Enhanced CRISPR-based DNA demethylation by Casilio-ME-mediated RNA-guided coupling of methylcytosine oxidation and DNA repair pathways

Evolved Cas9 variants with broad PAM compatibility and high DNA specificity

(2018) Johnny H. Hu et al.   NATURE

Minimal PAM specificity of a highly similar SpCas9 ortholog

(2018) Pranam Chatterjee et al.   Science Advances

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

The DNA methyltransferase family: a versatile toolkit for epigenetic regulation

(2017) Frank Lyko   NATURE REVIEWS GENETICS

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

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

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

Active DNA demethylation by DNA repair: Facts and uncertainties

(2016) David Schuermann et al.   DNA REPAIR

Gadd45a is a heterochromatin relaxer that enhances iPS cell generation

(2016) Keshi Chen et al.   EMBO REPORTS

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

(2016) Benjamin P. Kleinstiver et al.   NATURE

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

(2016) Sumiyo Morita et al.   NATURE BIOTECHNOLOGY

Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation

(2016) Lars Schomacher et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Biochemical reconstitution of TET1–TDG–BER-dependent active DNA demethylation reveals a highly coordinated mechanism

(2016) Alain R. Weber et al.   Nature Communications

Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation

(2016) Lars Schomacher et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

A CRISPR-based approach for targeted DNA demethylation

(2016) Xingxing Xu et al.   Cell Discovery

GADD45a physically and functionally interacts with TET1

(2015) Sabine Kienhöfer et al.   DIFFERENTIATION

Gadd45a promotes DNA demethylation through TDG

(2015) Zheng Li et al.   NUCLEIC ACIDS RESEARCH

Rationally engineered Cas9 nucleases with improved specificity

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

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

BiQ Analyzer HiMod: an interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives

(2014) Daniel Becker et al.   NUCLEIC ACIDS RESEARCH

TET-mediated oxidation of methylcytosine causes TDG or NEIL glycosylase dependent gene reactivation

(2014) Udo Müller et al.   NUCLEIC ACIDS RESEARCH

Artificial transcription factor-mediated regulation of gene expression

(2014) Niels van Tol et al.   PLANT SCIENCE

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

Modular assembly of designer PUF proteins for specific post-transcriptional regulation of endogenous RNA

(2014) Zhanar Abil et al.   Journal of Biological Engineering

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen 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

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

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

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

(2013) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Induced DNA demethylation by targeting Ten-Eleven Translocation 2 to the human ICAM-1 promoter

(2013) Hui Chen et al.   NUCLEIC ACIDS RESEARCH

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

One-Step Sequence- and Ligation-Independent Cloning as a Rapid and Versatile Cloning Method for Functional Genomics Studies

(2012) Jae-Yeon Jeong et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Thymine DNA glycosylase specifically recognizes 5-carboxylcytosine-modified DNA

(2012) Liang Zhang et al.   Nature Chemical Biology

Excision of 5-hydroxymethyluracil and 5-carboxylcytosine by the thymine DNA glycosylase domain: its structural basis and implications for active DNA demethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Active DNA demethylation by Gadd45 and DNA repair

(2012) Christof Niehrs et al.   TRENDS IN CELL BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Thymine DNA Glycosylase Can Rapidly Excise 5-Formylcytosine and 5-Carboxylcytosine

(2011) Atanu Maiti et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A hyperactive piggyBac transposase for mammalian applications

(2011) K. Yusa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Solution Structure of Human Growth Arrest and DNA Damage 45α (Gadd45α) and Its Interactions with Proliferating Cell Nuclear Antigen (PCNA) and Aurora A Kinase

(2010) Ricardo Sánchez et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

NER Factors Are Recruited to Active Promoters and Facilitate Chromatin Modification for Transcription in the Absence of Exogenous Genotoxic Attack

(2010) Nicolas Le May et al.   MOLECULAR CELL

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

TAF12 Recruits Gadd45a and the Nucleotide Excision Repair Complex to the Promoter of rRNA Genes Leading to Active DNA Demethylation

(2009) Kerstin-Maike Schmitz et al.   MOLECULAR CELL

Rethinking how DNA methylation patterns are maintained

(2009) Peter A. Jones et al.   NATURE REVIEWS GENETICS

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE