DNA sequence-dependent activity and base flipping mechanisms of DNMT1 regulate genome-wide DNA methylation

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

(2020) Sandra Catania et al.   CELL

Two distinct modes of DNMT1 recruitment ensure stable maintenance DNA methylation

(2020) Atsuya Nishiyama et al.   Nature Communications

Comprehensive structure-function characterization of DNMT3B and DNMT3A reveals distinctive de novo DNA methylation mechanisms

(2020) Linfeng Gao et al.   Nature Communications

Diversity of cytosine methylation across the fungal tree of life

(2019) Adam J. Bewick et al.   Nature Ecology & Evolution

Mutations of R882 change flanking sequence preferences of the DNA methyltransferase DNMT3A and cellular methylation patterns

(2019) Max Emperle et al.   NUCLEIC ACIDS RESEARCH

Biochemical Studies and Molecular Dynamic Simulations Reveal the Molecular Basis of Conformational Changes in DNA Methyltransferase-1

(2018) Fei Ye et al.   ACS Chemical Biology

Evolutionary analysis indicates that DNA alkylation damage is a byproduct of cytosine DNA methyltransferase activity

(2018) Silvana Rošić et al.   NATURE GENETICS

DNA methylation loss in late-replicating domains is linked to mitotic cell division

(2018) Wanding Zhou et al.   NATURE GENETICS

Global delay in nascent strand DNA methylation

(2018) Jocelyn Charlton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The DNMT3A R882H mutant displays altered flanking sequence preferences

(2018) Max Emperle et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Global delay in nascent strand DNA methylation

(2018) Jocelyn Charlton et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanisms of opening and closing of the bacterial replicative helicase

(2018) Jillian Chase et al.   eLife

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

(2018) Albert Jeltsch et al.   Genes

Targeting the cancer epigenome for therapy

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

Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm

(2016) Albert Jeltsch et al.   NUCLEIC ACIDS RESEARCH

Role of base excision repair in maintaining the genetic and epigenetic integrity of CpG sites

(2015) Alfonso Bellacosa et al.   DNA REPAIR

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

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

(2013) J. Zhang et al.   BIOINFORMATICS

DNA Methyltransferase Inhibition Reverses Epigenetically Embedded Phenotypes in Lung Cancer Preferentially Affecting Polycomb Target Genes

(2013) A. Hascher et al.   CLINICAL CANCER RESEARCH

DNA methylation dynamics in health and disease

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

DNAshape: a method for the high-throughput prediction of DNA structural features on a genomic scale

(2013) Tianyin Zhou et al.   NUCLEIC ACIDS RESEARCH

Specificity of Dnmt1 for Methylation of Hemimethylated CpG Sites Resides in Its Catalytic Domain

(2012) Pavel Bashtrykov et al.   CHEMISTRY & BIOLOGY

Mechanistic details of the DNA recognition by the Dnmt1 DNA methyltransferase

(2012) Pavel Bashtrykov et al.   FEBS LETTERS

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Structure-Based Mechanistic Insights into DNMT1-Mediated Maintenance DNA Methylation

(2012) J. Song et al.   SCIENCE

Approaches to Enzyme and Substrate Design of the Murine Dnmt3a DNA Methyltransferase

(2011) Renata Z. Jurkowska et al.   CHEMBIOCHEM

On the Evolutionary Origin of Eukaryotic DNA Methyltransferases and Dnmt2

(2011) Tomasz P. Jurkowski et al.   PLoS One

AIC model selection and multimodel inference in behavioral ecology: some background, observations, and comparisons

(2010) Kenneth P. Burnham et al.   BEHAVIORAL ECOLOGY AND SOCIOBIOLOGY

Manipulation of FASTQ data with Galaxy

(2010) D. Blankenberg et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Structure of DNMT1-DNA Complex Reveals a Role for Autoinhibition in Maintenance DNA Methylation

(2010) J. Song et al.   SCIENCE

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

DNMT3L Modulates Significant and Distinct Flanking Sequence Preference for DNA Methylation by DNMT3A and DNMT3B In Vivo

(2010) Bethany L. Wienholz et al.   PLoS Genetics

Modeling and Simulating Chemical Reactions

(2008) Desmond J. Higham   SIAM REVIEW