Defending the genome from the enemy within: mechanisms of retrotransposon suppression in the mouse germline

Non-canonical functions of the DNA methylome in gene regulation

(2013) James P. Reddington et al.   BIOCHEMICAL JOURNAL

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

(2013) Li Shen et al.   CELL

Endogenous Retrotransposition Activates Oncogenic Pathways in Hepatocellular Carcinoma

(2013) Ruchi Shukla et al.   CELL

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET

(2013) H. M. Rowe et al.   DEVELOPMENT

In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

(2013) Jia-Hui Ng et al.   DEVELOPMENTAL CELL

Combined Deficiency of Tet1 and Tet2 Causes Epigenetic Abnormalities but Is Compatible with Postnatal Development

(2013) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

The genome-defence gene Tex19.1 suppresses LINE-1 retrotransposons in the placenta and prevents intra-uterine growth retardation in mice

(2013) Judith Reichmann et al.   HUMAN MOLECULAR GENETICS

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

(2013) Edward B Chuong et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

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

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA

(2013) Anas Fadloun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic programming and reprogramming during development

(2013) Irene Cantone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

(2013) James P Reddington et al.   GENOME BIOLOGY

Revisiting the evolution of mouse LINE-1 in the genomic era

(2013) Akash Sookdeo et al.   Mobile DNA

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

Transposable Elements: An Abundant and Natural Source of Regulatory Sequences for Host Genes

(2012) Rita Rebollo et al.   Annual Review of Genetics

Loss of 5-Hydroxymethylcytosine Is an Epigenetic Hallmark of Melanoma

(2012) Christine Guo Lian et al.   CELL

Single-Neuron Sequencing Analysis of L1 Retrotransposition and Somatic Mutation in the Human Brain

(2012) Gilad D. Evrony et al.   CELL

piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism

(2012) Ergin Beyret et al.   CELL RESEARCH

Retroviruses and the Placenta

(2012) David Haig   CURRENT BIOLOGY

Active human retrotransposons: variation and disease

(2012) Dustin C Hancks et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Promoter DNA methylation couples genome-defence mechanisms to epigenetic reprogramming in the mouse germline

(2012) J. A. Hackett et al.   DEVELOPMENT

Replication-coupled passive DNA demethylation for the erasure of genome imprints in mice

(2012) Saya Kagiwada et al.   EMBO JOURNAL

Transcriptional regulation of human-specific SVAF1 retrotransposons by cis-regulatory MAST2 sequences

(2012) Anastasia A. Zabolotneva et al.   GENE

Global profiling of DNA methylation erasure in mouse primordial germ cells

(2012) S. Guibert et al.   GENOME RESEARCH

Moloney Leukemia Virus Type 10 Inhibits Reverse Transcription and Retrotransposition of Intracisternal A Particles

(2012) C. Lu et al.   JOURNAL OF VIROLOGY

RYBP Represses Endogenous Retroviruses and Preimplantation- and Germ Line-Specific Genes in Mouse Embryonic Stem Cells

(2012) K. Hisada et al.   MOLECULAR AND CELLULAR BIOLOGY

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

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

A Role for Fkbp6 and the Chaperone Machinery in piRNA Amplification and Transposon Silencing

(2012) Jordi Xiol et al.   MOLECULAR CELL

Latent Regulatory Potential of Human-Specific Repetitive Elements

(2012) Michelle C. Ward et al.   MOLECULAR CELL

Tet1 controls meiosis by regulating meiotic gene expression

(2012) Shinpei Yamaguchi et al.   NATURE

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

(2012) Zachary D. Smith et al.   NATURE

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis

(2012) Anastassios Vourekas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Expression of endogenous retroviruses is negatively regulated by the pluripotency marker Rex1/Zfp42

(2012) D. Guallar et al.   NUCLEIC ACIDS RESEARCH

DNA methylation dynamics during the mammalian life cycle

(2012) J. A. Hackett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenetic Disruption of the PIWI Pathway in Human Spermatogenic Disorders

(2012) Holger Heyn et al.   PLoS One

The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors

(2012) N. Mathioudakis et al.   RNA

MARF1 Regulates Essential Oogenic Processes in Mice

(2012) Y.-Q. Su et al.   SCIENCE

Germline DNA Demethylation Dynamics and Imprint Erasure Through 5-Hydroxymethylcytosine

(2012) J. A. Hackett et al.   SCIENCE

Microarray Analysis of LTR Retrotransposon Silencing Identifies Hdac1 as a Regulator of Retrotransposon Expression in Mouse Embryonic Stem Cells

(2012) Judith Reichmann et al.   PLoS Computational Biology

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

(2012) Hisato Kobayashi et al.   PLoS Genetics

Blockade of Pachytene piRNA Biogenesis Reveals a Novel Requirement for Maintaining Post-Meiotic Germline Genome Integrity

(2012) Ke Zheng et al.   PLoS Genetics

MOV10 RNA Helicase Is a Potent Inhibitor of Retrotransposition in Cells

(2012) John L. Goodier et al.   PLoS Genetics

Non-genotoxic carcinogen exposure induces defined changes in the 5-hydroxymethylome

(2012) John P Thomson et al.   GENOME BIOLOGY

Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies

(2011) Z. Li et al.   BLOOD

Generation and replication-dependent dilution of 5fC and 5caC during mouse preimplantation development

(2011) Azusa Inoue et al.   CELL RESEARCH

Tet1 Is Dispensable for Maintaining Pluripotency and Its Loss Is Compatible with Embryonic and Postnatal Development

(2011) Meelad M. Dawlaty et al.   Cell Stem Cell

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

DNA Methylation and SETDB1/H3K9me3 Regulate Predominantly Distinct Sets of Genes, Retroelements, and Chimeric Transcripts in mESCs

(2011) Mohammad M. Karimi et al.   Cell Stem Cell

Epigenetic reprogramming in mouse pre-implantation development and primordial germ cells

(2011) M. Saitou et al.   DEVELOPMENT

Pinpointing the expression of piRNAs and function of the PIWI protein subfamily during spermatogenesis in the mouse

(2011) Ergin Beyret et al.   DEVELOPMENTAL BIOLOGY

MITOPLD Is a Mitochondrial Protein Essential for Nuage Formation and piRNA Biogenesis in the Mouse Germline

(2011) Toshiaki Watanabe et al.   DEVELOPMENTAL CELL

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A

(2011) Todd S. Macfarlan et al.   GENES & DEVELOPMENT

Genome-wide analysis of translation reveals a critical role for deleted in azoospermia-like (Dazl) at the oocyte-to-zygote transition

(2011) J. Chen et al.   GENES & DEVELOPMENT

Tissue type is a major modifier of the 5-hydroxymethylcytosine content of human genes

(2011) C. E. Nestor et al.   GENOME RESEARCH

TDRD5 is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis in mice

(2011) Yukihiro Yabuta et al.   JOURNAL OF CELL BIOLOGY

Gamma-irradiation increased meiotic crossovers in mouse spermatocytes

(2011) X. Cai et al.   MUTAGENESIS

ATM controls meiotic double-strand-break formation

(2011) Julian Lange et al.   NATURE

The endonuclease activity of Mili fuels piRNA amplification that silences LINE1 elements

(2011) Serena De Fazio et al.   NATURE

Somatic retrotransposition alters the genetic landscape of the human brain

(2011) J. Kenneth Baillie et al.   NATURE

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing

(2011) Michael Reuter et al.   NATURE

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Ten-Eleven-Translocation 2 (TET2) negatively regulates homeostasis and differentiation of hematopoietic stem cells in mice

(2011) M. Ko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lsh, chromatin remodeling family member, modulates genome-wide cytosine methylation patterns at nonrepeat sequences

(2011) Y. Tao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptionally repressed genes become aberrantly methylated and distinguish tumors of different lineages in breast cancer

(2011) D. Sproul et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A pair of co-opted retroviral envelope syncytin genes is required for formation of the two-layered murine placental syncytiotrophoblast

(2011) A. Dupressoir et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Replication-Dependent Loss of 5-Hydroxymethylcytosine in Mouse Preimplantation Embryos

(2011) A. Inoue 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

SINEs

(2011) Dmitri A. Kramerov et al.   Wiley Interdisciplinary Reviews-RNA

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Meiosis and retrotransposon silencing during germ cell development in mice

(2010) Rupert Öllinger et al.   DIFFERENTIATION

DNA double strand break repair, chromosome synapsis and transcriptional silencing in meiosis

(2010) Akiko Inagaki et al.   Epigenetics

MVH in piRNA processing and gene silencing of retrotransposons

(2010) S. Kuramochi-Miyagawa et al.   GENES & DEVELOPMENT

Polycomb complexes act redundantly to repress genomic repeats and genes

(2010) M. Leeb et al.   GENES & DEVELOPMENT

Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?

(2010) N Zamudio et al.   HEREDITY

Repression of Retrotransposal Elements in Mouse Embryonic Stem Cells Is Primarily Mediated by a DNA Methylation-independent Mechanism

(2010) Leah K. Hutnick et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Human endogenous retrovirus protein Rec interacts with the testicular zinc-finger protein and androgen receptor

(2010) S. Kaufmann et al.   JOURNAL OF GENERAL VIROLOGY

P Body-Associated Protein Mov10 Inhibits HIV-1 Replication at Multiple Stages

(2010) R. Burdick et al.   JOURNAL OF VIROLOGY

Neuronal MeCP2 Is Expressed at Near Histone-Octamer Levels and Globally Alters the Chromatin State

(2010) Peter J. Skene et al.   MOLECULAR CELL

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

(2010) Myunggon Ko et al.   NATURE

Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells

(2010) Jose L. Garcia-Perez et al.   NATURE

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe et al.   NATURE

Genome-wide erasure of DNA methylation in mouse primordial germ cells is affected by AID deficiency

(2010) Christian Popp et al.   NATURE

L1 retrotransposition in neurons is modulated by MeCP2

(2010) Alysson R. Muotri et al.   NATURE

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

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

(2010) Shinsuke Ito et al.   NATURE

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control

(2010) Juliette Gimenez et al.   NUCLEIC ACIDS RESEARCH

The Impact of CpG Island on Defining Transcriptional Activation of the Mouse L1 Retrotransposable Elements

(2010) Sung-Hun Lee et al.   PLoS One

The Ubiquitin Ligase Ubr2, a Recognition E3 Component of the N-End Rule Pathway, Stabilizes Tex19.1 during Spermatogenesis

(2010) Fang Yang et al.   PLoS One

Dnmt3b recruitment through E2F6 transcriptional repressor mediates germ-line gene silencing in murine somatic tissues

(2010) G. Velasco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway

(2010) K. Zheng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs

(2010) R. J. A. Frost et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Reprogramming in the Mouse Germ Line Entails the Base Excision Repair Pathway

(2010) P. Hajkova et al.   SCIENCE

Potential mechanisms of endogenous retroviral-mediated genomic instability in human cancer

(2010) M.T. Romanish et al.   SEMINARS IN CANCER BIOLOGY

LINE-1 retrotransposons: mediators of somatic variation in neuronal genomes?

(2010) Tatjana Singer et al.   TRENDS IN NEUROSCIENCES

Epigenetic Regulation of a Murine Retrotransposon by a Dual Histone Modification Mark

(2010) Reinhard Brunmeir et al.   PLoS Genetics

Estimating enrichment of repetitive elements from high-throughput sequence data

(2010) Daniel S Day et al.   GENOME BIOLOGY

Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse

(2009) J. Rossant et al.   DEVELOPMENT

The TDRD9-MIWI2 Complex Is Essential for piRNA-Mediated Retrotransposon Silencing in the Mouse Male Germline

(2009) Masanobu Shoji et al.   DEVELOPMENTAL CELL

Transcription is required for establishment of germline methylation marks at imprinted genes

(2009) M. Chotalia et al.   GENES & DEVELOPMENT

Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members

(2009) V. V. Vagin et al.   GENES & DEVELOPMENT

L1 retrotransposition occurs mainly in embryogenesis and creates somatic mosaicism

(2009) H. Kano et al.   GENES & DEVELOPMENT

Embryonic stem cells use ZFP809 to silence retroviral DNAs

(2009) Daniel Wolf et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

Loss of the Mili-interacting Tudor domain–containing protein-1 activates transposons and alters the Mili-associated small RNA profile

(2009) Michael Reuter et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Methyl-CpG Binding Proteins Mecp2, Mbd2 and Kaiso Are Dispensable for Mouse Embryogenesis, but Play a Redundant Function in Neural Differentiation

(2009) Isabel Martín Caballero et al.   PLoS One

Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi

(2009) C. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

(2009) Elena Khazina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) M. Tahiliani et al.   SCIENCE

GASZ Is Essential for Male Meiosis and Suppression of Retrotransposon Expression in the Male Germline

(2009) Lang Ma et al.   PLoS Genetics

Cytoplasmic Compartmentalization of the Fetal piRNA Pathway in Mice

(2009) Alexei A. Aravin et al.   PLoS Genetics

Mice Deficient for a Small Cluster of Piwi-Interacting RNAs Implicate Piwi-Interacting RNAs in Transposon Control1

(2008) Mingang Xu et al.   BIOLOGY OF REPRODUCTION

xDnmt1 regulates transcriptional silencing in pre-MBT Xenopus embryos independently of its catalytic function

(2008) D. S. Dunican et al.   DEVELOPMENT

Mouse Maelstrom, a Component of Nuage, Is Essential for Spermatogenesis and Transposon Repression in Meiosis

(2008) Sarah F.C. Soper et al.   DEVELOPMENTAL CELL

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

Complex genome-wide transcription dynamics orchestrated by Blimp1 for the specification of the germ cell lineage in mice

(2008) K. Kurimoto et al.   GENES & DEVELOPMENT

An infectious progenitor for the murine IAP retrotransposon: Emergence of an intracellular genetic parasite from an ancient retrovirus

(2008) D. Ribet et al.   GENOME RESEARCH

MILI, a PIWI-interacting RNA-binding Protein, Is Required for Germ Line Stem Cell Self-renewal and Appears to Positively Regulate Translation

(2008) Yingdee Unhavaithaya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Extensive meiotic asynapsis in mice antagonises meiotic silencing of unsynapsed chromatin and consequently disrupts meiotic sex chromosome inactivation

(2008) Shantha K. Mahadevaiah et al.   JOURNAL OF CELL BIOLOGY

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

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

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?

(2008) Witold Filipowicz et al.   NATURE REVIEWS GENETICS

MicroRNA Biogenesis Is Required for Mouse Primordial Germ Cell Development and Spermatogenesis

(2008) Katsuhiko Hayashi et al.   PLoS One

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY

Deletion of the Pluripotency-Associated Tex19.1 Gene Causes Activation of Endogenous Retroviruses and Defective Spermatogenesis in Mice

(2008) Rupert Öllinger et al.   PLoS Genetics

Argonaute proteins: key players in RNA silencing

(2007) Gyorgy Hutvagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Tex19, a Mammalian-Specific Protein with a Restricted Expression in Pluripotent Stem Cells and Germ Line

(2007) Sandra Kuntz et al.   STEM CELLS