Enhancer responses to similarly distributed antagonistic gradients in development

PLoS Computational Biology

Volumn 3, Issue 5, 2007, Pages 0826-0835

  Zinzen, Robert P ^a,b   Papatsenko, Dmitri ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY;

CONTROL REGION; DROSOPHILA EMBRYOS; GENE CONTROL; GENE EXPRESSION PATTERNS; GENES EXPRESSION; MODEL-BASED OPC; PRINCIPLES OF INTERACTIONS; QUANTITATIVE MODELS; TRANSCRIPTIONAL REGULATOR; TRANSCRIPTIONAL RESPONSE;

TRANSCRIPTION;

TRANSCRIPTION FACTOR; DROSOPHILA PROTEIN;

ARTICLE; DEVELOPMENTAL GENE; DEVELOPMENTAL GENETICS; DNA SEQUENCE; DROSOPHILA; EMBRYO DEVELOPMENT; EMBRYO PATTERN FORMATION; ENHANCER REGION; GENE EXPRESSION; GENE REPRESSION; GENE TARGETING; INSECT DEVELOPMENT; MATHEMATICAL MODEL; NEUROECTODERM; TRANSCRIPTION REGULATION; ADAPTATION; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MORPHOGENESIS; PHYSIOLOGY; PRENATAL DEVELOPMENT; REGULATORY SEQUENCE;

ADAPTATION, PHYSIOLOGICAL; ANIMALS; BODY PATTERNING; COMPUTER SIMULATION; DROSOPHILA; DROSOPHILA PROTEINS; GENE EXPRESSION REGULATION, DEVELOPMENTAL; MODELS, BIOLOGICAL; REGULATORY SEQUENCES, NUCLEIC ACID; TRANSCRIPTION FACTORS;

EID: 34249722123     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030084     Document Type: Article

References (72)

1. Reinitz J, Hou S, Sharp DH (2003) Transcriptional control in Drosophila. Complexus 1: 54-56.
2. Bolouri H, Davidson EH (2003) Transcriptional regulatory cascades in development: Initial rates, not steady state, determine network kinetics. Proc Natl Acad Sci U S A 100: 9371-9376.
3. Ramsey S, Orrell D, Bolouri H (2005) Dizzy: Stochastic simulation of large-scale genetic regulatory networks. J Bioinform Comput Biol 3: 415-436.
4. Philippakis AA, Busser BW, Gisselbrecht SS, He FS, Estrada B, et al. (2006) Expression-guided in silico evaluation of candidate cis regulatory codes for Drosophila muscle founder cells. PLoS Comput Biol 2: e53.
5. Zhu Z, Shendure J, Church GM (2005) Discovering functional transcription-factor combinations in the human cell cycle. Genome Res 15: 848-855.
6. Zinzen RP, Senger K, Levine M, Papatsenko D (2006) Computational models for neurogenic gene expression in the Drosophila embryo. Curr Biol 16: 1358-1365.
7. Janssens H, Hou S, Jaeger J, Kim AR, Myasnikova E, et al. (2006) Quantitative and predictive model of transcriptional control of the Drosophila melanogaster even skipped gene. Nat Genet 38: 1159-1165.
8. Levine M, Davidson EH (2005) Gene regulatory networks for development. Proc Natl Acad Sci U S A 102: 4936-4942.
9. Stathopoulos A, Levine M (2005) Genomic regulatory networks and animal development. Dev Cell 9: 449-462.
10. Michelson AM, Bulyk ML (2006) Biological code breaking in the 21st century. Mol Syst Biol 2: 2006.0018.
11. Reeves GT, Muratov CB, Schupbach T, Shvartsman SY (2006) Quantitative models of developmental pattern formation. Dev Cell 11: 289-300.
12. Estrada B, Choe SE, Gisselbrecht SS, Michaud S, Raj L, et al. (2006) An integrated strategy for analyzing the unique developmental programs of different myoblast subtypes. PLoS Genet 2: e16.
13. Markstein M, Zinzen R, Markstein P, Yee KP, Erives A, et al. (2004) A regulatory code for neurogenic gene expression in the Drosophila embryo. Development 131: 2387-2394.
14. Ochoa-Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, et al. (2005) The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc Natl Acad Sci U S A 102: 4960-4965.
15. Makeev VJ, Lifanov AP, Nazina AG, Papatsenko DA (2003) Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res 31: 6016-6026.
16. Fu D, Wen Y, Ma J (2004) The co-activator CREB-binding protein participates in enhancer-dependent activities of bicoid. J Biol Chem 279: 48725-48733.
17. Erives A, Levine M (2004) Coordinate enhancers share common organizational features in the Drosophila genome. Proc Natl Acad Sci U S A 101: 3851-3856.
18. Papatsenko D, Levine M (2005) Quantitative analysis of binding motifs mediating diverse spatial readouts of the Dorsal gradient in the Drosophila embryo. Proc Natl Acad Sci U S A 102: 4966-4971.
19. Senger K, Armstrong GW, Rowell WJ, Kwan JM, Markstein M, et al. (2004) Immunity regulatory DNAs share common organizational features in Drosophila. Mol Cell 13: 19-32.
20. Cave JW, Loh F, Surpris JW, Xia L, Caudy MA (2005) A DNA transcription code for cell-specific gene activation by notch signaling. Curr Biol 15: 94-104.
21. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, et al. (2005) Transcriptional regulation by the numbers: Models. Curr Opin Genet Dev 15: 116-124.
22. Cai HN, Arnosti DN, Levine M (1996) Long-range repression in the Drosophila embryo. Proc Natl Acad Sci U S A 93: 9309-9314.
23. Kulkarni MM, Arnosti DN (2005) cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Mol Cell Biol 25: 3411-3420.
24. Struffi P, Arnosti DN (2005) Functional interaction between the Drosophila knirps short range transcriptional repressor and RPD3 histone deacetylase. J Biol Chem 280: 40757-40765.
25. Hvidsten TR, Wilczynski B, Kryshtafovych A, Tiuryn J, Komorowski J, et al. (2005) Discovering regulatory binding-site modules using rule-based learning. Genome Res 15: 856-866.
26. Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, et al. (2006) TRANSFAC and its module TRANSCompel: Transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34: D108-D110.
27. Ligr M, Siddharthan R, Cross F, Siggia E (2006) Gene expression from random libraries of yeast promoters. Genetics 172: 2113-2122.
28. Ludwig MZ, Bergman C, Patel NH, Kreitman M (2000) Evidence for stabilizing selection in a eukaryotic enhancer element. Nature 403: 564-567.
29. Ludwig MZ, Palsson A, Alekseeva E, Bergman CM, Nathan J, et al. (2005) Functional evolution of a cis-regulatory module. PLoS Biol 3: e93.
30. Berman BP, Pfeiffer BD, Laverty TR, Salzberg SL, Rubin GM, et al. (2004) Computational identification of developmental enhancers: Conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol 5: R61.
31. Papatsenko D, Kislyuk A, Levine M, Dubchak I (2006) Conservation patterns in different functional sequence categories of divergent Drosophila species. Genomics 88: 431-442.
32. Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, et al. (2006) Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124: 47-59.
33. Zhang H, Levine M (1999) Groucho and dCtBP mediate separate pathways of transcriptional repression in the Drosophila embryo. Proc Natl Acad Sci U S A 96: 535-540.
34. Merika M, Thanos D(2001) Enhanceosomes. Curr Opin Genet Dev 11: 205-208.
35. Blazek E, Mittler G, Meisterernst M (2005) The mediator of RNA polymerase II. Chromosoma 113: 399-408.
36. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, et al. (2005) Transcriptional regulation by the numbers: Applications. Curr Opin Genet Dev 15: 125-135.
37. Stanojevic D, Small S, Levine M (1991) Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo. Science 254: 1385-1387.
38. Stathopoulos A, Levine M (2004) Whole-genome analysis of Drosophila gastrulation. Curr Opin Genet Dev 14: 477-484.
39. Istrail S, Davidson EH (2005) Logic functions of the genomic cis-regulatory code. Proc Natl Acad Sci U S A 102: 4954-4959.
40. Ackers GK, Johnson AD, Shea MA (1982) Quantitative model for gene regulationby lambdaphage repressor. Proc Natl Acad SciUSA79: 1129-1133.
41. von Hippel PH, Berg OG (1989) Facilitated target location in biological systems. J Biol Chem 264: 675-678.
42. de Las Heras JM, Casanova J (2006) Spatially distinct downregulation of Capicua repression and tailless activation by the Torso RTK pathway in the Drosophila embryo. Mech Dev 123: 481-486.
43. Brakefield PM, Gates J, Keys D, Kesbeke F, Wijngaarden PJ, et al. (1996) Development, plasticity and evolution of butterfly eyespot patterns. Nature 384: 236-242.
44. Lifanov AP, Makeev VJ, Nazina AG, Papatsenko DA (2003) Homotypic regulatory clusters in Drosophila. Genome Res 13: 579-588.
45. Slutsky M, Mirny LA (2004) Kinetics of protein-DNA interaction: Facilitated target location in sequence-dependent potential. Biophys J 87: 4021-4035.
46. Small S, Kraut R, Hoey T, Warrior R, Levine M (1991) Transcriptional regulation of a pair-rule stripe in Drosophila. Genes Dev 5: 827-839.
47. Ptashne M (2005) Regulation of transcription: From lambda to eukaryotes. Trends Biochem Sci 30: 275-279.
48. Gray S, Szymanski P, Levine M (1994) Short-range repression permits multiple enhancers to function autonomously within a complex promoter. Genes Dev 8: 1829-1838.
49. Jaeger J, Reinitz J (2006) On the dynamic nature of positional information. Bioessays 28: 1102-1111.
50. Wu X, Vakani R, Small S (1998) Two distinct mechanisms for differential positioning of gene expression borders involving the Drosophila gap protein giant. Development 125: 3765-3774.
51. Ip YT, Park RE, Kosman D, Bier E, Levine M (1992) The dorsal gradient morphogen regulates stripes of rhomboid expression in the presumptive neuroectoderm of the Drosophila embryo. Genes Dev 6: 1728-1739.
52. Bergmann S, Sandler O, Sberro H, Shnider S, Schejter E, et al. (2007) Presteady-state decoding of the Bicoid morphogen gradient. PLoS Biol 5: e46.
53. Ishihara S, Fujimoto K, Shibata T (2005) Cross talking of network motifs in gene regulation that generates temporal pulses and spatial stripes. Genes Cells 10: 1025-1038.
54. Hulskamp M, Pfeifle C, Tautz D (1990) A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Kruppel and knirps in the early Drosophila embryo. Nature 346: 577-580.
55. Moussian B, Roth S (2005) Dorsoventral axis formation in the Drosophila embryo - Shaping and transducing a morphogen gradient. Curr Biol 15: R887-R899.
56. Pankratz MJ, Busch M, Hoch M, Seifert E, Jackle H (1992) Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system. Science 255: 986-989.
57. Rivera-Pomar R, Lu X, Perrimon N, Taubert H, Jackle H (1995) Activation of posterior gap gene expression in the Drosophila blastoderm. Nature 376: 253-256.
58. Schroeder MD, Pearce M, Fak J, Fan H, Unnerstall U, et al. (2004) Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol 2: E271.
59. Jaeger J, Sharp DH, Reinitz J (2007) Known maternal gradients are not sufficient for the establishment of gap domains in Drosophila melanogaster. Mech Dev 124: 108-128.
60. Poustelnikova E, Pisarev A, Blagov M, Samsonova M, Reinitz J (2004) A database for management of gene expression data in situ. Bioinformatics 20: 2212-2221.
61. McCarty AS, Kleiger G, Eisenberg D, Smale ST (2003) Selective dimerization of a C2H2 zinc finger subfamily. Mol Cell 11: 459-470.
62. Jaeger J, Surkova S, Blagov M, Janssens H, Kosman D, et al. (2004) Dynamic control of positional information in the early Drosophila embryo. Nature 430: 368-371.
63. Margolis JS, Borowsky ML, Steingrimsson E, Shim CW, Lengyel JA, et al. (1995) Posterior stripe expression of hunchback is driven from two promoters by a common enhancer element. Development 121: 3067-3077.
64. Greenwood S, Struhl G (1997) Different levels of Ras activity can specify distinct transcriptional and morphological consequences in early Drosophila embryos. Development 124: 4879-4886.
65. Reed RD, Serfas MS (2004) Butterfly wing pattern evolution is associated with changes in a Notch/Distal-less temporal pattern formation process. Curr Biol 14: 1159-1166.
66. Keys DN, Lewis DL, Selegue JE, Pearson BJ, Goodrich LV, et al. (1999) Recruitment of a hedgehog regulatory circuit in butterfly eyespot evolution. Science 283: 532-534.
67. Brunetti CR, Selegue JE, Monteiro A, French V, Brakefield PM, et al. (2001) The generation and diversification of butterfly eyespot color patterns. Curr Biol 11: 1578-1585.
68. Lall S, Ludwig MZ, Patel NH (2003) Nanos plays a conserved role in axial patterning outside of the Diptera. Curr Biol 13: 224-229.
69. Bolinger RA, Boekhoff-Falk G (2005) Distal-less functions in subdividing the Drosophila thoracic limb primordium. Dev Dyn 232: 801-816.
70. Myasnikova E, Samsonova M, Kosman D, Reinitz J (2005) Removal of background signal from in situ data on the expression of segmentation genes in Drosophila. Dev Genes Evol 215: 320-326.
71. Jiang J, Cai H, Zhou Q, Levine M (1993) Conversion of a dorsal-dependent silencer into an enhancer: Evidence for dorsal corepressors. EMBO J 12: 3201-3209.
72. Hosoyama N, Nasimul N, Iba H (2003) Layout search of a gene regulatory network for 3-D visualization. Genome Inform Ser 14: 104-113.