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

Placeholder Nucleosomes Underlie Germline-to-Embryo DNA Methylation Reprogramming

(2018) Patrick J. Murphy et al.   CELL

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

(2018) Lei Gao et al.   CELL

Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming

(2018) Rui Li et al.   GENES & DEVELOPMENT

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

(2018) Guifen Liu et al.   GENOME RESEARCH

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

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation

(2016) Makiko Iwafuchi-Doi et al.   MOLECULAR CELL

C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4

(2016) Bruno Di Stefano et al.   NATURE CELL BIOLOGY

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

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

(2015) Abdenour Soufi 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

Nonconsensus Protein Binding to Repetitive DNA Sequence Elements Significantly Affects Eukaryotic Genomes

(2015) Ariel Afek et al.   PLoS Computational Biology

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

(2014) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

Two independent transcription initiation codes overlap on vertebrate core promoters

(2014) Vanja Haberle et al.   NATURE

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2013) Warren A. Whyte et al.   CELL

Canonical nucleosome organization at promoters forms during genome activation

(2013) Y. Zhang et al.   GENOME RESEARCH

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

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

(2013) Miler T. Lee et al.   NATURE

C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells

(2013) Bruno Di Stefano et al.   NATURE

Nucleosomes accelerate transcription factor dissociation

(2013) Y. Luo et al.   NUCLEIC ACIDS RESEARCH

Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates

(2013) M. Leichsenring et al.   SCIENCE

Structural features based genome-wide characterization and prediction of nucleosome organization

(2012) Yanglan Gan et al.   BMC BIOINFORMATICS

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

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

DNA Sequence Correlations Shape Nonspecific Transcription Factor-DNA Binding Affinity

(2011) Itamar Sela et al.   BIOPHYSICAL JOURNAL

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Pou5f1 contributes to dorsoventral patterning by positive regulation of vox and modulation of fgf8a expression

(2011) Heinz-Georg Belting et al.   DEVELOPMENTAL BIOLOGY

Structural Constraints in Collaborative Competition of Transcription Factors against the Nucleosome

(2011) Georgette Moyle-Heyrman et al.   JOURNAL OF MOLECULAR BIOLOGY

A cis-Regulatory Signature in Ascidians and Flies, Independent of Transcription Factor Binding Sites

(2010) Pierre Khoueiry et al.   CURRENT BIOLOGY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development

(2010) Daria Onichtchouk et al.   Molecular Systems Biology

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Nucleosome dynamics define transcriptional enhancers

(2010) Housheng Hansen He et al.   NATURE GENETICS

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

High Nucleosome Occupancy Is Encoded at Human Regulatory Sequences

(2010) Desiree Tillo et al.   PLoS One

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

G+C content dominates intrinsic nucleosome occupancy

(2009) Desiree Tillo et al.   BMC BIOINFORMATICS

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

(2009) W. Tadros et al.   DEVELOPMENT

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Organization of developmental enhancers in the Drosophila embryo

(2009) Dmitri Papatsenko et al.   NUCLEIC ACIDS RESEARCH

Low nucleosome occupancy is encoded around functional human transcription factor binding sites

(2008) Floris Daenen et al.   BMC GENOMICS

Autoregulatory loop and retinoic acid repression regulatepou2/pou5f1 gene expression in the zebrafish embryonic brain

(2008) Mst. Shahnaj Parvin et al.   DEVELOPMENTAL DYNAMICS

Sequence-dependent Nucleosome Positioning

(2008) Ho-Ryun Chung et al.   JOURNAL OF MOLECULAR BIOLOGY

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

(2008) Hsiao-Lan Liang et al.   NATURE

The DNA-encoded nucleosome organization of a eukaryotic genome

(2008) Noam Kaplan et al.   NATURE

Distinct Modes of Regulation by Chromatin Encoded through Nucleosome Positioning Signals

(2008) Yair Field et al.   PLoS Computational Biology