Genome-wide Prediction of Mammalian Enhancers Based on Analysis of Transcription-Factor Binding Affinity

[1]  M S Waterman,et al.  Identification of common molecular subsequences. , 1981, Journal of molecular biology.

[2]  D. Crothers,et al.  Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. , 1981, Nucleic acids research.

[3]  B. Hogan,et al.  Manipulating the mouse embryo: A laboratory manual , 1986 .

[4]  W. Schulz,et al.  Dynamic expression pattern of the myc protooncogene in midgestation mouse embryos. , 1989, Science.

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

[6]  J. Ghysdael,et al.  Identification of nucleotide preferences in DNA sequences recognised specifically by c-Ets-1 protein. , 1992, Nucleic acids research.

[7]  AC Tose Cell , 1993, Cell.

[8]  C. Pabo,et al.  Crystal structure of a five-finger GLI-DNA complex: new perspectives on zinc fingers. , 1993, Science.

[9]  T. Honjo,et al.  Recognition sequence of a highly conserved DNA binding protein RBP-J kappa. , 1994, Nucleic acids research.

[10]  C. Babinet,et al.  The cis-acting elements known to regulate c-myc expression ex vivo are not sufficient for correct transcription in vivo. , 1994, Oncogene.

[11]  B. Brunk,et al.  Embryonic activation of the myoD gene is regulated by a highly conserved distal control element. , 1995, Development.

[12]  J. Darnell,et al.  A STAT protein domain that determines DNA sequence recognition suggests a novel DNA-binding domain. , 1995, Genes & development.

[13]  David Ish-Horowicz,et al.  Expression of a Delta homologue in prospective neurons in the chick , 1995, Nature.

[14]  M. Levine,et al.  Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. , 1996, Developmental biology.

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

[16]  K. Kinzler,et al.  Constitutive Transcriptional Activation by a β-Catenin-Tcf Complex in APC−/− Colon Carcinoma , 1997, Science.

[17]  A. Ruiz i Altaba,et al.  Gli1 is a target of Sonic hedgehog that induces ventral neural tube development. , 1997, Development.

[18]  N. Dahmane,et al.  Activation of the transcription factor Gli1 and the Sonic hedgehog signalling pathway in skin tumours , 1997, Nature.

[19]  M. Scott,et al.  Altered neural cell fates and medulloblastoma in mouse patched mutants. , 1997, Science.

[20]  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.

[21]  D. S. Fields,et al.  Specificity, free energy and information content in protein-DNA interactions. , 1998, Trends in biochemical sciences.

[22]  D. Schlessinger,et al.  Gpc3 expression correlates with the phenotype of the Simpson‐Golabi‐Behmel syndrome , 1998, Developmental dynamics : an official publication of the American Association of Anatomists.

[23]  A. Sparks,et al.  Identification of c-MYC as a target of the APC pathway. , 1998, Science.

[24]  Yasunori Tanaka,et al.  Sonic Hedgehog-induced Activation of the Gli1Promoter Is Mediated by GLI3* , 1999, The Journal of Biological Chemistry.

[25]  I. Conlon,et al.  Size Control in Animal Development , 1999, Cell.

[26]  A. McMahon,et al.  T (Brachyury) is a direct target of Wnt3a during paraxial mesoderm specification. , 1999, Genes & development.

[27]  H. Clevers,et al.  Linking Colorectal Cancer to Wnt Signaling , 2000, Cell.

[28]  Carmen Birchmeier,et al.  Requirement for beta-catenin in anterior-posterior axis formation in mice. , 2000 .

[29]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[30]  M. Scott,et al.  Effects of oncogenic mutations in Smoothened and Patched can be reversed by cyclopamine , 2000, Nature.

[31]  Gary D. Stormo,et al.  DNA binding sites: representation and discovery , 2000, Bioinform..

[32]  J. Taipale,et al.  The Hedgehog and Wnt signalling pathways in cancer , 2001, Nature.

[33]  Peter W. Markstein,et al.  Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[34]  P. T. Sharpe,et al.  Sonic hedgehog Regulates Epithelial Proliferation and Cell Survival in the Developing Tooth Germ , 2001, Journal of dental research.

[35]  P. Ingham,et al.  Hedgehog signaling in animal development: paradigms and principles. , 2001, Genes & development.

[36]  Michael R. Green,et al.  Expressing the human genome , 2001, Nature.

[37]  J. Tyson Does Indomethacin Prophylaxis Benefit Extremely Low Birth Weight Infants? Results of a Placebo-Controlled Multicenter Trial , 2002, Pediatric Research.

[38]  N. D. Clarke,et al.  Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. , 2002, Journal of molecular biology.

[39]  R. Behringer,et al.  Manipulating the Mouse Embryo: A Laboratory Manual , 2002 .

[40]  G. Evan,et al.  Suppression of Myc-Induced Apoptosis in β Cells Exposes Multiple Oncogenic Properties of Myc and Triggers Carcinogenic Progression , 2002, Cell.

[41]  Stella Pelengaris,et al.  c-MYC: more than just a matter of life and death , 2002, Nature Reviews Cancer.

[42]  P. Bucher,et al.  High-throughput SELEX–SAGE method for quantitative modeling of transcription-factor binding sites , 2002, Nature Biotechnology.

[43]  R. Kemler,et al.  Functional analysis of cis‐regulatory elements controlling initiation and maintenance of early Cdx1 gene expression in the mouse , 2002, Developmental dynamics : an official publication of the American Association of Anatomists.

[44]  G. Rubin,et al.  Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[45]  C. Emerson,et al.  Myf5 is a direct target of long-range Shh signaling and Gli regulation for muscle specification. , 2002, Genes & development.

[46]  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.

[47]  Massimo Vergassola,et al.  Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo , 2002, BMC Bioinformatics.

[48]  A. Michelson Deciphering genetic regulatory codes: A challenge for functional genomics , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[49]  Choun-Ki Joo,et al.  Wnt/β-Catenin/Tcf Signaling Induces the Transcription of Axin2, a Negative Regulator of the Signaling Pathway , 2002, Molecular and Cellular Biology.

[50]  Andrew P McMahon,et al.  Ectodermal Wnt3/beta-catenin signaling is required for the establishment and maintenance of the apical ectodermal ridge. , 2003, Genes & development.

[51]  P. Rigby,et al.  The initial somitic phase of Myf5 expression requires neither Shh signaling nor Gli regulation. , 2003, Genes & development.

[52]  Roderic Guigó,et al.  gff2aplot: Plotting sequence comparisons , 2003, Bioinform..

[53]  Michael D. Cole,et al.  Nmyc upregulation by sonic hedgehog signaling promotes proliferation in developing cerebellar granule neuron precursors , 2003, Development.

[54]  Denis Duboule,et al.  A Global Control Region Defines a Chromosomal Regulatory Landscape Containing the HoxD Cluster , 2003, Cell.

[55]  Robert J. Wechsler-Reya,et al.  Transcriptional profiling of the Sonic hedgehog response: A critical role for N-myc in proliferation of neuronal precursors , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Anders Gorm Pedersen,et al.  RevTrans: multiple alignment of coding DNA from aligned amino acid sequences , 2003, Nucleic Acids Res..

[57]  Michael D. Stone,et al.  Structural transitions and elasticity from torque measurements on DNA , 2003, Nature.

[58]  R. Young,et al.  Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays , 2004, Nature Genetics.

[59]  P. Kogerman,et al.  Expression of the PTCH1 tumor suppressor gene is regulated by alternative promoters and a single functional Gli-binding site. , 2004, Gene.

[60]  Ian P Newton,et al.  Loss of Apc in vivo immediately perturbs Wnt signaling, differentiation, and migration. , 2004, Genes & development.

[61]  K. Nakai,et al.  Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. , 2004, Genome research.

[62]  Wyeth W. Wasserman,et al.  JASPAR: an open-access database for eukaryotic transcription factor binding profiles , 2004, Nucleic Acids Res..

[63]  Saurabh Sinha,et al.  Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila , 2004, BMC Bioinformatics.

[64]  K. Lindblad-Toh,et al.  Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals , 2005, Nature.

[65]  Klaudia Walter,et al.  Open access, freely available online PLoS BIOLOGY Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development , 2022 .

[66]  N. D. Clarke,et al.  DIP-chip: rapid and accurate determination of DNA-binding specificity. , 2005, Genome research.