Drosophilapoised enhancers are generated during tissue patterning with the help of repression

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

(2016) Manuel Beltran et al.   GENOME RESEARCH

Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body

(2016) Masaki Hosogane et al.   Cell Reports

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

(2015) Allen Wang et al.   Cell Stem Cell

Morphogen rules: design principles of gradient-mediated embryo patterning

(2015) J. Briscoe et al.   DEVELOPMENT

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

Transcriptional regulators form diverse groups with context-dependent regulatory functions

(2015) Gerald Stampfel et al.   NATURE

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

BMP gradients: A paradigm for morphogen-mediated developmental patterning

(2015) E. Bier et al.   SCIENCE

Enhancer repertoires are reshaped independently of early priming and heterochromatin dynamics during B cell differentiation

(2015) Mohamed-Amin Choukrallah et al.   Nature Communications

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Su(H)-Mediated Repression Positions Gene Boundaries along the Dorsal-Ventral Axis of Drosophila Embryos

(2014) Anil Ozdemir et al.   DEVELOPMENTAL CELL

Transcriptional Activation Is a Conserved Feature of the Early Embryonic Factor Zelda That Requires a Cluster of Four Zinc Fingers for DNA Binding and a Low-complexity Activation Domain

(2014) Danielle C. Hamm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Ultrasensitivity part I: Michaelian responses and zero-order ultrasensitivity

(2014) James E. Ferrell et al.   TRENDS IN BIOCHEMICAL SCIENCES

Cooperativity, Specificity, and Evolutionary Stability of Polycomb Targeting in Drosophila

(2014) Bernd Schuettengruber et al.   Cell Reports

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

(2014) Xiao-Yong Li et al.   eLife

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

A Schnurri/Mad/Medea complex attenuates the dorsal–twist gradient readout at vnd

(2013) Justin Crocker et al.   DEVELOPMENTAL BIOLOGY

Occupying Chromatin: Polycomb Mechanisms for Getting to Genomic Targets, Stopping Transcriptional Traffic, and Staying Put

(2013) Jeffrey A. Simon et al.   MOLECULAR CELL

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Spatial expression of transcription factors in Drosophila embryonic organ development

(2013) Ann S Hammonds et al.   GENOME BIOLOGY

Pattern Formation by Graded and Uniform Signals in the Early Drosophila Embryo

(2012) Jitendra S. Kanodia et al.   BIOPHYSICAL JOURNAL

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage

(2012) Joseph A. Wamstad et al.   CELL

RTK signaling modulates the Dorsal gradient

(2012) A. Helman et al.   DEVELOPMENT

HOT regions function as patterned developmental enhancers and have a distinct cis-regulatory signature

(2012) E. Z. Kvon et al.   GENES & DEVELOPMENT

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Enhancer decommissioning by LSD1 during embryonic stem cell differentiation

(2012) Warren A. Whyte et al.   NATURE

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression

(2012) Bjoern Gaertner et al.   Cell Reports

Preferential Genome Targeting of the CBP Co-Activator by Rel and Smad Proteins in Early Drosophila melanogaster Embryos

(2012) Per-Henrik Holmqvist et al.   PLoS Genetics

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

(2011) Li M. Li et al.   CURRENT BIOLOGY

Pioneer transcription factors: establishing competence for gene expression

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

High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation

(2011) A. Ozdemir et al.   GENOME RESEARCH

Epigenetic signatures distinguish multiple classes of enhancers with distinct cellular functions

(2011) Gabriel E. Zentner et al.   GENOME RESEARCH

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

modMine: flexible access to modENCODE data

(2011) S. Contrino et al.   NUCLEIC ACIDS RESEARCH

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

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

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Groucho-Mediated Repression May Result from a Histone Deacetylase-Dependent Increase in Nucleosome Density

(2010) Clint J. Winkler et al.   PLoS One

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Anatomy of Polycomb and Trithorax Chromatin Landscapes in Drosophila Embryos

(2009) Bernd Schuettengruber et al.   PLOS BIOLOGY

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Signal-Induced Repression: The Exception or the Rule in Developmental Signaling?

(2008) Markus Affolter et al.   DEVELOPMENTAL CELL

Dynamic Regulation by Polycomb Group Protein Complexes Controls Pattern Formation and the Cell Cycle in Drosophila

(2008) Katarzyna Oktaba et al.   DEVELOPMENTAL CELL

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

(2008) Hsiao-Lan Liang et al.   NATURE

How the Dorsal gradient works: Insights from postgenome technologies

(2008) J.-W. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY