Genetic determinants and epigenetic effects of pioneer-factor occupancy

Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci

(2017) Ziying Liu et al.   MOLECULAR CELL

Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

(2016) Erin E. Swinstead et al.   CELL

Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & 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

Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering

(2016) Yu Zhang et al.   NATURE GENETICS

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

(2016) Kamila M. Jozwik et al.   Cell Reports

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

(2015) Abdenour Soufi et al.   CELL

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

TNFα Signaling Exposes Latent Estrogen Receptor Binding Sites to Alter the Breast Cancer Cell Transcriptome

(2015) Hector L. Franco et al.   MOLECULAR CELL

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Pioneer transcription factors in cell reprogramming

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

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

The simplest explanation: passive DNA demethylation in PGCs

(2013) Zachary D Smith et al.   EMBO JOURNAL

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

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

DNA methylation: roles in mammalian development

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

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

(2012) Abdenour Soufi et al.   CELL

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

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

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman 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

Inferring direct DNA binding from ChIP-seq

(2012) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Pioneer transcription factors: establishing competence for gene expression

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

Epigenetic switch involved in activation of pioneer factor FOXA1-dependent enhancers

(2011) A. A. Serandour et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

The nucleosome map of the mammalian liver

(2011) Zhaoyu Li et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comparative Epigenomic Analysis of Murine and Human Adipogenesis

(2010) Tarjei S. Mikkelsen et al.   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

FOXA1 is a key determinant of estrogen receptor function and endocrine response

(2010) Antoni Hurtado et al.   NATURE GENETICS

Nucleosome-binding affinity as a primary determinant of the nuclear mobility of the pioneer transcription factor FoxA

(2009) T. Sekiya et al.   GENES & DEVELOPMENT

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

(2008) Mathieu Lupien et al.   CELL

Visualizing Spatiotemporal Dynamics of Multicellular Cell-Cycle Progression

(2008) Asako Sakaue-Sawano et al.   CELL

Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site

(2008) Geetu Tuteja et al.   NUCLEIC ACIDS RESEARCH