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

Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

(2016) Erin E. Swinstead et al.   BIOESSAYS

Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development

(2016) Falong Lu et al.   CELL

Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming

(2016) Sören Boller et al.   IMMUNITY

OCT4 Acts as an Integrator of Pluripotency and Signal-Induced Differentiation

(2016) Zoltan Simandi et al.   MOLECULAR CELL

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

Genome-wide nucleosome specificity and function of chromatin remodellers in ES cells

(2016) Maud de Dieuleveult et al.   NATURE

The landscape of accessible chromatin in mammalian preimplantation embryos

(2016) Jingyi Wu et al.   NATURE

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Multiphasic and Dynamic Changes in Alternative Splicing during Induction of Pluripotency Are Coordinated by Numerous RNA-Binding Proteins

(2016) Benjamin Cieply et al.   Cell Reports

Hierarchical Oct4 Binding in Concert with Primed Epigenetic Rearrangements during Somatic Cell Reprogramming

(2016) Jun Chen et al.   Cell Reports

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

(2015) Abdenour Soufi et al.   CELL

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

(2015) Sarah J. Hainer et al.   GENES & DEVELOPMENT

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

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

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Pluripotency Transcription Factor Oct4 Mediates Stepwise Nucleosome Demethylation and Depletion

(2015) Arvind Shakya et al.   MOLECULAR AND CELLULAR BIOLOGY

Ascl1 Coordinately Regulates Gene Expression and the Chromatin Landscape during Neurogenesis

(2015) Alexandre A.S.F. Raposo et al.   Cell Reports

Regulation of Nucleosome Architecture and Factor Binding Revealed by Nuclease Footprinting of the ESC Genome

(2015) Sarah J. Hainer et al.   Cell Reports

The Chromatin Remodeler CHD8 Is Required for Activation of Progesterone Receptor-Dependent Enhancers

(2015) María Ceballos-Chávez et al.   PLoS Genetics

Unbiased chromatin accessibility profiling by RED-seq uncovers unique features of nucleosome variants in vivo

(2015) Poshen B Chen et al.   BMC GENOMICS

INO80 Facilitates Pluripotency Gene Activation in Embryonic Stem Cell Self-Renewal, Reprogramming, and Blastocyst Development

(2014) Li Wang et al.   Cell Stem Cell

Reorganization of Enhancer Patterns in Transition from Naive to Primed Pluripotency

(2014) Christa Buecker et al.   Cell Stem Cell

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila

(2014) Z. Xu et al.   GENES & DEVELOPMENT

Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

(2014) Simone Picelli et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Evolution of transcription factor binding in metazoans — mechanisms and functional implications

(2014) Diego Villar et al.   NATURE REVIEWS GENETICS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Mechanism governing a stem cell-generating cis-regulatory element

(2014) R. Sanalkumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

(2014) Shen-Hsi Yang et al.   Cell Reports

Transcriptional Repression by the BRG1-SWI/SNF Complex Affects the Pluripotency of Human Embryonic Stem Cells

(2014) Xiaoli Zhang et al.   Stem Cell Reports

Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons

(2013) Orly L. Wapinski et al.   CELL

Context-Dependent Wiring of Sox2 Regulatory Networks for Self-Renewal of Embryonic and Trophoblast Stem Cells

(2013) Kenjiro Adachi et al.   MOLECULAR CELL

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

Mechanisms and models of somatic cell reprogramming

(2013) Yosef Buganim et al.   NATURE REVIEWS GENETICS

Dynamic regulation of transcriptional states by chromatin and transcription factors

(2013) Ty C. Voss et al.   NATURE REVIEWS GENETICS

SWI/SNF Enzymes Promote SOX10- Mediated Activation of Myelin Gene Expression

(2013) Himangi G. Marathe et al.   PLoS One

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Abdenour Soufi et al.   CELL

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

Nucleosome-Driven Transcription Factor Binding and Gene Regulation

(2012) Cecilia Ballaré et al.   MOLECULAR CELL

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

(2012) Anca M Farcas et al.   eLife

Oct4 links multiple epigenetic pathways to the pluripotency network

(2011) Junjun Ding et al.   CELL RESEARCH

Pioneer transcription factors: establishing competence for gene expression

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

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

(2011) W. Wu et al.   GENOME RESEARCH

Transcription Factor AP1 Potentiates Chromatin Accessibility and Glucocorticoid Receptor Binding

(2011) Simon C. Biddie et al.   MOLECULAR CELL

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

(2011) Lena Ho et al.   NATURE CELL BIOLOGY

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

OCT4 establishes and maintains nucleosome-depleted regions that provide additional layers of epigenetic regulation of its target genes

(2011) J. S. You et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Concise Review: Oct4 and More: The Reprogramming Expressway

(2011) Jared Sterneckert et al.   STEM CELLS

Pioneer factors: directing transcriptional regulators within the chromatin environment

(2011) Luca Magnani et al.   TRENDS IN GENETICS

Combinatorial Binding in Human and Mouse Embryonic Stem Cells Identifies Conserved Enhancers Active in Early Embryonic Development

(2011) Jonathan Göke et al.   PLoS Computational Biology

Chromatin-Remodeling Components of the BAF Complex Facilitate Reprogramming

(2010) Nishant Singhal et al.   CELL

An Oct4-Centered Protein Interaction Network in Embryonic Stem Cells

(2010) Debbie L.C. van den Berg et al.   Cell Stem Cell

An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease

(2010) Mercedes Pardo et al.   Cell Stem Cell

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Chromatin Landscape Dictates HSF Binding to Target DNA Elements

(2010) Michael J. Guertin et al.   PLoS Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MEME SUITE: tools for motif discovery and searching

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

An embryonic stem cell chromatin remodeling complex, esBAF, is an essential component of the core pluripotency transcriptional network

(2009) L. Ho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Different gene regulation strategies revealed by analysis of binding motifs

(2009) Zeba Wunderlich et al.   TRENDS IN GENETICS

FoxA1 Translates Epigenetic Signatures into Enhancer-Driven Lineage-Specific Transcription

(2008) Mathieu Lupien et al.   CELL

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

SWI/SNF-Brg1 Regulates Self-Renewal and Occupies Core Pluripotency-Related Genes in Embryonic Stem Cells

(2008) Benjamin L. Kidder et al.   STEM CELLS