Genomic insights into chromatin reprogramming to totipotency in embryos

A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity

(2018) Michelle Percharde et al.   CELL

Chromatin Accessibility Landscape in Human Early Embryos and Its Association with Evolution

(2018) Lei Gao et al.   CELL

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

Pioneering the chromatin landscape

(2018) Kenneth S. Zaret   NATURE GENETICS

Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment

(2018) Qianhua Xu et al.   TRENDS IN CELL BIOLOGY

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

(2017) Moritz Mall et al.   NATURE

Maternal H3K27me3 controls DNA methylation-independent imprinting

(2017) Azusa Inoue et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Genome editing reveals a role for OCT4 in human embryogenesis

(2017) Norah M. E. Fogarty 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

Conservation and innovation in the DUX4-family gene network

(2017) Jennifer L Whiddon et al.   NATURE GENETICS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture

(2017) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

Shaping development by stochasticity and dynamics in gene regulation

(2017) Peng Dong et al.   Open Biology

rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline

(2017) Devanshi Jain et al.   PLoS Genetics

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

(2017) Hamish W King et al.   eLife

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

A Surveillance Mechanism Ensures Repair of DNA Lesions during Zygotic Reprogramming

(2016) Sabrina Ladstätter et al.   CELL

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

In Vivo Cellular Reprogramming: The Next Generation

(2016) Deepak Srivastava et al.   CELL

Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development

(2016) Máté Borsos et al.   GENES & DEVELOPMENT

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

Allelic reprogramming of the histone modification H3K4me3 in early mammalian development

(2016) Bingjie Zhang et al.   NATURE

Broad histone H3K4me3 domains in mouse oocytes modulate maternal-to-zygotic transition

(2016) John Arne Dahl et al.   NATURE

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

De novo DNA methylation drives 5hmC accumulation in mouse zygotes

(2016) Rachel Amouroux et al.   NATURE CELL BIOLOGY

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Transferable model for chromosome architecture

(2016) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The DNA methyltransferase DNMT3C protects male germ cells from transposon activity

(2016) Joan Barau et al.   SCIENCE

MERVL/Zscan4 Network Activation Results in Transient Genome-wide DNA Demethylation of mESCs

(2016) Mélanie A. Eckersley-Maslin et al.   Cell Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Making Sense of Transcription Networks

(2015) Trevor R. Sorrells et al.   CELL

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Continuous Histone Replacement by Hira Is Essential for Normal Transcriptional Regulation and De Novo DNA Methylation during Mouse Oogenesis

(2015) Buhe Nashun et al.   MOLECULAR CELL

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

(2015) Wenfei Jin et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Present and future challenges of induced pluripotent stem cells

(2015) Mari Ohnuki et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly

(2015) Takashi Ishiuchi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Maternal TET3 is dispensable for embryonic development but is required for neonatal growth

(2015) Yu-ichi Tsukada et al.   Scientific Reports

Haploinsufficiency, but Not Defective Paternal 5mC Oxidation, Accounts for the Developmental Defects of Maternal Tet3 Knockouts

(2015) Azusa Inoue et al.   Cell Reports

Histone H3 Variants and Their Chaperones During Development and Disease: Contributing to Epigenetic Control

(2014) Dan Filipescu et al.   Annual Review of Cell and Developmental Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao 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

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

(2014) Fan Guo et al.   Cell Stem Cell

Chemical Methods for Decoding Cytosine Modifications in DNA

(2014) Michael J. Booth et al.   CHEMICAL REVIEWS

Hira-Mediated H3.3 Incorporation Is Required for DNA Replication and Ribosomal RNA Transcription in the Mouse Zygote

(2014) Chih-Jen Lin et al.   DEVELOPMENTAL CELL

High-Resolution Mapping of Chromatin Packaging in Mouse Embryonic Stem Cells and Sperm

(2014) Benjamin R. Carone et al.   DEVELOPMENTAL CELL

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Gene regulatory networks and epigenetic modifications in cell differentiation

(2014) Siddhartha Roy et al.   IUBMB LIFE

The DNA methylation landscape of human early embryos

(2014) Hongshan Guo et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

Genome-wide Bisulfite Sequencing in Zygotes Identifies Demethylation Targets and Maps the Contribution of TET3 Oxidation

(2014) Julian R. Peat et al.   Cell Reports

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Chromatin dynamics during spermiogenesis

(2013) Christina Rathke et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

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

(2013) Cornelia G. Spruijt et al.   CELL

Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition

(2013) Miler T. Lee et al.   NATURE

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Totipotency: What It Is and What It Is Not

(2013) Maureen L. Condic   STEM CELLS AND DEVELOPMENT

Active demethylation in mouse zygotes involves cytosine deamination and base excision repair

(2013) Fátima Santos et al.   Epigenetics & Chromatin

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

(2013) Mario Iurlaro et al.   GENOME BIOLOGY

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

Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3-mediated 5-methylcytosine oxidation

(2012) Azusa Inoue et al.   CELL RESEARCH

Analysis of human embryos from zygote to blastocyst reveals distinct gene expression patterns relative to the mouse

(2012) Kathy K. Niakan et al.   DEVELOPMENTAL BIOLOGY

Time-lapse monitoring as a tool for clinical embryo assessment

(2012) K. Kirkegaard et al.   HUMAN REPRODUCTION

The promise of induced pluripotent stem cells in research and therapy

(2012) Daisy A. Robinton et al.   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Perceiving the epigenetic landscape through histone readers

(2012) Catherine A Musselman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

Epigenetic reprogramming and development: a unique heterochromatin organization in the preimplantation mouse embryo

(2011) A. Burton et al.   Briefings in Functional Genomics

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Genome-wide “Re”-Modeling of Nucleosome Positions

(2011) Ronen Sadeh et al.   CELL

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

(2011) Azusa Inoue et al.   CELL RESEARCH

Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development

(2011) R. Vassena et al.   DEVELOPMENT

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

The role of Tet3 DNA dioxygenase in epigenetic reprogramming by oocytes

(2011) Tian-Peng Gu et al.   NATURE

Gas6 Downregulation Impaired Cytoplasmic Maturation and Pronuclear Formation Independent to the MPF Activity

(2011) Kyeoung-Hwa Kim et al.   PLoS One

Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine

(2011) Khursheed Iqbal 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-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

(2011) Mark Wossidlo et al.   Nature Communications

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA

(2010) Colm Nestor et al.   BIOTECHNIQUES

Stepwise Histone Replacement by SWR1 Requires Dual Activation with Histone H2A.Z and Canonical Nucleosome

(2010) Ed Luk et al.   CELL

Lack of maternal Heat Shock Factor 1 results in multiple cellular and developmental defects, including mitochondrial damage and altered redox homeostasis, and leads to reduced survival of mammalian oocytes and embryos

(2010) Christiane Bierkamp et al.   DEVELOPMENTAL BIOLOGY

Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes

(2010) Mark Wossidlo et al.   EMBO JOURNAL

Non-invasive imaging of human embryos before embryonic genome activation predicts development to the blastocyst stage

(2010) Connie C Wong et al.   NATURE BIOTECHNOLOGY

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

(2010) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

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

(2010) Kashif Ahmed et al.   PLoS One

Prediction of embryonic developmental competence by time-lapse observation and ‘shortest-half’ analysis

(2010) Amir Arav et al.   REPRODUCTIVE BIOMEDICINE ONLINE

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

(2010) P. Hajkova et al.   SCIENCE

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

(2009) W. Tadros et al.   DEVELOPMENT

Nucleosome positioning: How is it established, and why does it matter?

(2009) Marta Radman-Livaja et al.   DEVELOPMENTAL BIOLOGY

Mouse ZAR1-like (XM_359149) colocalizes with mRNA processing components and its dominant-negative mutant caused two-cell-stage embryonic arrest

(2009) Jianjun Hu et al.   DEVELOPMENTAL DYNAMICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

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

(2009) M. Tahiliani et al.   SCIENCE

Essential role for Argonaute2 protein in mouse oogenesis

(2009) Masahiro Kaneda et al.   Epigenetics & Chromatin

Time-lapse cinematography of dynamic changes occurring during in vitro development of human embryos

(2008) Yasuyuki Mio et al.   AMERICAN JOURNAL OF OBSTETRICS AND GYNECOLOGY

Maternal and zygotic Dnmt1 are necessary and sufficient for the maintenance of DNA methylation imprints during preimplantation development

(2008) R. Hirasawa et al.   GENES & DEVELOPMENT

The four blastomeres of a 4-cell stage human embryo are able to develop individually into blastocysts with inner cell mass and trophectoderm

(2008) H. Van de Velde et al.   HUMAN REPRODUCTION

Maternal Argonaute 2 Is Essential for Early Mouse Development at the Maternal-Zygotic Transition

(2008) Karin Lykke-Andersen et al.   MOLECULAR BIOLOGY OF THE CELL

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE

Evidence for conserved DNA and histone H3 methylation reprogramming in mouse, bovine and rabbit zygotes

(2008) Konstantin Lepikhov et al.   Epigenetics & Chromatin