cad

Summary

Gene Symbol: cad
Description: caudal
Alias: 38E.19, CAD, CG1759, Cad, Dmel\CG1759, S67, anon-WO2004063362.83, CG1759 gene product from transcript CG1759-RC, CG1759-PA, CG1759-PB, CG1759-PC, cad-PA, cad-PB, cad-PC
Species: fruit fly

Top Publications

  1. ncbi What determines the specificity of action of Drosophila homeodomain proteins?
    S Hayashi
    National Institute of Genetics, Shizuoka ken, Japan
    Cell 63:883-94. 1990
  2. ncbi Homeobox genes and axial patterning
    W McGinnis
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
    Cell 68:283-302. 1992
  3. pmc FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
    Andrei Pisarev
    Department of Computational Biology, St Petersburg State Polytechnical University, St Petersburg 195251, Russia
    Nucleic Acids Res 37:D560-6. 2009
  4. ncbi Caudal is the Hox gene that specifies the most posterior Drosophile segment
    E Moreno
    Centro de Biologia Molecular CSIC UAM, Madrid, Spain
    Nature 400:873-7. 1999
  5. ncbi Activation of posterior gap gene expression in the Drosophila blastoderm
    R Rivera-Pomar
    Abteilung Molekulare Entwicklungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    Nature 376:253-6. 1995
  6. pmc Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila
    T E Haerry
    Biozentrum, University of Basel, Switzerland
    Proc Natl Acad Sci U S A 93:13884-9. 1996
  7. pmc The homeobox gene Caudal regulates constitutive local expression of antimicrobial peptide genes in Drosophila epithelia
    Ji Hwan Ryu
    Division of Molecular Life Science and Center for Cell Signaling Research, Ewha Womans University, Seoul, South Korea
    Mol Cell Biol 24:172-85. 2004
  8. ncbi Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila
    J Reinitz
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, New York 10027
    Dev Biol 140:57-72. 1990
  9. ncbi Effects of ectopic expression of caudal during Drosophila development
    M Mlodzik
    Department of Cell Biology, Biozentrum der Universitat, Basel, Switzerland
    Development 109:271-7. 1990
  10. ncbi Regulation of Krüppel expression in the anlage of the Malpighian tubules in the Drosophila embryo
    U Gaul
    Max Planck Institut fur Entwicklungsbiologie, Tubingen, F R G
    Mech Dev 33:57-67. 1990

Scientific Experts

Detail Information

Publications123 found, 100 shown here

  1. ncbi What determines the specificity of action of Drosophila homeodomain proteins?
    S Hayashi
    National Institute of Genetics, Shizuoka ken, Japan
    Cell 63:883-94. 1990
  2. ncbi Homeobox genes and axial patterning
    W McGinnis
    Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06511
    Cell 68:283-302. 1992
  3. pmc FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution
    Andrei Pisarev
    Department of Computational Biology, St Petersburg State Polytechnical University, St Petersburg 195251, Russia
    Nucleic Acids Res 37:D560-6. 2009
    ..5 h of development. FlyEx supports the data downloads and construction of personal reference datasets, that makes it possible to more effectively use and analyze data...
  4. ncbi Caudal is the Hox gene that specifies the most posterior Drosophile segment
    E Moreno
    Centro de Biologia Molecular CSIC UAM, Madrid, Spain
    Nature 400:873-7. 1999
    The homeobox gene caudal (cad) has a maternal embryonic function that establishes the antero-posterior body axis of Drosophila...
  5. ncbi Activation of posterior gap gene expression in the Drosophila blastoderm
    R Rivera-Pomar
    Abteilung Molekulare Entwicklungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    Nature 376:253-6. 1995
    ....
  6. pmc Intron of the mouse Hoxa-7 gene contains conserved homeodomain binding sites that can function as an enhancer element in Drosophila
    T E Haerry
    Biozentrum, University of Basel, Switzerland
    Proc Natl Acad Sci U S A 93:13884-9. 1996
    ..by the HB1-element of Hoxa-7, the expression pattern is altered and newly controlled by the homeotic gene caudal (cad)...
  7. pmc The homeobox gene Caudal regulates constitutive local expression of antimicrobial peptide genes in Drosophila epithelia
    Ji Hwan Ryu
    Division of Molecular Life Science and Center for Cell Signaling Research, Ewha Womans University, Seoul, South Korea
    Mol Cell Biol 24:172-85. 2004
    ..These results suggest that certain epithelial tissues have evolved a unique constitutive innate immune strategy by recruiting a developmental "master control" gene...
  8. ncbi Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila
    J Reinitz
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, New York 10027
    Dev Biol 140:57-72. 1990
    ..giant also regulates the establishment of the expression patterns of Antennapedia and Abdominal-B. In particular, giant is the factor that controls the anterior limit of early Antennapedia expression...
  9. ncbi Effects of ectopic expression of caudal during Drosophila development
    M Mlodzik
    Department of Cell Biology, Biozentrum der Universitat, Basel, Switzerland
    Development 109:271-7. 1990
    The effects of heat-shock-induced ectopic expression of the homeobox gene caudal (cad) at all stages of Drosophila development have been examined...
  10. ncbi Regulation of Krüppel expression in the anlage of the Malpighian tubules in the Drosophila embryo
    U Gaul
    Max Planck Institut fur Entwicklungsbiologie, Tubingen, F R G
    Mech Dev 33:57-67. 1990
    ..In addition, Krüppel activates different genes in the Malpighian tubules than in the central domain. Thus, both the regulation and the function of Krüppel in the Malpighian tubules differ strikingly from its role in segmentation...
  11. ncbi Expression of the caudal gene in the germ line of Drosophila: formation of an RNA and protein gradient during early embryogenesis
    M Mlodzik
    Cell 48:465-78. 1987
    The caudal (cad) gene of Drosophila encodes a maternal and a zygotic transcript which have different promoters. Both mRNAs contain the same open reading frame, including a homeo box...
  12. ncbi A molecular gradient in early Drosophila embryos and its role in specifying the body pattern
    P M Macdonald
    Nature 324:537-45. 1986
    After fertilization, the protein products of the Drosophila homeobox gene caudal (cad) accumulate in a concentration gradient spanning the anteroposterior axis of the developing embryo...
  13. pmc Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila
    E B Lewis
    Division of Biology, California Institute of Technology, Pasadena 91125, USA
    Proc Natl Acad Sci U S A 92:8403-7. 1995
    ..5 case is expected. Expected values are based on a third-order Markov chain, which is the optimal order for representing the BXCALL sequence...
  14. ncbi Zygotic caudal regulation by hunchback and its role in abdominal segment formation of the Drosophila embryo
    C Schulz
    Zoologisches Institut, Universitat, Munchen, Germany
    Development 121:1023-8. 1995
    caudal (cad) is a maternally and zygotically expressed gene in Drosophila whereby the two phases of expression can functionally replace each other...
  15. ncbi Analysis of the genes involved in organizing the tail segments of the Drosophila melanogaster embryo
    D T Kuhn
    Department of Biology, University of Central Florida, Orlando 32816, USA
    Mech Dev 53:3-13. 1995
    ..We documented the domains of engrailed (en), Abdominal-B (Abd-B) and caudal (cad) expression in the tail region...
  16. ncbi RNA recognition and translational regulation by a homeodomain protein
    J Dubnau
    Howard Hughes Medical Research Institute, Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, New York 10032, USA
    Nature 379:694-9. 1996
    ..binds RNA and acts as a translational repressor to generate an opposing gradient of the homeodomain protein caudal (cad)...
  17. ncbi RNA binding and translational suppression by bicoid
    R Rivera-Pomar
    Abteilung Molekulare Entwicklungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    Nature 379:746-9. 1996
    ..Its posterior counterpart, the homeodomain transcription factor caudal (cad), forms a concentration gradient in the opposite direction, emanating from evenly distributed messenger RNA in the ..
  18. ncbi From gradients to stripes in Drosophila embryogenesis: filling in the gaps
    R Rivera-Pomar
    Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    Trends Genet 12:478-83. 1996
    ..Recent progress has begun to reveal the mechanisms by which coherent positional information of maternal origin becomes transferred into serially repeated zygotic gene expression domains reflecting the metameric body plan of the larva...
  19. pmc Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo
    A La Rosée
    Abteilung Molekulare Entwicklungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    EMBO J 16:4403-11. 1997
    ..The results suggest that the gradients of Bicoid and Caudal combine their activities to activate segmentation genes along the entire axis of the embryo...
  20. ncbi Regulation of Drosophila spalt gene expression
    R P Kühnlein
    Max Planck Institut fur biophysikalische Chemie, Abteilung Molekulare Entwicklungsbiologie Am Fassberg, Gottingen, Germany
    Mech Dev 66:107-18. 1997
    ..In addition, we provide evidence that a zygotic gene product of the terminal system, Tailless, cooperates with the maternal gene product Caudal and thereby activates gene expression in the terminal region of the embryo...
  21. ncbi Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins
    D Kosman
    Brookdale Center for Molecular Biology, Box 1126, Mt Sinai School of Medicine, One Gustave L Levy Place, New York, NY 10029, USA
    Dev Genes Evol 208:290-4. 1998
    ..Antigenicity of the purified recombinant proteins may be increased by precipitation in double-distilled water. The results of using the serums obtained for fluorescent staining of Drosophila embryos are shown...
  22. ncbi A logical analysis of the Drosophila gap-gene system
    L Sanchez
    Centro de Investigaciones Biologicas, Velazquez 144, Madrid, 28006, Spain
    J Theor Biol 211:115-41. 2001
    ..qualitative, functional levels associated with each of the key regulatory factors (the three maternal Bcd, Hb and Cad products, and the four gap Gt, Hb, Kr and Kni products); (2) the most crucial interactions and regulatory circuits ..
  23. pmc Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    Benjamin P Berman
    Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 99:757-62. 2002
    ..We tested one of the newly identified clusters, mapping upstream of the gap gene giant (gt), and show that it acts as an enhancer that recapitulates the posterior expression pattern of gt...
  24. pmc Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers
    Dmitri A Papatsenko
    Department of Biology, New York University, New York, NY 10003 6688, USA
    Genome Res 12:470-81. 2002
    ..We also discuss the definition of true binding sites and the possible biological principles that govern patterning of regulatory regions and the distribution of transcriptional signals...
  25. pmc The caudal homeodomain protein activates Drosophila E2F gene expression
    Mi Sun Hwang
    Department of Molecular Biology, Pusan National University, Pusan 609 735, Korea
    Nucleic Acids Res 30:5029-35. 2002
    ..In addition, ectopic expression of Caudal with heat-shock promotion induced melanotic tumors in larvae. These results suggest that Caudal is involved in regulation of proliferation through transactivation of the E2F gene in Drosophila...
  26. ncbi Turnover of binding sites for transcription factors involved in early Drosophila development
    Javier Costas
    Instituto de Biologia Molecular e Celular IBMC, Universidade do Porto, Rua do Campo Alegre 823, 4150 180, Porto, Portugal
    Gene 310:215-20. 2003
    ..Finally, we detected a significant decrease in mean PWM scores for the D. virilis binding sites in the case of Hunchback. Possible explanations for this fact are discussed...
  27. pmc Transcriptional control in the segmentation gene network of Drosophila
    Mark D Schroeder
    Laboratory of Developmental Neurogenetics, Rockefeller University, New York, New York, USA
    PLoS Biol 2:E271. 2004
    ..The study demonstrates that computational methods are a powerful complement to experimental approaches in the analysis of transcription networks...
  28. pmc Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster
    Johannes Jaeger
    Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794 3600, USA
    Genetics 167:1721-37. 2004
    ..Our models predict activation of Kr by Cad and clarify several other regulatory interactions...
  29. pmc Engineering gene networks to emulate Drosophila embryonic pattern formation
    Mark Isalan
    European Molecular Biology Laboratory, Structures and Biocomputing, Heidelberg, Germany
    PLoS Biol 3:e64. 2005
    ..We anticipate that the system described here will be generally applicable to the study of any biological network with a spatial component...
  30. ncbi Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity
    Outi Hallikas
    Molecular and Cancer Biology Program, Biomedicum Helsinki, University of Helsinki, Finland
    Cell 124:47-59. 2006
    ....
  31. ncbi Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene
    Hilde Janssens
    Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, New York 11794 3600, USA
    Nat Genet 38:1159-65. 2006
    ..It also shows that the nonclassical expression of stripe 7 driven by this fragment is activated by the protein Caudal (Cad), and repressed by the proteins Tailless (Tll) and Giant (Gt).
  32. ncbi On the dynamic nature of positional information
    Johannes Jaeger
    Laboratory of Development and Evolution, Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Bioessays 28:1102-11. 2006
    ..Based on this analysis, we propose a revised French Flag, which incorporates the dynamic, feedback-driven nature of pattern formation in the Drosophila blastoderm...
  33. pmc Enhancer responses to similarly distributed antagonistic gradients in development
    Robert P Zinzen
    Department of Molecular and Cell Biology, Center for Integrative Genomics, University of California, Berkeley, California, United States of America
    PLoS Comput Biol 3:e84. 2007
    ....
  34. pmc Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes
    Maxim Nekrasov
    Gene Expression Programme, EMBL, Heidelberg, Germany
    EMBO J 26:4078-88. 2007
    ..Pcl-PRC2 is thus the HMTase that generates the high levels of H3-K27 trimethylation in Polycomb target genes that are needed to maintain a Polycomb-repressed chromatin state...
  35. ncbi Imaging in systems biology
    Sean G Megason
    Beckman Institute, Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
    Cell 130:784-95. 2007
    ..Here, we discuss the power of integrating imaging tools with more conventional -omic approaches to analyze the biological circuits of microorganisms, plants, and animals...
  36. pmc Characterization of the Drosophila segment determination morphome
    Svetlana Surkova
    Department of Computational Biology, Center for Advanced Studies, St Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St Petersburg, 195251, Russia
    Dev Biol 313:844-62. 2008
    ..As the first quantitatively characterized morphogenetic field, this system and its behavior constitute an extraordinarily rich set of materials for the study of canalization and embryonic regulation at the molecular level...
  37. pmc Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
    PLoS Biol 6:e27. 2008
    ....
  38. pmc Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation
    Emily E Hare
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 4:e1000106. 2008
    ..Together, these observations suggest that the local arrangement of binding sites relative to each other is more important than their overall arrangement into larger units of cis-regulatory function...
  39. pmc Parameter estimation and determinability analysis applied to Drosophila gap gene circuits
    Maksat Ashyraliyev
    CWI, Kruislaan 413, 1098 SJ Amsterdam, The Netherlands
    BMC Syst Biol 2:83. 2008
    ..Once the parameters are found by means of optimization, it is important to assess the quality of the parameter estimates, especially if parameter values are used to draw biological conclusions from the model...
  40. pmc Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images
    Svetlana Surkova
    Department of Computational Biology, Center for Advanced Studies, St Petersburg State Polytechnical University, St Petersburg, Russia
    Fly (Austin) 2:58-66. 2008
    ..5-minute resolution in time, as well as to construct a spatiotemporal atlas of segmentation gene expression. Each data pipeline step can be easily adapted to process a wide range of images of gene expression patterns...
  41. pmc Evolution of regulatory sequences in 12 Drosophila species
    Jaebum Kim
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, Illinois, United States of America
    PLoS Genet 5:e1000330. 2009
    ....
  42. pmc Canalization of gene expression and domain shifts in the Drosophila blastoderm by dynamical attractors
    - Manu
    Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America
    PLoS Comput Biol 5:e1000303. 2009
    ..The result confirms the idea that attractors are important for developmental stability and shows a richer variety of dynamical attractors in developmental systems than has been previously recognized...
  43. pmc Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution
    Xin He
    Department of Computer Science, University of Illinois Urbana Champaign, Urbana, IL, USA
    PLoS Comput Biol 5:e1000299. 2009
    ..Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context...
  44. pmc Statistical lower bounds on protein copy number from fluorescence expression images
    Lee Zamparo
    Department of Computer Science and Software Engineering, Concordia University, Montreal, Quebec, Canada
    Bioinformatics 25:2670-6. 2009
    ..While this is satisfactory for many applications, for certain kinds of quantitative network modeling and analysis of expression noise, absolute measures of expression are necessary...
  45. pmc Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions
    Stewart MacArthur
    Genomics Division, Lawrence Berkeley National Laboratory, Cyclotron Road MS 84 181, Berkeley, CA 94720, USA
    Genome Biol 10:R80. 2009
    ....
  46. pmc Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation
    - Manu
    Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, New York, United States of America
    PLoS Biol 7:e1000049. 2009
    ..More generally, we show that the complex multigenic phenomenon of canalization can be understood at a quantitative and predictive level by the application of a precise dynamical model...
  47. pmc Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis
    Yves Fomekong-Nanfack
    Section Computational Science, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands
    BMC Syst Biol 3:94. 2009
    ..Consequently, it is important to address the quality of the circuits in terms of model robustness...
  48. pmc Gene circuit analysis of the terminal gap gene huckebein
    Maksat Ashyraliyev
    Center for Mathematics and Computer Science, Centrum Wiskunde and Informatica, Amsterdam, The Netherlands
    PLoS Comput Biol 5:e1000548. 2009
    ..This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network...
  49. pmc Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species
    Robert K Bradley
    Department of Mathematics, University of California Berkeley, Berkeley, California, United States of America
    PLoS Biol 8:e1000343. 2010
    ....
  50. pmc Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
    Xin He
    Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, California, United States of America
    PLoS Comput Biol 6:. 2010
    ..Our implementation of the model, called GEMSTAT, is the first publicly available program for simultaneously modeling the regulatory activities of a given set of sequences...
  51. pmc Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
    Tommy Kaplan
    Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America
    PLoS Genet 7:e1001290. 2011
    ....
  52. pmc The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
    Xiao Yong Li
    Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84 171, Berkeley, CA 94720, USA
    Genome Biol 12:R34. 2011
    ..The primary biochemical mechanisms that drive these genome-wide occupancy patterns have yet to be established...
  53. pmc The Drosophila gap gene network is composed of two parallel toggle switches
    Dmitri Papatsenko
    Department of Gene and Cell Medicine, Mount Sinai School of Medicine, Black Family Stem Cell Institute, New York, New York, United States of America
    PLoS ONE 6:e21145. 2011
    ..The identified model solutions (parameter combinations) reproduced major dynamic features of the gap gradient system and explained gap expression in a variety of segmentation mutants...
  54. pmc Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains
    Jonathan Bieler
    The Institute of Bioengineering, School of Life Sciences, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
    Biophys J 101:287-96. 2011
    ....
  55. pmc Mechanisms of gap gene expression canalization in the Drosophila blastoderm
    Vitaly V Gursky
    Theoretical Department, Ioffe Physical Technical Institute of the Russian Academy of Sciences, St, Petersburg, 194021 Russia
    BMC Syst Biol 5:118. 2011
    ..The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system...
  56. pmc Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition
    Melissa M Harrison
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 7:e1002266. 2011
    ..This strong early association of ZLD with regions not active until the MZT suggests that ZLD is not only required for the earliest wave of transcription but also plays a major role in activating the genome at the MZT...
  57. pmc A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila
    Charless C Fowlkes
    Department of Computer Science, University of California Irvine, Irvine, California, USA
    PLoS Genet 7:e1002346. 2011
    ..Our results emphasize that transcriptional networks can diverge over short evolutionary timescales and that even small changes can lead to distinct output in terms of the placement and number of equivalent cells...
  58. pmc Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos
    Per Henrik Holmqvist
    The Wenner Gren Institute, Developmental Biology, Stockholm University, Stockholm, Sweden
    PLoS Genet 8:e1002769. 2012
    ..We conclude that CBP occupancy in Drosophila embryos preferentially overlaps factors controlling dorso-ventral patterning and that CBP binds silent genes without causing histone hyperacetylation...
  59. pmc Efficient reverse-engineering of a developmental gene regulatory network
    Anton Crombach
    EMBL CRG Research Unit in Systems Biology, Centre for Genomic Regulation CRG and Universitat Pompeu Fabra UPF, Barcelona, Spain
    PLoS Comput Biol 8:e1002589. 2012
    ..Only the quantitative investigation of a large number of developmental gene regulatory networks will allow us to discover whether there are rules or regularities governing development and evolution of complex multi-cellular organisms...
  60. doi A statistical fat-tail test of predicting regulatory regions in the Drosophila genome
    Jian Jun Shu
    School of Mechanical and Aerospace Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
    Comput Biol Med 42:935-41. 2012
    ..These two fatness coefficients may serve as valuable filtering indexes to predict CRMs experimentally...
  61. pmc Modeling of gap gene expression in Drosophila Kruppel mutants
    Konstantin Kozlov
    Department of Computational Biology Center for Advanced Studies, St Petersburg State Polytechnical University, St Petersburg, Russia
    PLoS Comput Biol 8:e1002635. 2012
    ..of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible ..
  62. pmc Mutual repression enhances the steepness and precision of gene expression boundaries
    Thomas R Sokolowski
    FOM Institute AMOLF, Amsterdam, The Netherlands
    PLoS Comput Biol 8:e1002654. 2012
    ..cooperative activation of hb by the anterior morphogen Bicoid (Bcd) and of kni by the posterior morphogen Caudal (Cad), as well as the diffusion of Hb and Kni between neighboring nuclei...
  63. pmc Lack of tailless leads to an increase in expression variability in Drosophila embryos
    Hilde Janssens
    EMBL CRG Research Unit in Systems Biology, CRG Centre de Regulacio Genomica, and Universitat Pompeu Fabra UPF, Dr Aiguader 88, 08003 Barcelona, Spain
    Dev Biol 377:305-17. 2013
    ..Our analysis provides evidence that loss of canalisation in mutants could be more widespread than previously thought...
  64. doi Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants
    Svetlana Surkova
    Department of Computational Biology, Center for Advanced Studies, St Petersburg State Polytechnical University, 29 Polytehnicheskaya Street, St Petersburg 195251, Russia
    Dev Biol 376:99-112. 2013
    ..This is a surprising result in view of the role that mutual repression is thought to play in the gap gene system...
  65. doi Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data
    Abul Hassan Samee
    Department of Computer Science, University of Illinois at Urbana Champaign, Urbana, IL, USA
    Methods 62:79-90. 2013
    ..Finally, we show how fitting quantitative models on data sets comprising a handful of enhancers, as reported in earlier work, may lead to unreliable models...
  66. ncbi Polycomb group proteins and heritable silencing of Drosophila Hox genes
    D Beuchle
    Max Planck Institut fur Entwicklungsbiologie, Spemannstr 35 III, 72076 Tubingen, Germany
    Development 128:993-1004. 2001
    ..Some PcG proteins may be required to define and propagate this mark; others may function to repress the transcription of Hox genes that bear the mark...
  67. pmc Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
    Vsevolod J Makeev
    Scientific Center Genetika, Moscow 113545, Russia
    Nucleic Acids Res 31:6016-26. 2003
    ..We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes...
  68. pmc The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila
    Amanda Ochoa-Espinosa
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Proc Natl Acad Sci U S A 102:4960-5. 2005
    ..We propose that the key design principle in AP patterning is the differential integration of positive and negative transcriptional information at the level of individual CRMs for each target gene...
  69. pmc Organization of developmental enhancers in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular Cell Biology, Division of Genetics, Genomics and Development, Center for Integrative Genomics, University of California, Berkeley, CA 94720 200, USA
    Nucleic Acids Res 37:5665-77. 2009
    ..We conclude that grammar of gene control regions is pervasively used in the patterning of the Drosophila embryo...
  70. ncbi The caudal gene product is a direct activator of fushi tarazu transcription during Drosophila embryogenesis
    C R Dearolf
    Division of Chemistry, California Institute of Technology, Pasadena 91125
    Nature 341:340-3. 1989
    ..Here we report that the homoeodomain-containing protein encoded by caudal (cad) is one such regulator...
  71. doi Gene and epigene networks: two levels in organizing the hereditary system
    R N Tchuraev
    Institute of Biology, Ufa Research Center, Russian Academy of Sciences, 69 Prospect Oktyabrya, Ufa 450054, Russia
    J Theor Biol 259:659-69. 2009
    ..In addition, the experimental results are given on construction an artificial epigene...
  72. pmc Refining transcriptional regulatory networks using network evolutionary models and gene histories
    Xiuwei Zhang
    Laboratory for Computational Biology and Bioinformatics, Ecole Polytechnique Federale de Lausanne, EPFL IC LCBB, INJ230, Station 14, CH 1015 Lausanne, Switzerland
    Algorithms Mol Biol 5:1. 2010
    ....
  73. ncbi The homeodomain: a new face for the helix-turn-helix?
    J Treisman
    Howard Hughes Medical Institute, Rockefeller University, New York
    Bioessays 14:145-50. 1992
    ..We propose that this intrinsic complexity of the HD, as well as its frequent association with other DNA binding domains, explains the functional specificity achieved by genes encoding highly related HDs...
  74. ncbi Role of gap genes in early Drosophila development
    U Gaul
    Max Planck Institut fur Entwicklungsbiologie, Tubingen, Federal Republic of Germany
    Adv Genet 27:239-75. 1990
  75. ncbi Homeodomain proteins and the regulation of gene expression
    M Affolter
    Biozentrum, University of Basel, Switzerland
    Curr Opin Cell Biol 2:485-95. 1990
  76. ncbi Transcriptional regulation of the Drosophila segmentation gene fushi tarazu (ftz)
    C R Dearolf
    Division of Chemistry, California Institute of Technology, Pasadena 91125
    Bioessays 12:109-13. 1990
    ..We discuss the transcriptional mechanism which causes ftz to be expressed in a seven stripe pattern during embryogenesis...
  77. ncbi Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression
    B C Goodwin
    Department of Biology, Open University, Milton Keynes, U K
    J Theor Biol 144:303-19. 1990
    ..This model has implications for the general stability properties of evolving epigenetic systems...
  78. ncbi The segmentation gene Krüppel of Drosophila melanogaster has homeotic properties
    R Harbecke
    Zoologisches Institut der Universitat, Munster, FRG
    Genes Dev 3:114-22. 1989
    ..Therefore, we conclude that the Krüppel gene exhibits a homeotic function in addition to its role as a segmentation gene and is involved in separating hindgut and Malpighian tubule cells and in the elongation process as well...
  79. ncbi Structure of the segmentation gene paired and the Drosophila PRD gene set as part of a gene network
    G Frigerio
    Cell 47:735-46. 1986
    ..The observed linking of gene sets through combinations of homologies coding for protein domains is consistent with a general network concept of gene action...
  80. ncbi Arthropod evolution: Brine shrimp add salt to the stew
    T A Williams
    Department of Zoology, University of Texas, Austin 78712, USA
    Curr Biol 5:1330-3. 1995
  81. ncbi Translational regulation of maternal mRNAs
    P M Macdonald
    Department of Biological Sciences, Stanford University, Stanford, California 94305 5020, USA
    Curr Opin Genet Dev 6:403-7. 1996
    ..Substantial progress has also been reported in the identification and characterization of the cis-acting elements and trans-acting factors that mediate translational regulation and their interactions with one another...
  82. ncbi Expression patterns of developmental genes reveal segment and parasegment organization of D. melanogaster genital discs
    D E Freeland
    Department of Biology, University of Central Florida, Orlando 32816, USA
    Mech Dev 56:61-72. 1996
    ..the edge of the posterior lobes, leaving open the possibility that A11 may contribute to the genital discs, caudal (cad) was expressed segmentally in the anal primordium of A10, extending through the Abd-B unstained region, wingless (..
  83. ncbi Visualization of gene expression in living adult Drosophila
    M Calleja
    Centro de Biologia Molecular, Universidad Autonoma de Madrid, Consejo Superior de Investigaciones Cientificas, Madrid 28049, Spain
    Science 274:252-5. 1996
    ..The boundary between two of these domains coincides with localized expression of the signaling molecule wingless...
  84. ncbi A sequence conserved in vertebrate Hox gene introns functions as an enhancer regulated by posterior homeotic genes in Drosophila imaginal discs
    L P Keegan
    Department of Cell Biology, Basel University Biozentrum, Switzerland
    Mech Dev 63:145-57. 1997
    ..Testing a reporter gene construct with mutated binding sites in mouse embryos shows that HB1 is also active in the expression domains of posterior Hox genes in the mouse neural tube...
  85. ncbi The DPE, a conserved downstream core promoter element that is functionally analogous to the TATA box
    T W Burke
    Department of Biology, University of California, San Diego, La Jolla 92093 0347, USA
    Cold Spring Harb Symp Quant Biol 63:75-82. 1998
  86. ncbi A comparison of homologous developmental genes from Drosophila and Tribolium reveals major differences in length and trinucleotide repeat content
    K J Schmid
    Institut fur Genetik, Universitat zu Koln, Weyertal 121, 50931 Koln, Germany
    J Mol Evol 49:558-66. 1999
    ....
  87. ncbi Drosophila: flying high in Zürich
    A S Wilkins
    BioEssays Editorial Office, 10 11 Tredgold Lane, Napier St, Cambridge CB1 1HN, UK
    Bioessays 22:305-7. 2000
  88. ncbi Body-plan evolution in the Bilateria: early antero-posterior patterning and the deuterostome-protostome dichotomy
    L Z Holland
    Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, 92093 0202, USA
    Curr Opin Genet Dev 10:434-42. 2000
    ..Comparisons with Drosophila and Cnidarians suggest a scheme for evolution of the Bilaterian body plan and emphasize the pressing need for similar studies in a wider variety of organisms, especially more basal protostomes...
  89. ncbi Fragmented forests, evolving flies: molecular variation in African populations of Drosophila teissieri
    M Cobb
    Laboratoire d Ecologie, CNRS UMR 7625 et Ecole Pratique des Hautes Etudes, Universite Paris 6, Bât A Case 237, 7 quai St Bernard, 75005 Paris, France
    Mol Ecol 9:1591-7. 2000
    ..It seems probable that the species has undergone abrupt changes involving isolation, merging and migration of populations, as a consequence of repeated waves of forest fragmentation and coalescence...
  90. ncbi Sex comes in from the cold: the integration of sex and pattern
    Audrey E Christiansen
    Department Biological Sciences, Stanford University, Stanford, CA 94305, USA
    Trends Genet 18:510-6. 2002
    ....
  91. ncbi Development of the Drosophila genital disc requires interactions between its segmental primordia
    Nicole Gorfinkiel
    Centro de Biologia Molecular Severo Ochoa, C S I C, Universidad Autonoma de Madrid, Cantoblanco, E 28049 Madrid, Spain
    Development 130:295-305. 2003
    ..Collectively, these findings suggest that interaction between segmental primordia is required for the normal development of the genital disc...
  92. ncbi The ken and barbie gene encoding a putative transcription factor with a BTB domain and three zinc finger motifs functions in terminalia development of Drosophila
    Tamas Lukacsovich
    ERATO Yamamoto Behavior Genes Project at Mitsubishi Kagaku Institute of Life Sciences, Tokyo, Japan
    Arch Insect Biochem Physiol 54:77-94. 2003
    ..All defects in ken and barbie mutants are fully rescued by the expression of a wild-type genomic construct, which establishes the causality between phenotypes and the gene...
  93. ncbi Translational repression by Bicoid: competition for the cap
    Paul M Macdonald
    Cell 121:321-2. 2005
    ..In this issue of Cell, solve a puzzle surrounding the action of the Drosophila Bicoid morphogen in formation of the Caudal protein gradient and in doing so describe a novel mechanism of translational repression...
  94. ncbi A new paradigm for translational control: inhibition via 5'-3' mRNA tethering by Bicoid and the eIF4E cognate 4EHP
    Park F Cho
    Department of Biochemistry, McGill Cancer Center, McGill University, 3655 Promenade Sir William Osler, Montreal, Quebec H3G 1Y6, Canada
    Cell 121:411-23. 2005
    ..In the Drosophila embryo, cap-dependent translation of the uniformly distributed caudal (cad) mRNA is inhibited in the anterior by Bicoid (Bcd) to create an asymmetric distribution of Cad protein...
  95. ncbi How to get ahead: the origin, evolution and function of bicoid
    Alistair P McGregor
    Department of Ecology and Evolutionary Biology, Princeton University, New Jersey 08540, USA
    Bioessays 27:904-13. 2005
    ..I suggest further comparative studies may allow us to identify the intermediate steps in bcd evolution. This will make bcd a paradigm for the origin and evolution of genes and regulatory networks...
  96. pmc aPKC controls microtubule organization to balance adherens junction symmetry and planar polarity during development
    Tony J C Harris
    Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
    Dev Cell 12:727-38. 2007
    ..aPKC apparently regulates this balance. Without aPKC, abnormally strong microtubule interactions break AJ symmetry and epithelial structure is lost...
  97. doi Age-related upregulation of Drosophila caudal gene via NF-kappaB in the adult posterior midgut
    Yoon Jeong Choi
    Department of Molecular Biology, College of Natural Science, Pusan National University, Busan 609 735, Republic of Korea
    Biochim Biophys Acta 1780:1093-100. 2008
    ..Our results may contribute to an understanding of the mechanisms of age-related changes in the number and activity of intestinal stem cells and progenitors in the Drosophila adult midgut...
  98. ncbi Accuracy of positional information provided by multiple morphogen gradients with correlated noise
    Yoshihiro Morishita
    Department of Biology, Faculty of Sciences, Kyushu University, Fukuoka 812 8581, Japan
    Phys Rev E Stat Nonlin Soft Matter Phys 79:061905. 2009
    ....
  99. pmc Homeo box gene expression in anterior and posterior regions of the Drosophila embryo
    T Hoey
    Proc Natl Acad Sci U S A 83:4809-13. 1986
    ..In this report we describe the isolation and properties of two additional homeo box genes, F90-2 and S67. Transcripts encoded by the two genes are detected in embryonic tissues that derive from regions near the anterior ..
  100. ncbi Expression of the homeo box gene family in Drosophila
    M Levine
    Cold Spring Harb Symp Quant Biol 50:209-22. 1985
  101. ncbi The gene serpent has homeotic properties and specifies endoderm versus ectoderm within the Drosophila gut
    R Reuter
    Max Planck Institut fur Entwicklungsbiologie, Abteilung V, Tubingen, FR Germany
    Development 120:1123-35. 1994
    ..serpent appears to act as a homeotic gene downstream of the terminal gap gene huckebein and to promote morphogenesis and differentiation of anterior and posterior midgut...