Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation

Chromatin accessibility and the regulatory epigenome

(2019) Sandy L. Klemm et al.   NATURE REVIEWS GENETICS

An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

(2019) Longqi Liu et al.   Nature Communications

A cell cycle-coordinated Polymerase II transcription compartment encompasses gene expression before global genome activation

(2019) Yavor Hadzhiev et al.   Nature Communications

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

(2019) Marina Veil et al.   GENOME RESEARCH

Genetic compensation triggered by mutant mRNA degradation

(2019) Mohamed A. El-Brolosy et al.   NATURE

The maternal-to-zygotic transition revisited

(2019) Nadine L. Vastenhouw et al.   DEVELOPMENT

Brd4 and P300 Confer Transcriptional Competency during Zygotic Genome Activation

(2019) Shun Hang Chan et al.   DEVELOPMENTAL CELL

Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

(2019) Michael P. Meers et al.   MOLECULAR CELL

Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis

(2019) Yuko Sato et al.   DEVELOPMENT

Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals

(2019) George E. Gentsch et al.   Nature Communications

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

Inherited DNA methylation primes the establishment of accessible chromatin during genome activation

(2018) Guifen Liu et al.   GENOME RESEARCH

Pioneer transcription factors shape the epigenetic landscape

(2018) Alexandre Mayran et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single-cell multi-omics sequencing of human early embryos

(2018) Lin Li et al.   NATURE CELL BIOLOGY

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo

(2018) Jenna E. Haines et al.   PLoS Genetics

TALE factors use two distinct functional modes to control an essential zebrafish gene expression program

(2018) Franck Ladam et al.   eLife

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Widespread Enhancer Dememorization and Promoter Priming during Parental-to-Zygotic Transition

(2018) Bingjie Zhang et al.   MOLECULAR CELL

Chromatin accessibility dynamics across C. elegans development and ageing

(2018) Jürgen Jänes et al.   eLife

Crowding-induced transcriptional bursts dictate polymerase and nucleosome density profiles along genes

(2017) Aafke A. van den Berg et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

In Vivo Regulation of the Zebrafish Endoderm Progenitor Niche by T-Box Transcription Factors

(2017) Andrew C. Nelson et al.   Cell Reports

mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay

(2017) Jennifer L. Anderson et al.   PLoS Genetics

A high-resolution mRNA expression time course of embryonic development in zebrafish

(2017) Richard J White et al.   eLife

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

(2017) Shai R Joseph et al.   eLife

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes

(2016) Yuvia A. Pérez-Rico et al.   GENOME RESEARCH

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

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

(2015) Abdenour Soufi et al.   CELL

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

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

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Genetic compensation induced by deleterious mutations but not gene knockdowns

(2015) Andrea Rossi et al.   NATURE

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

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

Response to Nodal morphogen gradient is determined by the kinetics of target gene induction

(2015) Julien Dubrulle et al.   eLife

Global identification of Smad2 and Eomesodermin targets in zebrafish identifies a conserved transcriptional network in mesendoderm and a novel role for Eomesodermin in repression of ectodermal gene expression

(2014) Andrew C Nelson et al.   BMC BIOLOGY

Histone-Fold Domain Protein NF-Y Promotes Chromatin Accessibility for Cell Type-Specific Master Transcription Factors

(2014) Andrew J. Oldfield et al.   MOLECULAR CELL

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

Chromatin state dynamics during blood formation

(2014) D. Lara-Astiaso et al.   SCIENCE

The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species

(2014) Patricia Heyn et al.   Cell Reports

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

(2013) Daniel J. McKay et al.   DEVELOPMENTAL CELL

Pou5f1 protein expression and posttranslational modification during early zebrafish development

(2013) Bernadette Lippok et al.   DEVELOPMENTAL DYNAMICS

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

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

(2013) Miler T. Lee et al.   NATURE

A unique Oct4 interface is crucial for reprogramming to pluripotency

(2013) Daniel Esch et al.   NATURE CELL BIOLOGY

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

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

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

(2012) Abdenour Soufi et al.   CELL

Nanog-like Regulates Endoderm Formation through the Mxtx2-Nodal Pathway

(2012) Cong Xu et al.   DEVELOPMENTAL CELL

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

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

(2012) O. Bogdanovic et al.   GENOME RESEARCH

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins

(2012) Natalia Tapia et al.   Nature Communications

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

(2012) Ingrid S Andersen et al.   GENOME BIOLOGY

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 chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

no tail integrates two modes of mesoderm induction

(2010) S. A. Harvey et al.   DEVELOPMENT

Chromatin signature of embryonic pluripotency is established during genome activation

(2010) Nadine L. Vastenhouw et al.   NATURE

RNA polymerase complexes cooperate to relieve the nucleosomal barrier and evict histones

(2010) O. I. Kulaeva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

B1 SOX Coordinate Cell Specification with Patterning and Morphogenesis in the Early Zebrafish Embryo

(2010) Yuichi Okuda et al.   PLoS Genetics

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY