Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

ZNF445 is a primary regulator of genomic imprinting

(2019) Nozomi Takahashi et al.   GENES & DEVELOPMENT

Differential roles of Stella in the modulation of DNA methylation during oocyte and zygotic development

(2019) Longsen Han et al.   Cell Discovery

Stella protein facilitates DNA demethylation by disrupting the chromatin association of the RING finger–type E3 ubiquitin ligase UHRF1

(2019) Wenlong Du et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolutionary transition between invertebrates and vertebrates via methylation reprogramming in embryogenesis

(2019) Xiaocui Xu et al.   National Science Review

Paradoxical association of TET loss of function with genome-wide DNA hypomethylation

(2019) Isaac F. López-Moyado et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retention of paternal DNA methylome in the developing zebrafish germline

(2019) Ksenia Skvortsova et al.   Nature Communications

Zebrafish preserve global germline DNA methylation while sex-linked rDNA is amplified and demethylated during feminisation

(2019) Oscar Ortega-Recalde et al.   Nature Communications

DNA Methylation: Shared and Divergent Features across Eukaryotes

(2019) Robert J. Schmitz et al.   TRENDS IN GENETICS

Convergent evolution of a vertebrate-like methylome in a marine sponge

(2019) Alex de Mendoza et al.   Nature Ecology & Evolution

Evolution of imprinting via lineage-specific insertion of retroviral promoters

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

PAM: A Framework for Integrated Analysis of Imaging, Single-Molecule, and Ensemble Fluorescence Data

(2018) Waldemar Schrimpf et al.   BIOPHYSICAL JOURNAL

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

Neutral Theory, Transposable Elements, and Eukaryotic Genome Evolution

(2018) Irina R Arkhipova   MOLECULAR BIOLOGY AND EVOLUTION

Delay in maternal transcript degradation in ovine embryos derived from low competence oocytes

(2018) Laura Masala et al.   MOLECULAR REPRODUCTION AND DEVELOPMENT

Embryonic defects induced by maternal obesity in mice derive from Stella insufficiency in oocytes

(2018) Longsen Han et al.   NATURE GENETICS

Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq

(2018) Johannes W. Bagnoli et al.   Nature Communications

Heterogeneous localisation of membrane proteins in Staphylococcus aureus

(2018) Felix Weihs et al.   Scientific Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

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(2018) Swati Parekh et al.   GigaScience

Genomic insights into chromatin reprogramming to totipotency in embryos

(2018) Sabrina Ladstätter et al.   JOURNAL OF CELL BIOLOGY

Nimble and Ready to Mingle: Transposon Outbursts of Early Development

(2018) Diego Rodriguez-Terrones et al.   TRENDS IN GENETICS

Single cell transcriptome analysis of human, marmoset and mouse embryos reveals common and divergent features of preimplantation development

(2018) Thorsten Boroviak et al.   DEVELOPMENT

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1

(2018) Yingfeng Li et al.   NATURE

Ubiquitome Analysis Reveals PCNA-Associated Factor 15 (PAF15) as a Specific Ubiquitination Target of UHRF1 in Embryonic Stem Cells

(2017) Elisabeth Karg et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance

(2017) Satoshi Ishiyama et al.   MOLECULAR CELL

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer

(2017) Zachary D. Smith et al.   NATURE

KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks

(2017) Michaël Imbeault et al.   NATURE

Lineage-specific functions of TET1 in the postimplantation mouse embryo

(2017) Rita Khoueiry et al.   NATURE GENETICS

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

(2017) Nipun Verma et al.   NATURE GENETICS

Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons

(2017) Peter G Hendrickson et al.   NATURE GENETICS

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

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Transposable Element Domestication As an Adaptation to Evolutionary Conflicts

(2017) Diwash Jangam et al.   TRENDS IN GENETICS

Co-option of endogenous viral sequences for host cell function

(2017) John A .Frank et al.   Current Opinion in Virology

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition

(2017) Yun Huang et al.   eLife

MAD2L2 Promotes Open Chromatin in Embryonic Stem Cells and Derepresses the Dppa3 Locus

(2017) Ali Rahjouei et al.   Stem Cell Reports

Endogenous Retroviruses: With Us and against Us

(2017) Thomas J. Meyer et al.   Frontiers in Chemistry

Transposable elements: Self-seekers of the germline, team-players of the soma

(2016) David Haig   BIOESSAYS

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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Activation of Endogenous Retroviruses in Dnmt1 −/− ESCs Involves Disruption of SETDB1-Mediated Repression by NP95 Binding to Hemimethylated DNA

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Persistent virus and addiction modules: an engine of symbiosis

(2016) Luis P Villarreal   CURRENT OPINION IN MICROBIOLOGY

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

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

Cooperative Action between SALL4A and TET Proteins in Stepwise Oxidation of 5-Methylcytosine

(2016) Jun Xiong et al.   MOLECULAR CELL

Impairment of DNA Methylation Maintenance Is the Main Cause of Global Demethylation in Naive Embryonic Stem Cells

(2016) Ferdinand von Meyenn et al.   MOLECULAR CELL

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

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Tet proteins influence the balance between neuroectodermal and mesodermal fate choice by inhibiting Wnt signaling

(2016) Xiang Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Zygote arrest 1, nucleoplasmin 2, and developmentally associated protein 3 mRNA profiles throughout porcine embryo development in vitro

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Super-Enhancers at the Nanog Locus Differentially Regulate Neighboring Pluripotency-Associated Genes

(2016) Steven Blinka et al.   Cell Reports

Post-translational Regulation of Cas9 during G1 Enhances Homology-Directed Repair

(2016) Tony Gutschner et al.   Cell Reports

Hemi-methylated DNA regulates DNA methylation inheritance through allosteric activation of H3 ubiquitylation by UHRF1

(2016) Joseph S Harrison et al.   eLife

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(2016) Stephen R. Frankenberg et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Age-Dependent Levels of 5-Methyl-, 5-Hydroxymethyl-, and 5-Formylcytosine in Human and Mouse Brain Tissues

(2015) Mirko Wagner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The Developmental Control of Transposable Elements and the Evolution of Higher Species

(2015) Marc Friedli et al.   Annual Review of Cell and Developmental Biology

Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines

(2015) Eric Kowarz et al.   Biotechnology Journal

DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts

(2015) David Roulois et al.   CELL

DNA methylation requires a DNMT1 ubiquitin interacting motif (UIM) and histone ubiquitination

(2015) Weihua Qin et al.   CELL RESEARCH

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates

(2015) Ian A. Warren et al.   CHROMOSOME RESEARCH

Lineage-Specific Profiling Delineates the Emergence and Progression of Naive Pluripotency in Mammalian Embryogenesis

(2015) Thorsten Boroviak et al.   DEVELOPMENTAL CELL

Phosphorylation of TET Proteins Is Regulated viaO-GlcNAcylation by theO-LinkedN-Acetylglucosamine Transferase (OGT)

(2015) Christina Bauer et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Live-cell observation of cytosolic HIV-1 assembly onset reveals RNA-interacting Gag oligomers

(2015) Jelle Hendrix et al.   JOURNAL OF CELL BIOLOGY

Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells

(2015) Edward J. Grow et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells

(2015) Jing Liao et al.   NATURE GENETICS

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(2015) Christopher B. Mulholland et al.   NUCLEIC ACIDS RESEARCH

Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy

(2015) Vincent J. Lynch et al.   Cell Reports

Early Developmental and Evolutionary Origins of Gene Body DNA Methylation Patterns in Mammalian Placentas

(2015) Diane I. Schroeder et al.   PLoS Genetics

Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines

(2015) Eric Kowarz et al.   Biotechnology Journal

Tbx3 Controls Dppa3 Levels and Exit from Pluripotency toward Mesoderm

(2015) Avinash Waghray et al.   Stem Cell Reports

Inhibition of maintenance DNA methylation by Stella

(2014) Soichiro Funaki et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

Reprogramming the Methylome: Erasing Memory and Creating Diversity

(2014) Heather J. Lee et al.   Cell Stem Cell

Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes

(2014) Li Shen et al.   Cell Stem Cell

Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote

(2014) Fan Guo et al.   Cell Stem Cell

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons

(2014) Frank M. J. Jacobs et al.   NATURE

DNA methylation dynamics of the human preimplantation embryo

(2014) Zachary D. Smith et al.   NATURE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

Data-based filtering for replicated high-throughput transcriptome sequencing experiments

(2013) Andrea Rau et al.   BIOINFORMATICS

Effects of Dppa3 on DNA Methylation Dynamics During Primordial Germ Cell Development in Mice1

(2013) Hiroyuki Nakashima et al.   BIOLOGY OF REPRODUCTION

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

(2013) Li Shen et al.   CELL

PRDM14 Ensures Naive Pluripotency through Dual Regulation of Signaling and Epigenetic Pathways in Mouse Embryonic Stem Cells

(2013) Masashi Yamaji et al.   Cell Stem Cell

FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency

(2013) Gabriella Ficz et al.   Cell Stem Cell

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

PRDM14 promotes active DNA demethylation through the Ten-eleven translocation (TET)-mediated base excision repair pathway in embryonic stem cells

(2013) N. Okashita et al.   DEVELOPMENT

Prdm14 promotes germline fate and naive pluripotency by repressing FGF signalling and DNA methylation

(2013) Nils Grabole et al.   EMBO REPORTS

Multivalent histone engagement by the linked tandem Tudor and PHD domains of UHRF1 is required for the epigenetic inheritance of DNA methylation

(2013) S. B. Rothbart et al.   GENES & DEVELOPMENT

Uhrf1-dependent H3K23 ubiquitylation couples maintenance DNA methylation and replication

(2013) Atsuya Nishiyama et al.   NATURE

A tripartite transcription factor network regulates primordial germ cell specification in mice

(2013) Erna Magnúsdóttir et al.   NATURE CELL BIOLOGY

Endogenous retroviruses function as species-specific enhancer elements in the placenta

(2013) Edward B Chuong et al.   NATURE GENETICS

Generation of eggs from mouse embryonic stem cells and induced pluripotent stem cells

(2013) Katsuhiko Hayashi et al.   Nature Protocols

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Naive pluripotency is associated with global DNA hypomethylation

(2013) Harry G Leitch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Visualization and targeted disruption of protein interactions in living cells

(2013) Henry D. Herce et al.   Nature Communications

The Majority of Primate-Specific Regulatory Sequences Are Derived from Transposable Elements

(2013) Pierre-Étienne Jacques et al.   PLoS Genetics

Differential Evolutionary Fate of an Ancestral Primate Endogenous Retrovirus Envelope Gene, the EnvV Syncytin, Captured for a Function in Placentation

(2013) Cécile Esnault et al.   PLoS Genetics

Synergistic Mechanisms of DNA Demethylation during Transition to Ground-State Pluripotency

(2013) Jamie A. Hackett et al.   Stem Cell Reports

Transposable element recruitments in the mammalian placenta: impacts and mechanisms

(2012) D. Emera et al.   Briefings in Functional Genomics

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

5-hydroxymethyl-cytosine enrichment of non-committed cells is not a universal feature of vertebrate development

(2012) Rimple D. Almeida et al.   Epigenetics

SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components

(2012) Richard A. Scheltema et al.   JOURNAL OF PROTEOME RESEARCH

PGC7 binds histone H3K9me2 to protect against conversion of 5mC to 5hmC in early embryos

(2012) Toshinobu Nakamura et al.   NATURE

Embryonic stem cell potency fluctuates with endogenous retrovirus activity

(2012) Todd S. Macfarlan et al.   NATURE

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Association of UHRF1 with methylated H3K9 directs the maintenance of DNA methylation

(2012) Scott B Rothbart et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

From ancestral infectious retroviruses to bona fide cellular genes: Role of the captured syncytins in placentation

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Implication of DNA Demethylation and Bivalent Histone Modification for Selective Gene Regulation in Mouse Primordial Germ Cells

(2012) Kentaro Mochizuki et al.   PLoS One

Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

(2012) K. Arita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The role of genes domesticated from LTR retrotransposons and retroviruses in mammals

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(2012) Patrick Boyle et al.   GENOME BIOLOGY

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Developmental features of DNA methylation during activation of the embryonic zebrafish genome

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Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Prediction of novel families of enzymes involved in oxidative and other complex modifications of bases in nucleic acids

(2011) Lakshminarayan M. Iyer et al.   CELL CYCLE

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

(2011) Ozren Bogdanović et al.   GENOME RESEARCH

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals

(2011) Vincent J Lynch et al.   NATURE GENETICS

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

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Dynamic control of endogenous retroviruses during development

(2011) Helen M. Rowe et al.   VIROLOGY

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

(2011) Mark Wossidlo et al.   Nature Communications

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

Role of Tet proteins in 5mC to 5hmC conversion, ES-cell self-renewal and inner cell mass specification

(2010) Shinsuke Ito et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Sequence-specific regulator Prdm14 safeguards mouse ESCs from entering extraembryonic endoderm fates

(2010) Ziyang Ma et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

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

Evolution of Genomic Imprinting: Insights from Marsupials and Monotremes

(2009) Marilyn B. Renfree et al.   Annual Review of Genomics and Human Genetics

Detecting Protein Complexes in Living Cells from Laser Scanning Confocal Image Sequences by the Cross Correlation Raster Image Spectroscopy Method

(2009) Michelle A. Digman et al.   BIOPHYSICAL JOURNAL

Releasing cohesin from chromosome arms in early mitosis: opposing actions of Wapl-Pds5 and Sgo1

(2009) K. Shintomi et al.   GENES & DEVELOPMENT

Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates

(2009) Lajos Mátés et al.   NATURE GENETICS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

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

(2009) M. Tahiliani et al.   SCIENCE

Dynamic Equilibrium and Heterogeneity of Mouse Pluripotent Stem Cells with Distinct Functional and Epigenetic States

(2008) Katsuhiko Hayashi et al.   Cell Stem Cell

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY