Individual retrotransposon integrants are differentially controlled by KZFP/KAP1-dependent histone methylation, DNA methylation and TET-mediated hydroxymethylation in naïve embryonic stem cells

The 5-Hydroxymethylcytosine (5hmC) Reader UHRF2 Is Required for Normal Levels of 5hmC in Mouse Adult Brain and Spatial Learning and Memory

(2017) Ruoyu Chen et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2017) Michaël Imbeault et al.   NATURE

DUX-family transcription factors regulate zygotic genome activation in placental mammals

(2017) Alberto De Iaco 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

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

(2016) Jafar Sharif et al.   Cell Stem Cell

Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues

(2016) Gabriela Ecco et al.   DEVELOPMENTAL 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

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Regulatory activities of transposable elements: from conflicts to benefits

(2016) Edward B. Chuong et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Regulatory evolution of innate immunity through co-option of endogenous retroviruses

(2016) E. B. Chuong et al.   SCIENCE

Causes and Consequences of Multi-Locus Imprinting Disturbances in Humans

(2016) Marta Sanchez-Delgado et al.   TRENDS IN GENETICS

An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells

(2016) Marius Walter et al.   eLife

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

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

The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses

(2015) Gernot Wolf et al.   GENES & DEVELOPMENT

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo

(2015) Julia Arand et al.   Epigenetics & Chromatin

TRIM28 Controls Genomic Imprinting through Distinct Mechanisms during and after Early Genome-wide Reprogramming

(2015) Katherine A. Alexander et al.   Cell Reports

TRIM28 Represses Transcription of Endogenous Retroviruses in Neural Progenitor Cells

(2015) Liana Fasching et al.   Cell Reports

Imprinting disorders: a group of congenital disorders with overlapping patterns of molecular changes affecting imprinted loci

(2015) Thomas Eggermann et al.   Clinical Epigenetics

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

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

(2014) Fan Guo et al.   Cell Stem Cell

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Evolutionally dynamic L1 regulation in embryonic stem cells

(2014) N. Castro-Diaz et al.   GENES & DEVELOPMENT

DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos

(2014) D. M. Messerschmidt et al.   GENES & DEVELOPMENT

Deep Vertebrate Roots for Mammalian Zinc Finger Transcription Factor Subfamilies

(2014) Hui Liu et al.   Genome Biology and Evolution

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Interplay of TRIM28 and DNA methylation in controlling human endogenous retroelements

(2014) Priscilla Turelli et al.   GENOME RESEARCH

Regulation of DNA methylation turnover at LTR retrotransposons and imprinted loci by the histone methyltransferase Setdb1

(2014) D. Leung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

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

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

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

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

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

Tet Proteins Connect the O-Linked N-acetylglucosamine Transferase Ogt to Chromatin in Embryonic Stem Cells

(2013) Pietro Vella et al.   MOLECULAR CELL

Differential L1 regulation in pluripotent stem cells of humans and apes

(2013) Maria C. N. Marchetto et al.   NATURE

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

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

The Microprocessor controls the activity of mammalian retrotransposons

(2013) Sara R Heras et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Naive pluripotency is associated with global DNA hypomethylation

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

Epigenetic programming and reprogramming during development

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

Single-Cell DNA-Methylation Analysis Reveals Epigenetic Chimerism in Preimplantation Embryos

(2013) C. Lorthongpanich et al.   SCIENCE

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells

(2013) Francesco Neri et al.   GENOME BIOLOGY

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

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

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

Proteins involved in establishment and maintenance of imprinted methylation marks

(2012) R. Strogantsev et al.   Briefings in Functional Genomics

The Transcriptional and Epigenomic Foundations of Ground State Pluripotency

(2012) Hendrik Marks et al.   CELL

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Trim28 Is Required for Epigenetic Stability During Mouse Oocyte to Embryo Transition

(2012) D. M. Messerschmidt et al.   SCIENCE

Pluripotency in the Embryo and in Culture

(2012) J. Nichols et al.   Cold Spring Harbor Perspectives in Biology

The KRAB-ZFP/KAP1 System Contributes to the Early Embryonic Establishment of Site-Specific DNA Methylation Patterns Maintained during Development

(2012) Simon Quenneville et al.   Cell Reports

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

Zinc Finger Protein ZFP57 Requires Its Co-factor to Recruit DNA Methyltransferases and Maintains DNA Methylation Imprint in Embryonic Stem Cells via Its Transcriptional Repression Domain

(2011) Xiaopan Zuo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional Analysis of KAP1 Genomic Recruitment

(2011) S. Iyengar et al.   MOLECULAR AND CELLULAR BIOLOGY

Maintenance of Silent Chromatin through Replication Requires SWI/SNF-like Chromatin Remodeler SMARCAD1

(2011) Samuel P. Rowbotham 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

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Dynamic CpG island methylation landscape in oocytes and preimplantation embryos

(2011) Sébastien A Smallwood et al.   NATURE GENETICS

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

(2011) Miguel R. Branco et al.   NATURE REVIEWS GENETICS

Genomic imprinting: the emergence of an epigenetic paradigm

(2011) Anne C. Ferguson-Smith   NATURE REVIEWS GENETICS

Mammalian Genomic Imprinting

(2011) M. S. Bartolomei et al.   Cold Spring Harbor Perspectives in Biology

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

KAP1 controls endogenous retroviruses in embryonic stem cells

(2010) Helen M. Rowe 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

GaGa: A parsimonious and flexible model for differential expression analysis

(2009) David Rossell   Annals of Applied Statistics

The HP1α–CAF1–SetDB1-containing complex provides H3K9me1 for Suv39-mediated K9me3 in pericentric heterochromatin

(2009) Alejandra Loyola et al.   EMBO REPORTS

Chromatin mechanisms in genomic imprinting

(2009) Slim Kacem et al.   MAMMALIAN GENOME

Intracisternal A particle genes: Distribution in the mouse genome, active subtypes, and potential roles as species-specific mediators of susceptibility to cancer

(2009) Chunhua Qin et al.   MOLECULAR CARCINOGENESIS

A Maternal-Zygotic Effect Gene, Zfp57, Maintains Both Maternal and Paternal Imprints

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

Hypomethylation of multiple imprinted loci in individuals with transient neonatal diabetes is associated with mutations in ZFP57

(2008) Deborah J G Mackay et al.   NATURE GENETICS

QUMA: quantification tool for methylation analysis

(2008) Y. Kumaki et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY