Pawel Nowialis et al.   Nature Communications

Editing the Epigenome: Reshaping the Genomic Landscape

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

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

DNA Sequence Recognition of Human CXXC Domains and Their Structural Determinants

(2018) Chao Xu et al.   STRUCTURE

Genome-wide tracking of dCas9-methyltransferase footprints

(2018) Christina Galonska et al.   Nature Communications

Mammalian DNA methyltransferases: new discoveries and open questions

(2018) Humaira Gowher et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Gain-of-function DNMT3A mutations cause microcephalic dwarfism and hypermethylation of Polycomb-regulated regions

(2018) Patricia Heyn et al.   NATURE GENETICS

Targets and genomic constraints of ectopic Dnmt3b expression

(2018) Yingying Zhang et al.   eLife

Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes

(2018) Albert Jeltsch et al.   Genes

Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA

(2017) Xueyin Wang 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

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

Molecular analysis of PRC2 recruitment to DNA in chromatin and its inhibition by RNA

(2017) Xueyin Wang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ChAsE: chromatin analysis and exploration tool

(2016) Hamid Younesy et al.   BIOINFORMATICS

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

(2016) Angelo Amabile et al.   CELL

Role of TET enzymes in DNA methylation, development, and cancer

(2016) Kasper Dindler Rasmussen et al.   GENES & DEVELOPMENT

The molecular hallmarks of epigenetic control

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

Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm

(2016) Albert Jeltsch et al.   NUCLEIC ACIDS RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

(2016) Hannah K. Long et al.   NUCLEIC ACIDS RESEARCH

Repurposing the CRISPR-Cas9 system for targeted DNA methylation

(2016) Aleksandar Vojta et al.   NUCLEIC ACIDS RESEARCH

Dynamics of epigenetic regulation at the single-cell level

(2016) L. Bintu et al.   SCIENCE

Epigenome Editing: State of the Art, Concepts, and Perspectives

(2016) Goran Kungulovski et al.   TRENDS IN GENETICS

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

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

Quantitative Proteomic Analysis of Histone Modifications

(2015) He Huang et al.   CHEMICAL REVIEWS

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition

(2015) Philipp Rathert et al.   NATURE

Restricted epigenetic inheritance of H3K9 methylation

(2015) P. N. C. B. Audergon et al.   SCIENCE

Comprehensive Catalog of Currently Documented Histone Modifications

(2015) Yingming Zhao et al.   Cold Spring Harbor Perspectives in Biology

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

(2015) Goran Kungulovski et al.   Epigenetics & Chromatin

Understanding the relationship between DNA methylation and histone lysine methylation

(2014) Nathan R. Rose et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

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

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

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

Epigenetic inheritance uncoupled from sequence-specific recruitment

(2014) K. Ragunathan et al.   SCIENCE

New concepts in DNA methylation

(2014) Albert Jeltsch et al.   TRENDS IN BIOCHEMICAL SCIENCES

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs

(2013) Francesco Neri et al.   CELL

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

(2012) Aaron L. Statham et al.   GENOME RESEARCH

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

EpiExplorer: live exploration and global analysis of large epigenomic datasets

(2012) Konstantin Halachev et al.   GENOME BIOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The structural basis for selective binding of non-methylated CpG islands by the CFP1 CXXC domain

(2011) Chao Xu et al.   Nature Communications

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Active DNA demethylation: many roads lead to Rome

(2010) Susan C. Wu et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Molecular coupling of DNA methylation and histone methylation

(2010) Hideharu Hashimoto et al.   Epigenomics

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation Analysis of Chromosome 21 Gene Promoters at Single Base Pair and Single Allele Resolution

(2009) Yingying Zhang et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY