Low-affinity transcription factor binding sites shape morphogen responses and enhancer evolution

Olig2 Targets Chromatin Remodelers to Enhancers to Initiate Oligodendrocyte Differentiation

(2013) Yang Yu et al.   CELL

In Vivo Epigenomic Profiling of Germ Cells Reveals Germ Cell Molecular Signatures

(2013) Jia-Hui Ng et al.   DEVELOPMENTAL CELL

Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

(2013) C. D. Arnold et al.   SCIENCE

Characterization of Enhancer Function from Genome-Wide Analyses

(2012) Glenn A. Maston et al.   Annual Review of Genomics and Human Genetics

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

(2012) Guillaume Junion et al.   CELL

Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube

(2012) Nikolaos Balaskas et al.   CELL

Mechanistic Differences in the Transcriptional Interpretation of Local and Long-Range Shh Morphogen Signaling

(2012) Tony Oosterveen et al.   DEVELOPMENTAL CELL

Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning

(2012) K. A. Peterson et al.   GENES & DEVELOPMENT

What does our genome encode?

(2012) J. A. Stamatoyannopoulos   GENOME RESEARCH

A model of spatially restricted transcription in opposing gradients of activators and repressors

(2012) Michael A White et al.   Molecular Systems Biology

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wnt/Wingless Signaling in Drosophila

(2012) S. Swarup et al.   Cold Spring Harbor Perspectives in Biology

Gli Proteins in Development and Disease

(2011) Chi-chung Hui et al.   Annual Review of Cell and Developmental Biology

Evolution of Gene Regulatory Networks Controlling Body Plan Development

(2011) Isabelle S. Peter et al.   CELL

Rapid Evolutionary Rewiring of a Structurally Constrained Eye Enhancer

(2011) Christina I. Swanson et al.   CURRENT BIOLOGY

Spatiotemporal mechanisms of morphogen gradient interpretation

(2011) Marcos Nahmad et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Animal Transcription Networks as Highly Connected, Quantitative Continua

(2011) Mark D. Biggin   DEVELOPMENTAL CELL

Evolutionary Origins of Transcription Factor Binding Site Clusters

(2011) Xin He et al.   MOLECULAR BIOLOGY AND EVOLUTION

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Mechanisms and functions of Hedgehog signalling across the metazoa

(2011) Philip W. Ingham et al.   NATURE REVIEWS GENETICS

Understanding morphogenetic growth control — lessons from flies

(2011) Ortrud Wartlick et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity

(2011) D. S. Parker et al.   Science Signaling

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

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

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

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Structural Rules and Complex Regulatory Circuitry Constrain Expression of a Notch- and EGFR-Regulated Eye Enhancer

(2010) Christina I. Swanson et al.   DEVELOPMENTAL CELL

Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity

(2010) S. Rowan et al.   GENES & DEVELOPMENT

Vectors for efficient and high-throughput construction of fluorescent drosophila reporters using the PhiC31 site-specific integration system

(2010) Aurelia L. Boy et al.   GENESIS

Conservation and regulatory associations of a wide affinity range of mouse transcription factor binding sites

(2010) Savina A. Jaeger et al.   GENOMICS

Positional information and patterning revisited

(2010) Lewis Wolpert   JOURNAL OF THEORETICAL BIOLOGY

ChIP-Seq identification of weakly conserved heart enhancers

(2010) Matthew J Blow et al.   NATURE GENETICS

Conserved noncoding elements and the evolution of animal body plans

(2009) Tanya Vavouri et al.   BIOESSAYS

Comparative genomics of gene regulation—conservation and divergence of cis-regulatory information

(2009) Antonio CA Meireles-Filho et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Wingless and Hedgehog signaling pathways regulate orthodenticle and eyes absent during ocelli development in Drosophila

(2009) Jorge Blanco et al.   DEVELOPMENTAL BIOLOGY

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Rapid detection and curation of conserved DNA via enhanced-BLAT and EvoPrinterHD analysis

(2008) Amarendra S Yavatkar et al.   BMC GENOMICS

Cellular Trafficking of the Glypican Dally-like Is Required for Full-Strength Hedgehog Signaling and Wingless Transcytosis

(2008) Armel Gallet et al.   DEVELOPMENTAL CELL

GLI2-specific Transcriptional Activation of the Bone Morphogenetic Protein/Activin Antagonist Follistatin in Human Epidermal Cells

(2008) Thomas Eichberger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Evolution of Eukaryotic Transcription Circuits

(2008) B. B. Tuch et al.   SCIENCE