gt

Summary

Gene Symbol: gt
Description: giant
Alias: CG7952, DM17, Dmel\CG7952, EG:BACH7M4.5, GIAN_DROME, Giant, l(1)3Aa, l(1)giant, CG7952 gene product from transcript CG7952-RB, CG7952-PB, gt-PB
Species: fruit fly

Top Publications

  1. 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
  2. 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
  3. 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
  4. ncbi Complex regulation of early paired expression: initial activation by gap genes and pattern modulation by pair-rule genes
    T Gutjahr
    Institute of Molecular Biology II, University of Zurich, Switzerland
    Development 117:609-23. 1993
  5. pmc dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo
    Y Nibu
    Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    EMBO J 17:7009-20. 1998
  6. ncbi Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes
    G Riddihough
    Imperial Cancer Research Fund, Department of Zoology, University of Oxford, UK
    Genes Dev 5:840-54. 1991
  7. pmc Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
    Cris L Luengo Hendriks
    Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 7:R123. 2006
  8. 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
  9. ncbi Conservation of regulatory elements controlling hairy pair-rule stripe formation
    J A Langeland
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, Madison 53706
    Development 117:585-96. 1993
  10. ncbi A cascade of transcriptional control leading to axis determination in Drosophila
    D Niessing
    Abteilung Molekulare Entwick lungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    J Cell Physiol 173:162-7. 1997

Research Grants

  1. Computational and Functional Analysis of Gene Networks
    MARC HALFON; Fiscal Year: 2006
  2. BH3-only protein BNIP3 in tumor progression
    GOVINDASWAMY CHINNADURAI; Fiscal Year: 2006
  3. Apoptosis Signaling: BH3 to BH123 Proteins
    GOVINDASWAMY CHINNADURAI; Fiscal Year: 2008
  4. SUMO conjugation in cell biology and Development
    Albert J Courey; Fiscal Year: 2010

Scientific Experts

Detail Information

Publications147 found, 100 shown here

  1. 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...
  2. 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
    ....
  3. 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...
  4. ncbi Complex regulation of early paired expression: initial activation by gap genes and pattern modulation by pair-rule genes
    T Gutjahr
    Institute of Molecular Biology II, University of Zurich, Switzerland
    Development 117:609-23. 1993
    ..runt and hairy, and in all gap mutants suggests that the products of the gap genes hunchback, Krüppel, knirps and giant activate paired expression in stripes...
  5. pmc dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo
    Y Nibu
    Department of Molecular and Cellular Biology, Division of Genetics, 401 Barker Hall, University of California, Berkeley, CA 94720, USA
    EMBO J 17:7009-20. 1998
    ..We propose that dCtBP represents a major form of transcriptional repression in development, and that the Groucho and dCtBP co-repressors mediate separate pathways of repression...
  6. ncbi Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes
    G Riddihough
    Imperial Cancer Research Fund, Department of Zoology, University of Oxford, UK
    Genes Dev 5:840-54. 1991
    ..Our results suggest that different but overlapping subsets of gap genes regulate each stripe and that activation and repression are both important in generating the stripe pattern...
  7. pmc Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline
    Cris L Luengo Hendriks
    Berkeley Drosophila Transcription Network Project, Life Sciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, CA 94720, USA
    Genome Biol 7:R123. 2006
    ..To model and thoroughly understand animal transcription networks, it is essential to derive accurate spatial and temporal descriptions of developing gene expression patterns with cellular resolution...
  8. 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...
  9. ncbi Conservation of regulatory elements controlling hairy pair-rule stripe formation
    J A Langeland
    Howard Hughes Medical Institute, Laboratory of Molecular Biology, University of Wisconsin, Madison 53706
    Development 117:585-96. 1993
    ..approach, coupled with the analysis of reporter gene expression in gap mutant embryos suggests that the Kr and gt proteins establish the anterior and posterior borders of h stripe 5, respectively, through spatial repression...
  10. ncbi A cascade of transcriptional control leading to axis determination in Drosophila
    D Niessing
    Abteilung Molekulare Entwick lungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    J Cell Physiol 173:162-7. 1997
  11. 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
    ....
  12. ncbi Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo
    D Stanojevic
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, NY 10027
    Science 254:1385-7. 1991
    ..suggested that even-skipped (eve) stripe 2 is controlled by three gap genes, hunchback (hb), Kruppel (Kr), and giant (gt), and by the maternal morphogen bicoid (bcd)...
  13. pmc Diffusion and scaling during early embryonic pattern formation
    Thomas Gregor
    Howard Hughes Medical Institute, Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
    Proc Natl Acad Sci U S A 102:18403-7. 2005
    ..Our results, together with constraints imposed by the time scales of development, suggest that the mechanism for scaling is a species-specific adaptation of the Bcd lifetime...
  14. ncbi Mechanism of eve stripe formation
    J Reinitz
    Brookdale Center for Molecular Biology, Mt Sinai School of Medicine, New York, NY 10029, USA
    Mech Dev 49:133-58. 1995
    ..Third is the use of least squares fits to gene expression data to measure phenomenological parameters occurring in the gene circuit...
  15. 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...
  16. ncbi Region-specific defects in l(1)giant embryos of Drosophila melanogaster
    J P Petschek
    Dev Biol 119:175-89. 1987
    Lack of zygotic expression of the l(1)giant locus (l(1)gt;3A1), produces embryos with defects in abdominal A5, 6, and 7 and within the head...
  17. ncbi Positioning adjacent pair-rule stripes in the posterior Drosophila embryo
    J A Langeland
    Howard Hughes Medical Institute, R M Bock Laboratories, University of Wisconsin, Madison 53706, USA
    Development 120:2945-55. 1994
    ..stripe boundaries are established by gap protein repressors unique to each stripe: h stripe 5 is repressed by the giant (gt) protein on its posterior border and h stripe 6 is repressed by the hunchback (hb) protein on its posterior ..
  18. pmc Dual regulation by the Hunchback gradient in the Drosophila embryo
    Dmitri Papatsenko
    Department of Molecular and Cell Biology, Division of Genetics, Genomics, and Development, and Center for Integrative Genomics, University of California, Berkeley, CA 94720, USA
    Proc Natl Acad Sci U S A 105:2901-6. 2008
    ..The subsequent refinement of the Kr pattern depends on the combination of Hb and the Giant (Gt) repressor...
  19. pmc Anterior-posterior positional information in the absence of a strong Bicoid gradient
    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 106:3823-8. 2009
    ....
  20. 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...
  21. 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...
  22. 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
    ..We model the early mRNA and protein dynamics of the gap genes hunchback, Kruppel, giant, and knirps, taking as regulatory inputs the maternal Bicoid and Caudal gradients, plus the zygotic Tailless and ..
  23. ncbi Trans- and cis-acting requirements for blastodermal expression of the head gap gene buttonhead
    E A Wimmer
    Abteilung Molekulare Entwicklungsbiologie, Max Planck Institut fur biophysikalische Chemie, Gottingen, Germany
    Mech Dev 53:235-45. 1995
    ..Finally, the terminal system takes part in the regulation of btd head stripe expression by enhancing activation at low levels of activity and repression at high levels of activity...
  24. ncbi Segmentation
    Diethard Tautz
    Institut für Genetik der Universität zu Köln, Weyertal 121, 50931, Germany
    Dev Cell 7:301-12. 2004
    ..An old concept of comparative anatomy, the enterocoele theory, is compatible with a single origin of segmentation mechanisms and could therefore provide a conceptual framework for assessing these molecular similarities...
  25. pmc Regulation of even-skipped stripe 2 in the Drosophila embryo
    S Small
    Biology Department, UCSD, La Jolla 92093 0322
    EMBO J 11:4047-57. 1992
    ..The maternal morphogen bicoid (bcd) and the gap proteins hunchback (hb), Kruppel (Kr) and giant (gt) all bind with high affinity to closely linked sites within this small promoter element...
  26. pmc l(1)trol and l(1)devl, loci affecting the development of the adult central nervous system in Drosophila melanogaster
    S Datta
    Department of Biology, Yale University, New Haven, Connecticut 06511 8112
    Genetics 130:523-37. 1992
    ..Two of these, including one that is allelic to l(1)zw1, were chosen for further analysis...
  27. ncbi The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes
    M Capovilla
    Department of Cell Biology, Baylor College of Medicine, Houston, Texas 77030
    Development 114:99-112. 1992
    The sequence of a cDNA from the giant gene of Drosophila shows that its product has a basic domain followed by a leucine zipper motif. Both features contain characteristic conserved elements of the b-ZIP family of DNA-binding proteins...
  28. ncbi Interactions of the Drosophila gap gene giant with maternal and zygotic pattern-forming genes
    E D Eldon
    Department of Cell Biology, Baylor College of Medicine, Texas Medical Center, Houston 77030
    Development 111:367-78. 1991
    The Drosophila gene giant (gt) is a segmentation gene that affects anterior head structures and abdominal segments A5-A7...
  29. ncbi Spatial regulation of the gap gene giant during Drosophila development
    R Kraut
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, NY 10027
    Development 111:601-9. 1991
    We describe the regulated expression of the segmentation gene giant (gt) during early embryogenesis. The gt protein is expressed in two broad gradients in precellular embryos, one in anterior regions and the other in posterior regions...
  30. ncbi Mutually repressive interactions between the gap genes giant and Krüppel define middle body regions of the Drosophila embryo
    R Kraut
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, NY 10027
    Development 111:611-21. 1991
    ..Here we present evidence that the segmentation gene giant is a bona fide gap gene that is likely to act in concert with hunchback, Krüppel and knirps to initiate stripes ..
  31. ncbi Transcriptional regulation of a pair-rule stripe in Drosophila
    S Small
    Department of Biological Sciences, Fairchild Center, Columbia University, New York, New York 10027
    Genes Dev 5:827-39. 1991
    ..hunchback (hb), while the borders of the stripe are formed by selective repression, involving the gap protein giant (gt) in anterior regions and the Krüppel (Kr) protein in posterior regions...
  32. ncbi Zebra patterns in fly embryos: activation of stripes or repression of interstripes?
    S B Carroll
    Laboratory of Molecular Biology, University of Wisconsin, Madison 53706
    Cell 60:9-16. 1990
    ..Different gap proteins control different subsets of stripes and interstripes. Combinations of gap proteins regulate transcription by binding to far upstream elements that contain different numbers and types of binding sites...
  33. 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
    ..this system, we show that the cad domain functions by activating the expression of the abdominal gap genes knirps (kni) and giant (gt). We conclude that cad is the so far missing region-specific activator of abdominal segmentation genes.
  34. ncbi Model for cooperative control of positional information in Drosophila by bicoid and maternal hunchback
    J Reinitz
    Center for Medical Informatics, Yale Medical School, New Haven, Connecticut 06510
    J Exp Zool 271:47-56. 1995
    ..The model shows that positional information in the presumptive middle body is cooperatively determined by maternal products of the bicoid and hunchback genes...
  35. ncbi Gap gene properties of the pair-rule gene runt during Drosophila segmentation
    C Tsai
    Department of Biochemistry and Cell Biology, State University of New York at Stony Brook 11794 5215
    Development 120:1671-83. 1994
    ..Finally, genetic experiments demonstrated that regulation of gap gene expression by runt is a normal component of the regulatory program that generates the segmented body pattern of the Drosophila embryo...
  36. ncbi Morphogens, compartments, and pattern: lessons from drosophila?
    P A Lawrence
    Medical Research Council Laboratory of Molecular Biology, Cambridge, United Kingdom
    Cell 85:951-61. 1996
  37. ncbi The Dichaete gene of Drosophila melanogaster encodes a SOX-domain protein required for embryonic segmentation
    S R Russell
    Department of Genetics, University of Cambridge, UK
    Development 122:3669-76. 1996
    ....
  38. 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...
  39. 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...
  40. ncbi Segmentation: painting stripes from flies to vertebrates
    L Pick
    Brookdale Center for Developmental and Molecular Biology, Mt Sinai School of Medicine, New York, NY 10029, USA
    Dev Genet 23:1-10. 1998
  41. ncbi Stripe forming architecture of the gap gene system
    J Reinitz
    Brookdale Center for Molecular Biology, Mt Sinai School of Medicine, NY 10029, USA
    Dev Genet 23:11-27. 1998
    ..It is argued that the constraints on gap gene architecture identified here are a consequence of selective pressures that minimize the number of gap genes required to determine segments in long-germ band insects...
  42. 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
    ..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 of the earliest stages of the ..
  43. 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...
  44. ncbi Decoding cis-regulatory DNAs in the Drosophila genome
    Michele Markstein
    Department of Molecular Cell Biology, Division of Genetics and Development, 401 Barker Hall, University of California, Berkeley, California 94720, USA
    Curr Opin Genet Dev 12:601-6. 2002
    ..These methods change the way that cis-DNAs will be analyzed in future studies and offer the promise of unraveling complex gene networks...
  45. pmc Homotypic regulatory clusters in Drosophila
    Alexander P Lifanov
    Institute of Chemical Physics, Moscow, 117421 Russia
    Genome Res 13:579-88. 2003
    ..We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators...
  46. 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
    ..Finally, our models suggest a correlation between timing of gap domain boundary formation and regulatory contributions from the terminal maternal system...
  47. ncbi Different combinations of gap repressors for common stripes in Anopheles and Drosophila embryos
    Yury Goltsev
    Department of Molecular and Cellular Biology, Division of Genetics and Development, University of California, Berkeley, CA 94720, USA
    Dev Biol 275:435-46. 2004
    ..The gap genes hunchback and giant display inverted patterns of expression in posterior regions of Anopheles embryos, while tailless exhibits an ..
  48. ncbi Control of Drosophila body pattern by the hunchback morphogen gradient
    G Struhl
    Howard Hughes Medical Institute, Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, New York 10032
    Cell 69:237-249. 1992
    ..are specified early in embryogenesis by the overlapping activities of the hunchback (hb), Krüppel, knirps, and giant gap genes...
  49. ncbi Control and function of terminal gap gene activity in the posterior pole region of the Drosophila embryo
    G Bronner
    Institut fur Genetik und Mikrobiologie, Universitat Munchen, F R G
    Mech Dev 35:205-11. 1991
    ..This, in turn, suggests that the terminal gap gene activities prevent metamerization by repression of central gap genes, thereby distinguishing the segmented trunk from the nonsegmented tail region of the embryo...
  50. 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
    ..We have analyzed the pattern of expression of a variety of homeotic, pair-rule, and gap genes in tailless and giant gap mutants. tailless acts in two domains, one anterodorsal and one posterior...
  51. pmc A novel spatial transcription pattern associated with the segmentation gene, giant, of Drosophila
    J Mohler
    Department of Cell Biology, Baylor College of Medicine, Houston, TX 77030
    EMBO J 8:1539-48. 1989
    The segmentation gene, giant, is located in 3A1 within a cloned chromosome region surrounding the zeste locus...
  52. ncbi Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues
    T Goto
    Department of Biochemistry, Harvard University, Cambridge, Massachusetts 02138
    Cell 57:413-22. 1989
    ..As a consequence of this two-step regulatory program, eve functions both in the establishment of the periodic pattern of gene expression and in the subsequent specification of parasegmental boundaries...
  53. 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
    ..factor, but rather prevents the repressor hunchback from acting in the posterior half so that the gap genes giant (gt) and knirps (kni) are activated by an as yet unknown transcription factor...
  54. pmc A role of polycomb group genes in the regulation of gap gene expression in Drosophila
    F Pelegri
    Whitehead Institute, Howard Hughes Medical Institute, Cambridge, Massachusetts
    Genetics 136:1341-53. 1994
    ..In the absence of nanos high levels of Hb protein repress the abdomen-specific genes knirps and giant. In suppressor-of-nanos mutants, knirps and giant are expressed in spite of high Hb levels...
  55. ncbi The eve stripe 2 enhancer employs multiple modes of transcriptional synergy
    D N Arnosti
    Department of Biology, UCSD, La Jolla 92093 0347, USA
    Development 122:205-14. 1996
    ..to activate the stripe in the anterior half of the embryo, bcd also coordinates the expression of two repressors, giant (gt) and Kruppel (Kr), which define the anterior and posterior borders of the stripe, respectively...
  56. ncbi Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo
    S Small
    Department of Biology, New York University, New York 10003, USA
    Dev Biol 175:314-24. 1996
    ..These findings suggest a general model for the regulation of segmentation stripes, whereby enhancers integrate positional information provided by broadly distributed activators and spatially restricted repressors...
  57. ncbi Disperse versus compact elements for the regulation of runt stripes in Drosophila
    M Klingler
    Zoologisches Institut, Luisenstrasse 14, Munich, D 80333, Germany
    Dev Biol 177:73-84. 1996
    ..Such disperse elements mediating pair-rule gene interactions may have escaped detection in other segmentation genes and may involve molecular mechanisms different from those mediating regulation by gap genes...
  58. ncbi Orthodenticle regulation during embryonic head development in Drosophila
    Q Gao
    University of Pennsylvania School of Medicine, Department of Neuroscience, Philadelphia, PA 19104, USA
    Mech Dev 56:3-15. 1996
    ..Finally, we identify a novel pathway mediated by the gap gene huckebein through which three maternal systems cooperate to repress otd expression at the anterior terminus of the embryo...
  59. ncbi Concentration-dependent patterning by an ectopic expression domain of the Drosophila gap gene knirps
    D Kosman
    Department of Biology, New York University, NY 10003, USA
    Development 124:1343-54. 1997
    ..Evidence is presented that the level and timing of expression, as well as protein diffusion, are important for determining the specific responses of target genes...
  60. ncbi Different levels of Ras activity can specify distinct transcriptional and morphological consequences in early Drosophila embryos
    S Greenwood
    Howard Hughes Medical Institute, and Department of Genetics and Development, Columbia University College of Physicians and Surgeons, New York, NY 10032, USA
    Development 124:4879-86. 1997
    ....
  61. ncbi Two distinct mechanisms for differential positioning of gene expression borders involving the Drosophila gap protein giant
    X Wu
    Department of Biology, New York University, New York, NY 10003, USA
    Development 125:3765-74. 1998
    We have combined genetic experiments and a targeted misexpression approach to examine the role of the gap gene giant (gt) in patterning anterior regions of the Drosophila embryo...
  62. pmc Analysis of an even-skipped rescue transgene reveals both composite and discrete neuronal and early blastoderm enhancers, and multi-stripe positioning by gap gene repressor gradients
    M Fujioka
    Department of Microbiology and Immunology, Kimmel Cancer Institute, Thomas Jefferson University, Philadelphia, PA 19107, USA
    Development 126:2527-38. 1999
    ..analysis in gap gene mutants showed that stripe 5 is restricted anteriorly by Krüppel and posteriorly by giant, the same repressors that regulate stripe 2...
  63. ncbi Functional analysis of repressor binding sites in the iab-2 regulatory region of the abdominal-A homeotic gene
    M J Shimell
    Department of Genetics, University of Minnesota, Minneapolis, Minnesota, 55455, USA
    Dev Biol 218:38-52. 2000
    ..We also show that the gap repressor Giant (GT) initially establishes a posterior expression limit at PS9, which shifts posteriorly after the blastoderm ..
  64. ncbi Transcriptional repression: the long and the short of it
    A J Courey
    Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
    Genes Dev 15:2786-96. 2001
  65. ncbi Drosophila atrophin homolog functions as a transcriptional corepressor in multiple developmental processes
    Sheng Zhang
    Howard Hughes Medical Institute, Department of Genetics, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06535, USA
    Cell 108:45-56. 2002
    ..We propose that Atrophin proteins function as versatile transcriptional corepressors and discuss a model that deregulation of transcription may contribute to the pathogenesis of neurodegeneration...
  66. 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.
  67. ncbi Establishment of developmental precision and proportions in the early Drosophila embryo
    Bahram Houchmandzadeh
    Howard Hughes Medical Institute, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, USA
    Nature 415:798-802. 2002
    ..We show that genes known to interact directly with Hb are not responsible for its spatial precision, but that the maternal gene staufen may be crucial...
  68. ncbi Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms
    Luiz Paulo Moura Andrioli
    Department of Biology, New York University, 1009 Main Building, 100 Washington Square East, New York 10003 6688, USA
    Development 129:4931-40. 2002
    ..The gap gene giant (gt) is involved in a repression mechanism that sets the anterior stripe border, but genetic removal of gt (or ..
  69. ncbi FlyMove--a new way to look at development of Drosophila
    Katrin Weigmann
    Institut fur Neurobiologie, Universitat Munster, Badestrasse 9, D 48149 Munster, Germany
    Trends Genet 19:310-1. 2003
    ..Here, we introduce FlyMove (http://flymove.uni-muenster.de), a new database combining movies, animated schemata, interactive "modules" and pictures that will greatly facilitate the understanding of Drosophila development...
  70. pmc Functional similarity of Knirps CtBP-dependent and CtBP-independent transcriptional repressor activities
    Jae Ryeon Ryu
    Department of Biochemistry and Molecular Biology and Program in Genetics, Michigan State University, East Lansing, MI 48824 1319, USA
    Nucleic Acids Res 31:4654-62. 2003
    ....
  71. 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...
  72. ncbi Dynamic control of positional information in the early Drosophila embryo
    Johannes Jaeger
    Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, New York 11794 3600, USA
    Nature 430:368-71. 2004
    ....
  73. 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...
  74. 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...
  75. 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...
  76. pmc cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster
    Meghana M Kulkarni
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 1319, USA
    Mol Cell Biol 25:3411-20. 2005
    ..This cis-regulatory "grammar" may aid the identification of enhancers regulated by short-range repressors and facilitate bioinformatic prediction of the functional output of transcriptional regulatory sequences...
  77. pmc Bicoid cooperative DNA binding is critical for embryonic patterning in Drosophila
    Danielle Lebrecht
    Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, NY 12208, USA
    Proc Natl Acad Sci U S A 102:13176-81. 2005
    ..The mutants did not faithfully stimulate transcription of downstream target genes such as hunchback (hb), giant, and Krüppel...
  78. ncbi Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes
    Shuji Ishihara
    Department of Pure and Applied Sciences, University of Tokyo, Komaba, Tokyo 153 8902, Japan
    Genes Cells 10:1025-38. 2005
    ..Our database study of gene regulatory networks indicates that most feed-forward loops actually cross talk. We discuss how the feed-forward loops and their cross talks can play important roles in morphogenesis...
  79. ncbi Developmental mechanisms and cis-regulatory codes
    Amanda Ochoa-Espinosa
    New York University, 100 Washington Square East, New York, NY 10003, USA
    Curr Opin Genet Dev 16:165-70. 2006
    ..They also suggest that CRMs involved in specific types of developmental events have common binding site architectures, which can be linked to their specific functions...
  80. ncbi Sexual reproduction selects for robustness and negative epistasis in artificial gene networks
    Ricardo B R Azevedo
    Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204 5001, USA
    Nature 440:87-90. 2006
    ..Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path...
  81. 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...
  82. pmc Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution II: dynamics
    Soile V E Keränen
    Berkeley Drosophila Transcription Network Project, Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA
    Genome Biol 7:R124. 2006
    ..To accurately describe gene expression and computationally model animal transcriptional networks, it is essential to determine the changing locations of cells in developing embryos...
  83. pmc Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster
    Johannes Jaeger
    Department of Applied Mathematics and Statistics, and Center for Developmental Genetics, Stony Brook University, Stony Brook, NY 11794 3600, USA
    Mech Dev 124:108-28. 2007
    ..present new, quantitative data on the mRNA expression patterns for the gap genes Krüppel (Kr), knirps (kni) and giant (gt) during the early blastoderm stage of Drosophila development...
  84. pmc Pre-steady-state decoding of the Bicoid morphogen gradient
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 5:e46. 2007
    ..This can explain the surprisingly small shifts in gap and pair-rule gene expression domains observed in response to alterations in bcd dosage...
  85. 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
    ....
  86. pmc Canalization of segmentation and its evolution in Drosophila
    Susan E Lott
    Committee on Genetics, Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA
    Proc Natl Acad Sci U S A 104:10926-31. 2007
    ..Specifically, we ask whether spatial localization of gap genes Kruppel (Kr) and giant (gt) and the pair-rule gene even-skipped (eve) during cellularization is robust to genetic variation in embryo ..
  87. 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...
  88. doi A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm
    Charless C Fowlkes
    Berkeley Drosophila Transcription Network Project, University of California, Irvine, CA 92697, USA
    Cell 133:364-74. 2008
    ..We present a VirtualEmbryo containing data for 95 genes at six time cohorts. We show that known gene-regulatory interactions can be automatically recovered from this data set and predict hundreds of new interactions...
  89. pmc Precise registration of gene expression boundaries by a repressive morphogen in Drosophila
    Danyang Yu
    Department of Biology, New York University, 100 Washington Square East, New York, NY 10003, USA
    Curr Biol 18:868-76. 2008
    ..Despite intensive study, it is still unclear how the concentration profiles within gradients are spatially related to the critical patterning thresholds they generate...
  90. 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...
  91. 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
    ....
  92. 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...
  93. pmc Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo
    Walid D Fakhouri
    Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 1319, USA
    Mol Syst Biol 6:341. 2010
    ..uncovered unexpected features of these proteins' activity that allow accurate predictions of regulation by the Giant, Knirps, Krüppel, and Snail repressors, including modeling of an endogenous enhancer...
  94. pmc Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers
    Richard W Lusk
    Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
    PLoS Genet 6:e1000829. 2010
    ..melanogaster enhancers. Thus, this study calls into question the common practice of inferring "cis-regulatory grammars" from the organization and evolutionary dynamics of developmental enhancers...
  95. pmc Precision and scaling in morphogen gradient read-out
    Aitana Morton de Lachapelle
    Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
    Mol Syst Biol 6:351. 2010
    ..Our measurements confirm this trend, indicating almost perfect scaling except for anterior most expression domains, which overcompensate fluctuations in embryo length...
  96. 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
    ....
  97. 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...
  98. 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...
  99. 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...
  100. pmc Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo
    Michael W Perry
    Department of Integrative Biology, Biophysics Graduate Group, University of California, Berkeley, CA 94720 3200, USA
    Proc Natl Acad Sci U S A 108:13570-5. 2011
    ..We present different models for "enhancer synergy," whereby two enhancers with overlapping activities produce authentic patterns of gene expression...
  101. 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...

Research Grants4

  1. Computational and Functional Analysis of Gene Networks
    MARC HALFON; Fiscal Year: 2006
    ..abstract_text> ..
  2. BH3-only protein BNIP3 in tumor progression
    GOVINDASWAMY CHINNADURAI; Fiscal Year: 2006
    ..Our results may also provide the experimental support to suggest that BNIP3 may be a new prognostic marker for human cancer. [unreadable] [unreadable]..
  3. Apoptosis Signaling: BH3 to BH123 Proteins
    GOVINDASWAMY CHINNADURAI; Fiscal Year: 2008
    ..The knowledge gained would be valuable in modulating the activity of BAX in cancer and in degenerative diseases. ..
  4. SUMO conjugation in cell biology and Development
    Albert J Courey; Fiscal Year: 2010
    ..Consequently, the research proposed here will advance our understanding of human disease. ..