The epigenome in pluripotency and differentiation

X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming

(2013) Derek Lessing et al.   Annual Review of Genomics and Human Genetics

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

X-Inactivation, Imprinting, and Long Noncoding RNAs in Health and Disease

(2013) Jeannie T. Lee et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer

(2013) Masahito Tachibana et al.   CELL

Tight correlation of 5-hydroxymethylcytosine and Polycomb marks in health and disease

(2013) Michael Haffner et al.   CELL CYCLE

Dynamic Chromatin Remodeling Mediated by Polycomb Proteins Orchestrates Pancreatic Differentiation of Human Embryonic Stem Cells

(2013) Ruiyu Xie et al.   Cell Stem Cell

Epigenetic and genetic alterations of the imprinting disorder Beckwith–Wiedemann syndrome and related disorders

(2013) Hidenobu Soejima et al.   JOURNAL OF HUMAN GENETICS

AID stabilizes stem-cell phenotype by removing epigenetic memory of pluripotency genes

(2013) Ritu Kumar et al.   NATURE

XACT, a long noncoding transcript coating the active X chromosome in human pluripotent cells

(2013) Céline Vallot et al.   NATURE GENETICS

DNA methylation: roles in mammalian development

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

DNA methylation dynamics in health and disease

(2013) Yehudit Bergman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Coordinate Regulation of DNA Methylation and H3K27me3 in Mouse Embryonic Stem Cells

(2013) James A. Hagarman et al.   PLoS One

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Identification of Novel Imprinted Differentially Methylated Regions by Global Analysis of Human-Parthenogenetic-Induced Pluripotent Stem Cells

(2013) Yonatan Stelzer et al.   Stem Cell Reports

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

(2012) Miao Yu et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Site-Specific Silencing of Regulatory Elements as a Mechanism of X Inactivation

(2012) J. Mauro Calabrese et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Derivation Conditions Impact X-Inactivation Status in Female Human Induced Pluripotent Stem Cells

(2012) Kiichiro Tomoda et al.   Cell Stem Cell

Molecular Signatures of Human Induced Pluripotent Stem Cells Highlight Sex Differences and Cancer Genes

(2012) Montserrat C. Anguera et al.   Cell Stem Cell

Recurrent Variations in DNA Methylation in Human Pluripotent Stem Cells and Their Differentiated Derivatives

(2012) Kristopher L. Nazor et al.   Cell Stem Cell

Erosion of Dosage Compensation Impacts Human iPSC Disease Modeling

(2012) Shila Mekhoubad et al.   Cell Stem Cell

X-chromosome inactivation in monkey embryos and pluripotent stem cells

(2012) Masahito Tachibana et al.   DEVELOPMENTAL BIOLOGY

The landscape for epigenetic/epigenomic biomedical resources

(2012) Kabita Shakya et al.   Epigenetics

Prader-Willi syndrome

(2012) Suzanne B. Cassidy et al.   GENETICS IN MEDICINE

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA

(2012) Aaron L. Statham et al.   GENOME RESEARCH

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

R-Loop Formation Is a Distinctive Characteristic of Unmethylated Human CpG Island Promoters

(2012) Paul A. Ginno et al.   MOLECULAR CELL

The functions of microRNAs in pluripotency and reprogramming

(2012) Trevor R. Leonardo et al.   NATURE CELL BIOLOGY

Global DNA Hypomethylation Prevents Consolidation of Differentiation Programs and Allows Reversion to the Embryonic Stem Cell State

(2012) Christine S. Schmidt et al.   PLoS One

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

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

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Epigenetic Regulation of Nanog by MiR-302 Cluster-MBD2 Completes Induced Pluripotent Stem Cell Reprogramming

(2012) Man Ryul Lee et al.   STEM CELLS

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

Dynamic Changes in the Copy Number of Pluripotency and Cell Proliferation Genes in Human ESCs and iPSCs during Reprogramming and Time in Culture

(2011) Louise C. Laurent et al.   Cell Stem Cell

Unexpected X Chromosome Skewing during Culture and Reprogramming of Human Somatic Cells Can Be Alleviated by Exogenous Telomerase

(2011) Oz Pomp 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

Transcription and histone methylation changes correlate with imprint acquisition in male germ cells

(2011) Amandine Henckel et al.   EMBO JOURNAL

The effects of culture on genomic imprinting profiles in human embryonic and fetal mesenchymal stem cells

(2011) Jennifer M. Frost et al.   Epigenetics

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

Eutherian mammals use diverse strategies to initiate X-chromosome inactivation during development

(2011) Ikuhiro Okamoto et al.   NATURE

Somatic coding mutations in human induced pluripotent stem cells

(2011) Athurva Gore et al.   NATURE

Copy number variation and selection during reprogramming to pluripotency

(2011) Samer M. Hussein et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Regulation of X-chromosome inactivation by the X-inactivation centre

(2011) Sandrine Augui et al.   NATURE REVIEWS GENETICS

Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation

(2011) Anton Wutz   NATURE REVIEWS GENETICS

Neuronal maturation defect in induced pluripotent stem cells from patients with Rett syndrome

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

De novo DNA methylation: a germ cell perspective

(2011) Sébastien A. Smallwood et al.   TRENDS IN GENETICS

Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes

(2011) Angela M. Mabb et al.   TRENDS IN NEUROSCIENCES

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS Genetics

Derivation of Pre-X Inactivation Human Embryonic Stem Cells under Physiological Oxygen Concentrations

(2010) Christopher J. Lengner et al.   CELL

A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells

(2010) Maria C.N. Marchetto et al.   CELL

Female Human iPSCs Retain an Inactive X Chromosome

(2010) Jason Tchieu et al.   Cell Stem Cell

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

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

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Variations of X Chromosome Inactivation Occur in Early Passages of Female Human Embryonic Stem Cells

(2010) Tamar Dvash et al.   PLoS One

Human embryonic stem cells with biological and epigenetic characteristics similar to those of mouse ESCs

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

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

Chromatin Signatures in Multipotent Human Hematopoietic Stem Cells Indicate the Fate of Bivalent Genes during Differentiation

(2009) Kairong Cui et al.   Cell Stem Cell

Histone Deacetylase Inhibition Elicits an Evolutionarily Conserved Self-Renewal Program in Embryonic Stem Cells

(2009) Carol B. Ware et al.   Cell Stem Cell

KDM1B is a histone H3K4 demethylase required to establish maternal genomic imprints

(2009) David N. Ciccone et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Reprogramming towards pluripotency requires AID-dependent DNA demethylation

(2009) Nidhi Bhutani et al.   NATURE

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

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

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

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL

X-inactivation reveals epigenetic anomalies in most hESC but identifies sublines that initiate as expected

(2008) Lisa L. Hall et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

X-chromosome inactivation and epigenetic fluidity in human embryonic stem cells

(2008) S. S. Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations

(2008) Y. Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA