patterning provide context and positional information in Shh-directed neural Neural-specific Sox 2 input and differential Gli-binding affinity

[1]  J. Ericson,et al.  Mechanistic differences in the transcriptional interpretation of local and long-range Shh morphogen signaling. , 2012, Developmental cell.

[2]  Johan Ericson,et al.  Genome-wide characterization of Foxa2 targets reveals upregulation of floor plate genes and repression of ventrolateral genes in midbrain dopaminergic progenitors , 2012, Development.

[3]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[4]  A. McMahon,et al.  An embryonic stem cell‐based system for rapid analysis of transcriptional enhancers , 2012, Genesis.

[5]  James Briscoe,et al.  Gene Regulatory Logic for Reading the Sonic Hedgehog Signaling Gradient in the Vertebrate Neural Tube , 2012, Cell.

[6]  R. Sandberg,et al.  Sequentially acting Sox transcription factors in neural lineage development. , 2011, Genes & development.

[7]  Hui Wang,et al.  Tcf/Lef repressors differentially regulate Shh-Gli target gene activation thresholds to generate progenitor patterning in the developing CNS , 2011, Development.

[8]  A. McMahon,et al.  Overlapping roles and collective requirement for the coreceptors GAS1, CDO, and BOC in SHH pathway function. , 2011, Developmental cell.

[9]  Matt Thomson,et al.  Pluripotency Factors in Embryonic Stem Cells Regulate Differentiation into Germ Layers , 2011, Cell.

[10]  Andrea I. Ramos,et al.  The cis-Regulatory Logic of Hedgehog Gradient Responses: Key Roles for Gli Binding Affinity, Competition, and Cooperativity , 2011, Science Signaling.

[11]  E. Metzakopian,et al.  Foxa1 and Foxa2 positively and negatively regulate Shh signalling to specify ventral midbrain progenitor identity , 2011, Mechanisms of Development.

[12]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[13]  James Briscoe,et al.  Distinct Sonic Hedgehog signaling dynamics specify floor plate and ventral neuronal progenitors in the vertebrate neural tube. , 2010, Genes & development.

[14]  James Briscoe,et al.  Dynamic Assignment and Maintenance of Positional Identity in the Ventral Neural Tube by the Morphogen Sonic Hedgehog , 2010, PLoS biology.

[15]  Martha L Bulyk,et al.  Precise temporal control of the eye regulatory gene Pax6 via enhancer-binding site affinity. , 2010, Genes & development.

[16]  M. Berger,et al.  Universal protein-binding microarrays for the comprehensive characterization of the DNA-binding specificities of transcription factors , 2009, Nature Protocols.

[17]  Hongkai Ji,et al.  A genome-scale analysis of the cis-regulatory circuitry underlying sonic hedgehog-mediated patterning of the mammalian limb. , 2008, Genes & development.

[18]  Scott A. Rifkin,et al.  Imaging individual mRNA molecules using multiple singly labeled probes , 2008, Nature Methods.

[19]  James Briscoe,et al.  Pattern formation in the vertebrate neural tube: a sonic hedgehog morphogen-regulated transcriptional network , 2008, Development.

[20]  A. McMahon,et al.  Notochord-derived Shh concentrates in close association with the apically positioned basal body in neural target cells and forms a dynamic gradient during neural patterning , 2008, Development.

[21]  James Briscoe,et al.  Interpretation of the sonic hedgehog morphogen gradient by a temporal adaptation mechanism , 2007, Nature.

[22]  C. Fan,et al.  Gas1 extends the range of hedgehog action by facilitating its signaling , 2007 .

[23]  Andrew P. McMahon,et al.  Genomic characterization of Gli-activator targets in sonic hedgehog-mediated neural patterning , 2007, Development.

[24]  Toyoaki Tenzen,et al.  The Hedgehog-binding proteins Gas1 and Cdo cooperate to positively regulate Shh signaling during mouse development. , 2007, Genes & development.

[25]  A. Philippakis,et al.  Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities , 2006, Nature Biotechnology.

[26]  M. Matise,et al.  Wnt signaling inhibitors regulate the transcriptional response to morphogenetic Shh-Gli signaling in the neural tube. , 2006, Developmental cell.

[27]  Toyoaki Tenzen,et al.  The cell surface membrane proteins Cdo and Boc are components and targets of the Hedgehog signaling pathway and feedback network in mice. , 2006, Developmental cell.

[28]  A. Joyner,et al.  Sonic hedgehog Signaling Regulates Gli2 Transcriptional Activity by Suppressing Its Processing and Degradation , 2006, Molecular and Cellular Biology.

[29]  E. Ukkonen,et al.  Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity , 2006, Cell.

[30]  Yanyun Li,et al.  Evidence for the direct involvement of βTrCP in Gli3 protein processing , 2006 .

[31]  Dmitri Papatsenko,et al.  Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  J. Briscoe,et al.  The floor plate: multiple cells, multiple signals , 2005, Nature Reviews Neuroscience.

[33]  L. Pevny,et al.  SOX genes and neural progenitor identity , 2005, Current Opinion in Neurobiology.

[34]  A. McMahon,et al.  Growth and pattern of the mammalian neural tube are governed by partially overlapping feedback activities of the hedgehog antagonists patched 1 and Hhip1 , 2004, Development.

[35]  B. Novitch,et al.  Vertebrate neurogenesis is counteracted by Sox1–3 activity , 2003, Nature Neuroscience.

[36]  H. Wichterle,et al.  A Requirement for Retinoic Acid-Mediated Transcriptional Activation in Ventral Neural Patterning and Motor Neuron Specification , 2003, Neuron.

[37]  Kuniya Abe,et al.  Identification of Cis-regulatory elements in the mouse Pax9/Nkx2-9 genomic region: implication for evolutionary conserved synteny. , 2003, Genetics.

[38]  L. Pevny,et al.  SOX2 Functions to Maintain Neural Progenitor Identity , 2003, Neuron.

[39]  B. Oostra,et al.  A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. , 2003, Human molecular genetics.

[40]  A. McMahon,et al.  A direct requirement for Hedgehog signaling for normal specification of all ventral progenitor domains in the presumptive mammalian spinal cord. , 2002, Genes & development.

[41]  Jens Böse,et al.  Dorsal-ventral patterning of the spinal cord requires Gli3 transcriptional repressor activity. , 2002, Genes & development.

[42]  Jussi Taipale,et al.  Small molecule modulation of Smoothened activity , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[43]  H. Wichterle,et al.  Directed Differentiation of Embryonic Stem Cells into Motor Neurons , 2002, Cell.

[44]  S. Mango,et al.  Regulation of Organogenesis by the Caenorhabditis elegans FoxA Protein PHA-4 , 2002, Science.

[45]  T. Jessell,et al.  Coordinate Regulation of Motor Neuron Subtype Identity and Pan-Neuronal Properties by the bHLH Repressor Olig2 , 2001, Neuron.

[46]  A. McMahon,et al.  The whereabouts of a morphogen: direct evidence for short- and graded long-range activity of hedgehog signaling peptides. , 2001, Developmental biology.

[47]  T. Jessell Neuronal specification in the spinal cord: inductive signals and transcriptional codes , 2000, Nature Reviews Genetics.

[48]  T. Jessell,et al.  A Homeodomain Protein Code Specifies Progenitor Cell Identity and Neuronal Fate in the Ventral Neural Tube , 2000, Cell.

[49]  Philip A Beachy,et al.  Hedgehog-Regulated Processing of Gli3 Produces an Anterior/Posterior Repressor Gradient in the Developing Vertebrate Limb , 2000, Cell.

[50]  A. Joyner,et al.  Regionalization of Sonic hedgehog transcription along the anteroposterior axis of the mouse central nervous system is regulated by Hnf3-dependent and -independent mechanisms. , 1999, Development.

[51]  A. Joyner,et al.  Gli2 is required for induction of floor plate and adjacent cells, but not most ventral neurons in the mouse central nervous system. , 1998, Development.

[52]  J. Rossant,et al.  Diminished Sonic hedgehog signaling and lack of floor plate differentiation in Gli2 mutant mice. , 1998, Development.

[53]  M. Nakafuku,et al.  A binding site for Gli proteins is essential for HNF-3beta floor plate enhancer activity in transgenics and can respond to Shh in vitro. , 1997, Development.

[54]  P. Beachy,et al.  Cyclopia and defective axial patterning in mice lacking Sonic hedgehog gene function , 1996, Nature.

[55]  M. Scott,et al.  Conservation of the hedgehog/patched signaling pathway from flies to mice: induction of a mouse patched gene by Hedgehog. , 1996, Genes & development.

[56]  A. McMahon,et al.  Requirement of 19K form of Sonic hedgehog for induction of distinct ventral cell types in CNS explants , 1995, Nature.

[57]  T. Jessell,et al.  Floor plate and motor neuron induction by different concentrations of the amino-terminal cleavage product of sonic hedgehog autoproteolysis , 1995, Cell.

[58]  Michael Levine,et al.  Binding affinities and cooperative interactions with bHLH activators delimit threshold responses to the dorsal gradient morphogen , 1993, Cell.

[59]  K. Kinzler,et al.  The GLI gene encodes a nuclear protein which binds specific sequences in the human genome , 1990, Molecular and cellular biology.

[60]  Martin Renqiang Min,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[61]  W. Wong,et al.  The analysis of ChIP-Seq data. , 2011, Methods in enzymology.

[62]  A. Joyner,et al.  All mouse ventral spinal cord patterning by hedgehog is Gli dependent and involves an activator function of Gli3. , 2004, Developmental cell.