NSD1-deposited H3K36me2 directs de novo methylation in the mouse male germline and counteracts Polycomb-associated silencing

ZNF445 is a primary regulator of genomic imprinting

(2019) Nozomi Takahashi et al.   GENES & DEVELOPMENT

SETD2 regulates the maternal epigenome, genomic imprinting and embryonic development

(2019) Qianhua Xu et al.   NATURE GENETICS

Highly efficient single-stranded DNA ligation technique improves low-input whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2019) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Gintarė Sendžikaitė et al.   Nature Communications

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

(2019) Daniel N. Weinberg et al.   NATURE

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Broad Heterochromatic Domains Open in Gonocyte Development Prior to De Novo DNA Methylation

(2019) Soichiro Yamanaka et al.   DEVELOPMENTAL CELL

H3K36me2/3 Binding and DNA Binding of the DNA Methyltransferase DNMT3A PWWP Domain Both Contribute to its Chromatin Interaction

(2019) Michael Dukatz et al.   JOURNAL OF MOLECULAR BIOLOGY

Evolution of imprinting via lineage-specific insertion of retroviral promoters

(2019) Aaron B. Bogutz et al.   Nature Communications

The histone methyltransferase SETD2 is required for expression of acrosin-binding protein 1 and protamines and essential for spermiogenesis in mice

(2018) Xiaoli Zuo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells

(2018) Gundula Streubel et al.   MOLECULAR CELL

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

(2018) Wanding Zhou et al.   NATURE GENETICS

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MLL2 conveys transcription-independent H3K4 trimethylation in oocytes

(2018) Courtney W. Hanna et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies

(2018) Rohan N. Shah et al.   MOLECULAR CELL

LTR retrotransposons transcribed in oocytes drive species-specific and heritable changes in DNA methylation

(2018) Julie Brind’Amour et al.   Nature Communications

Genetics meets DNA methylation in rare diseases

(2018) Guillaume Velasco et al.   CLINICAL GENETICS

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

(2018) Patricia Heyn et al.   NATURE GENETICS

Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas

(2017) Simon Papillon-Cavanagh et al.   NATURE GENETICS

Switching of dominant retrotransposon silencing strategies from posttranscriptional to transcriptional mechanisms during male germ-cell development in mice

(2017) Kota Inoue et al.   PLoS Genetics

Dual Chromatin and Cytoskeletal Remodeling by SETD2

(2016) In Young Park et al.   CELL

Global Landscape and Regulatory Principles of DNA Methylation Reprogramming for Germ Cell Specification by Mouse Pluripotent Stem Cells

(2016) Kenjiro Shirane et al.   DEVELOPMENTAL CELL

SETD2andDNMT3Ascreen in the Sotos-like syndrome French cohort

(2016) Camille Tlemsani et al.   JOURNAL OF MEDICAL GENETICS

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity

(2016) Joan Barau et al.   SCIENCE

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

(2016) C. Lu et al.   SCIENCE

The histone H3.3K36M mutation reprograms the epigenome of chondroblastomas

(2016) D. Fang et al.   SCIENCE

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells

(2016) Andrew D. King et al.   Cell Reports

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

VisRseq: R-based visual framework for analysis of sequencing data

(2015) Hamid Younesy et al.   BMC BIOINFORMATICS

DNA methylation and gene expression dynamics during spermatogonial stem cell differentiation in the early postnatal mouse testis

(2015) Naoki Kubo et al.   BMC GENOMICS

Dynamic changes in histone modifications precede de novo DNA methylation in oocytes

(2015) Kathleen R. Stewart et al.   GENES & DEVELOPMENT

Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide

(2015) Adrian T. Grzybowski et al.   MOLECULAR CELL

Genomic profiling of DNA methyltransferases reveals a role for DNMT3B in genic methylation

(2015) Tuncay Baubec et al.   NATURE

An ultra-low-input native ChIP-seq protocol for genome-wide profiling of rare cell populations

(2015) Julie Brind’Amour et al.   Nature Communications

NSD1 mutations generate a genome-wide DNA methylation signature

(2015) S. Choufani et al.   Nature Communications

In vivo targeting of de novo DNA methylation by histone modifications in yeast and mouse

(2015) Marco Morselli et al.   eLife

Allele-specific binding of ZFP57 in the epigenetic regulation of imprinted and non-imprinted monoallelic expression

(2015) Ruslan Strogantsev et al.   GENOME BIOLOGY

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Setdb1is required for germline development and silencing of H3K9me3-marked endogenous retroviruses in primordial germ cells

(2014) Sheng Liu et al.   GENES & DEVELOPMENT

Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability

(2014) Katrina Tatton-Brown et al.   NATURE GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice

(2013) H. Kobayashi et al.   GENOME RESEARCH

DNA methylation: roles in mammalian development

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

Molecular determinants of nucleosome retention at CpG-rich sequences in mouse spermatozoa

(2013) Serap Erkek et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells

(2013) James A. Hagarman et al.   PLoS One

De Novo DNA Methylation in the Male Germ Line Occurs by Default but Is Excluded at Sites of H3K4 Methylation

(2013) Purnima Singh et al.   Cell Reports

Mouse Oocyte Methylomes at Base Resolution Reveal Genome-Wide Accumulation of Non-CpG Methylation and Role of DNA Methyltransferases

(2013) Kenjiro Shirane et al.   PLoS Genetics

Redistribution of H3K27me3 upon DNA hypomethylation results in de-repression of Polycomb target genes

(2013) James P Reddington et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

Total kinetic analysis reveals how combinatorial methylation patterns are established on lysines 27 and 36 of histone H3

(2012) Y. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks

(2012) Hisato Kobayashi et al.   PLoS Genetics

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

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes

(2011) S.-i. Tomizawa et al.   DEVELOPMENT

H3K36 Methylation Antagonizes PRC2-mediated H3K27 Methylation

(2011) Wen Yuan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

(2011) Frank W. Schmitges et al.   MOLECULAR CELL

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

Role for piRNAs and Noncoding RNA in de Novo DNA Methylation of the Imprinted Mouse Rasgrf1 Locus

(2011) T. Watanabe et al.   SCIENCE

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

(2010) Hong-Qiang Wang et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   CELL

The Dnmt3a PWWP Domain Reads Histone 3 Lysine 36 Trimethylation and Guides DNA Methylation

(2010) Arunkumar Dhayalan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

DNMT3AMutations in Acute Myeloid Leukemia

(2010) Timothy J. Ley et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes

(2010) H. Wu et al.   SCIENCE

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes

(2008) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

GDNF-mediated signaling via RET tyrosine 1062 is essential for maintenance of spermatogonial stem cells

(2008) Mayumi Jijiwa et al.   GENES TO CELLS

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

Epigenetic events in mammalian germ-cell development: reprogramming and beyond

(2008) Hiroyuki Sasaki et al.   NATURE REVIEWS GENETICS