Active DNA demethylation at enhancers during the vertebrate phylotypic period

Tex10 Coordinates Epigenetic Control of Super-Enhancer Activity in Pluripotency and Reprogramming

(2015) Junjun Ding et al.   Cell Stem Cell

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Dynamics of DNA Hydroxymethylation in Zebrafish

(2015) Jorke H. Kamstra et al.   Zebrafish

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

(2015) Hyung Joo Lee et al.   Nature Communications

Embryonic transcription is controlled by maternally defined chromatin state

(2015) Saartje Hontelez et al.   Nature Communications

Overlapping Requirements for Tet2 and Tet3 in Normal Development and Hematopoietic Stem Cell Emergence

(2015) Cheng Li et al.   Cell Reports

TET3 Is Recruited by REST for Context-Specific Hydroxymethylation and Induction of Gene Expression

(2015) Arshan Perera et al.   Cell Reports

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

(2014) Miler T. Lee et al.   Annual Review of Cell and Developmental Biology

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   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

TET2 Plays an Essential Role in Erythropoiesis by Regulating Lineage-Specific Genes via DNA Oxidative Demethylation in a Zebrafish Model

(2014) L. Ge et al.   MOLECULAR AND CELLULAR BIOLOGY

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

Synthetic CpG islands reveal DNA sequence determinants of chromatin structure

(2014) Elisabeth Wachter et al.   eLife

High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions

(2014) Arnaud R Krebs et al.   eLife

A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development

(2013) Sarita S Paranjpe et al.   BMC GENOMICS

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Sperm, but Not Oocyte, DNA Methylome Is Inherited by Zebrafish Early Embryos

(2013) Lan Jiang et al.   CELL

Dynamic Readers for 5-(Hydroxy)Methylcytosine and Its Oxidized Derivatives

(2013) Cornelia G. Spruijt et al.   CELL

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

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

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

The Hourglass and the Early Conservation Models—Co-Existing Patterns of Developmental Constraints in Vertebrates

(2013) Barbara Piasecka et al.   PLoS Genetics

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Tet3 CXXC Domain and Dioxygenase Activity Cooperatively Regulate Key Genes for Xenopus Eye and Neural Development

(2012) Yufei Xu 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

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

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

(2012) Zachary D. Smith et al.   NATURE

Reprogramming DNA methylation in the mammalian life cycle: building and breaking epigenetic barriers

(2012) S. Seisenberger et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2012) Ingrid S Andersen et al.   GENOME BIOLOGY

Tet2 Loss Leads to Increased Hematopoietic Stem Cell Self-Renewal and Myeloid Transformation

(2011) Kelly Moran-Crusio et al.   CANCER CELL

Primate CpG Islands Are Maintained by Heterogeneous Evolutionary Regimes Involving Minimal Selection

(2011) Netta Mendelson Cohen et al.   CELL

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

Prepatterning of Developmental Gene Expression by Modified Histones before Zygotic Genome Activation

(2011) Leif C. Lindeman et al.   DEVELOPMENTAL CELL

Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis

(2011) A. Pauli et al.   GENOME RESEARCH

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Dual functions of Tet1 in transcriptional regulation in mouse embryonic stem cells

(2011) Hao Wu et al.   NATURE

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

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

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

(2011) Naoki Irie et al.   Nature Communications

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Gene expression divergence recapitulates the developmental hourglass model

(2010) Alex T. Kalinka et al.   NATURE

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns

(2010) Tomislav Domazet-Lošo et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton 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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Combination of FASP and StageTip-Based Fractionation Allows In-Depth Analysis of the Hippocampal Membrane Proteome

(2009) Jacek R. Wiśniewski et al.   JOURNAL OF PROTEOME RESEARCH

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

DNA Demethylation in Zebrafish Involves the Coupling of a Deaminase, a Glycosylase, and Gadd45

(2008) Kunal Rai et al.   CELL

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

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

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH