The epigenome in early vertebrate development

Cell Fate Potential of Human Pluripotent Stem Cells Is Encoded by Histone Modifications

(2011) Seok-Ho Hong et al.   Cell Stem Cell

An essential role for transcription before the MBT in Xenopus laevis

(2011) Jennifer Skirkanich et al.   DEVELOPMENTAL BIOLOGY

Nucleotide composition-linked divergence of vertebrate core promoter architecture

(2011) S. J. van Heeringen et al.   GENOME RESEARCH

Temporal uncoupling of the DNA methylome and transcriptional repression during embryogenesis

(2011) Ozren Bogdanović et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Histone Methylation by PRC2 Is Inhibited by Active Chromatin Marks

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

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Methods for making induced pluripotent stem cells: reprogramming à la carte

(2011) Federico González et al.   NATURE REVIEWS GENETICS

Stage-Specific Histone Modification Profiles Reveal Global Transitions in the Xenopus Embryonic Epigenome

(2011) Tobias D. Schneider et al.   PLoS One

Xenopus research: metamorphosed by genetics and genomics

(2011) Richard M. Harland et al.   TRENDS IN GENETICS

An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation

(2011) Juan J. Tena et al.   Nature Communications

TBP-related factors: a paradigm of diversity in transcription initiation

(2011) Waseem Akhtar et al.   Cell and Bioscience

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Genomic Prevalence of Heterochromatic H3K9me2 and Transcription Do Not Discriminate Pluripotent from Terminally Differentiated Cells

(2011) Florian Lienert et al.   PLoS Genetics

The ground state of pluripotency

(2010) Jason Wray et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

What an epigenome remembers

(2010) Ulrike C. Lange et al.   BIOESSAYS

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Tracing the Derivation of Embryonic Stem Cells from the Inner Cell Mass by Single-Cell RNA-Seq Analysis

(2010) Fuchou Tang et al.   Cell Stem Cell

Geminin cooperates with Polycomb to restrain multi-lineage commitment in the early embryo

(2010) J.-W. Lim et al.   DEVELOPMENT

Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst

(2010) Guoji Guo et al.   DEVELOPMENTAL CELL

β-Catenin Primes Organizer Gene Expression by Recruiting a Histone H3 Arginine 8 Methyltransferase, Prmt2

(2010) Shelby A. Blythe et al.   DEVELOPMENTAL CELL

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

ChIP-Chip Designs to Interrogate the Genome of Xenopus Embryos for Transcription Factor Binding and Epigenetic Regulation

(2010) Robert C. Akkers et al.   PLoS One

Histone H3 Lysine 27 Methylation Asymmetry on Developmentally-Regulated Promoters Distinguish the First Two Lineages in Mouse Preimplantation Embryos

(2010) John Arne Dahl et al.   PLoS One

Targeting of De Novo DNA Methylation Throughout the Oct-4 Gene Regulatory Region in Differentiating Embryonic Stem Cells

(2010) Rodoniki Athanasiadou et al.   PLoS One

Global Chromatin Architecture Reflects Pluripotency and Lineage Commitment in the Early Mouse Embryo

(2010) Kashif Ahmed et al.   PLoS One

Characterization of somatic cell nuclear reprogramming by oocytes in which a linker histone is required for pluripotency gene reactivation

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

Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo

(2010) P. J. Rugg-Gunn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Genome of the Western Clawed Frog Xenopus tropicalis

(2010) U. Hellsten et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Spatio-Temporal Plasticity in Chromatin Organization in Mouse Cell Differentiation and during Drosophila Embryogenesis

(2009) Dipanjan Bhattacharya et al.   BIOPHYSICAL JOURNAL

TBP2 is a substitute for TBP in Xenopus oocyte transcription

(2009) Waseem Akhtar et al.   BMC BIOLOGY

Jarid2/Jumonji Coordinates Control of PRC2 Enzymatic Activity and Target Gene Occupancy in Pluripotent Cells

(2009) Jamy C. Peng et al.   CELL

Molecules that Promote or Enhance Reprogramming of Somatic Cells to Induced Pluripotent Stem Cells

(2009) Bo Feng et al.   Cell Stem Cell

Naive and Primed Pluripotent States

(2009) Jennifer Nichols et al.   Cell Stem Cell

DNA methylation and methyl-CpG binding proteins: developmental requirements and function

(2009) Ozren Bogdanović et al.   CHROMOSOMA

Kruppel-like factor 2 cooperates with the ETS family protein ERG to activate Flk1 expression during vascular development

(2009) S. M. Meadows et al.   DEVELOPMENT

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

A Hierarchy of H3K4me3 and H3K27me3 Acquisition in Spatial Gene Regulation in Xenopus Embryos

(2009) Robert C. Akkers et al.   DEVELOPMENTAL CELL

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis

(2009) J. Armisen et al.   GENOME RESEARCH

Predictive chromatin signatures in the mammalian genome

(2009) G. C. Hon et al.   HUMAN MOLECULAR GENETICS

Histone modifications at human enhancers reflect global cell-type-specific gene expression

(2009) Nathaniel D. Heintzman et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Role of the polycomb protein EED in the propagation of repressive histone marks

(2009) Raphael Margueron et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line

(2009) Harukazu Suzuki et al.   NATURE GENETICS

Massive transcriptional start site analysis of human genes in hypoxia cells

(2009) Katsuya Tsuchihara et al.   NUCLEIC ACIDS RESEARCH

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

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Epigenetic Landscaping During hESC Differentiation to Neural Cells

(2009) Anna Golebiewska et al.   STEM CELLS

Promoter CpG Methylation Contributes to ES Cell Gene Regulation in Parallel with Oct4/Nanog, PcG Complex, and Histone H3 K4/K27 Trimethylation

(2008) Shaun D. Fouse et al.   Cell Stem Cell

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

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

Coordinated regulation of transcriptional repression by the RBP2 H3K4 demethylase and Polycomb-Repressive Complex 2

(2008) D. Pasini et al.   GENES & DEVELOPMENT

Long-range chromosomal interactions and gene regulation

(2008) Adriana Miele et al.   Molecular BioSystems

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

A model for transmission of the H3K27me3 epigenetic mark

(2008) Klaus H. Hansen et al.   NATURE CELL BIOLOGY

Polycomb Repressive Complex 2 Is Dispensable for Maintenance of Embryonic Stem Cell Pluripotency

(2008) Stormy J. Chamberlain et al.   STEM CELLS