Gene Symbol: kni
Description: knirps
Alias: CG4717, Dmel\CG4717, KNI, KNIRPS, Kni, NR0A1, knr, knirps, CG4717-PA, CG4717-PB, kni-PA, kni-PB, radius incompletus
Species: fruit fly
Products:     kni

Top Publications

  1. Houchmandzadeh B, Wieschaus E, Leibler S. Establishment of developmental precision and proportions in the early Drosophila embryo. Nature. 2002;415:798-802 pubmed
    ..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. ..
  2. Gao Q, Wang Y, Finkelstein R. Orthodenticle regulation during embryonic head development in Drosophila. Mech Dev. 1996;56:3-15 pubmed
    ..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. ..
  3. Isalan M, Lemerle C, Serrano L. Engineering gene networks to emulate Drosophila embryonic pattern formation. PLoS Biol. 2005;3:e64 pubmed
    ..We anticipate that the system described here will be generally applicable to the study of any biological network with a spatial component. ..
  4. Kim A, Martinez C, Ionides J, Ramos A, Ludwig M, Ogawa N, et al. Rearrangements of 2.5 kilobases of noncoding DNA from the Drosophila even-skipped locus define predictive rules of genomic cis-regulatory logic. PLoS Genet. 2013;9:e1003243 pubmed publisher
  5. Papatsenko D, Makeev V, Lifanov A, Regnier M, Nazina A, Desplan C. Extraction of functional binding sites from unique regulatory regions: the Drosophila early developmental enhancers. Genome Res. 2002;12:470-81 pubmed
    ..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. ..
  6. Ajuria L, Nieva C, Winkler C, Kuo D, Samper N, Andreu M, et al. Capicua DNA-binding sites are general response elements for RTK signaling in Drosophila. Development. 2011;138:915-24 pubmed publisher
    ..We conclude that Capicua octamers are general response elements for RTK signaling in Drosophila. ..
  7. Ribeiro C, Ebner A, Affolter M. In vivo imaging reveals different cellular functions for FGF and Dpp signaling in tracheal branching morphogenesis. Dev Cell. 2002;2:677-83 pubmed
    ..Bnl/FGF signaling affects the formation of dynamic filopodia, possibly controlling cytoskeletal activity and motility as such, and Dpp controls cellular functions allowing branch morphogenesis and outgrowth. ..
  8. Yu D, Small S. Precise registration of gene expression boundaries by a repressive morphogen in Drosophila. Curr Biol. 2008;18:868-76 pubmed publisher
  9. Bronner G, Jackle H. Control and function of terminal gap gene activity in the posterior pole region of the Drosophila embryo. Mech Dev. 1991;35:205-11 pubmed
    ..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. ..

More Information


  1. Wang L, Rajan H, Pitman J, McKeown M, Tsai C. Histone deacetylase-associating Atrophin proteins are nuclear receptor corepressors. Genes Dev. 2006;20:525-30 pubmed
    ..Using the established regulation of knirps by tll as a paradigm, we report that repression of knirps by Tll involves Atrophin, which is related to vertebrate ..
  2. Surkova S, Kosman D, Kozlov K, Manu -, Myasnikova E, Samsonova A, et al. Characterization of the Drosophila segment determination morphome. Dev Biol. 2008;313:844-62 pubmed
    ..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...
  3. Hooper K, Parkhurst S, Ish Horowicz D. Spatial control of hairy protein expression during embryogenesis. Development. 1989;107:489-504 pubmed
    ..Our observations suggest that pair-rule striping may be under redundant control, and we discuss possible implications for hierarchical models of pair-rule gene action. ..
  4. Schroeder M, Pearce M, Fak J, Fan H, Unnerstall U, Emberly E, et al. Transcriptional control in the segmentation gene network of Drosophila. PLoS Biol. 2004;2:E271 pubmed
    ..The study demonstrates that computational methods are a powerful complement to experimental approaches in the analysis of transcription networks. ..
  5. Marco A, Konikoff C, Karr T, Kumar S. Relationship between gene co-expression and sharing of transcription factor binding sites in Drosophila melanogaster. Bioinformatics. 2009;25:2473-7 pubmed publisher
    ..We discuss these results in light of reverse engineering approaches to computationally predict regulatory sequences by using comparative genomics. ..
  6. Shu J, Li Y. A statistical fat-tail test of predicting regulatory regions in the Drosophila genome. Comput Biol Med. 2012;42:935-41 pubmed publisher
    ..These two fatness coefficients may serve as valuable filtering indexes to predict CRMs experimentally. ..
  7. Wappner P, Gabay L, Shilo B. Interactions between the EGF receptor and DPP pathways establish distinct cell fates in the tracheal placodes. Development. 1997;124:4707-16 pubmed
    ..Antagonistic interactions between the two pathways are demonstrated. The opposing activities of two pathways may refine the final determination of tracheal branch fates. ..
  8. Vincent S, Ruberte E, Grieder N, Chen C, Haerry T, Schuh R, et al. DPP controls tracheal cell migration along the dorsoventral body axis of the Drosophila embryo. Development. 1997;124:2741-50 pubmed
    ..It is required to control the dorsal expression of the BNL ligand; in addition, the DPP signal recruits groups of dorsal and ventral tracheal cells and programs them to migrate in dorsal and ventral directions. ..
  9. Samee A, Sinha S. Evaluating thermodynamic models of enhancer activity on cellular resolution gene expression data. Methods. 2013;62:79-90 pubmed publisher
    ..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. ..
  10. Ingham P, Martinez Arias A. Boundaries and fields in early embryos. Cell. 1992;68:221-35 pubmed
  11. Pankratz M, Busch M, Hoch M, Seifert E, Jackle H. Spatial control of the gap gene knirps in the Drosophila embryo by posterior morphogen system. Science. 1992;255:986-9 pubmed
    ..The gap gene knirps, required for patterning in the posterior region of the embryo, can be activated throughout the wild-type embryo ..
  12. Nibu Y, Zhang H, Bajor E, Barolo S, Small S, Levine M. dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo. EMBO J. 1998;17:7009-20 pubmed
    ..Here we present evidence that three different repressors, Knirps, Krüppel and Snail, recruit a different co-repressor, dCtBP...
  13. Fomekong Nanfack Y, Postma M, Kaandorp J. Inferring Drosophila gap gene regulatory network: a parameter sensitivity and perturbation analysis. BMC Syst Biol. 2009;3:94 pubmed publisher
    ..Our study suggests that multi-objective optimization based on robustness and sensitivity analysis has to be considered. ..
  14. Kozlov K, Surkova S, Myasnikova E, Reinitz J, Samsonova M. Modeling of gap gene expression in Drosophila Kruppel mutants. PLoS Comput Biol. 2012;8:e1002635 pubmed publisher
    ..This result also clearly indicates that the oversimplified representation of transcriptional regulation in the previous models is one of the reasons for unsuccessful attempts of mutant simulations. ..
  15. Lunde K, Trimble J, Guichard A, Guss K, Nauber U, Bier E. Activation of the knirps locus links patterning to morphogenesis of the second wing vein in Drosophila. Development. 2003;130:235-48 pubmed
    The adjacent knirps (kni) and knirps-related (knrl) genes encode functionally related zinc finger transcription factors that collaborate to initiate development of the second longitudinal wing vein (L2)...
  16. Bieler J, Pozzorini C, Naef F. Whole-embryo modeling of early segmentation in Drosophila identifies robust and fragile expression domains. Biophys J. 2011;101:287-96 pubmed publisher
    ..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 Huckebein ..
  17. Fowlkes C, Hendriks C, Keränen S, Weber G, Rübel O, Huang M, et al. A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell. 2008;133:364-74 pubmed publisher
    ..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...
  18. Makeev V, Lifanov A, Nazina A, Papatsenko D. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res. 2003;31:6016-26 pubmed
    ..preferences in the arrangement of binding motifs for five transcription factors (Bicoid, Krüppel, Hunchback, Knirps and Caudal) in a large set of Drosophila cis-regulatory modules (CRMs)...
  19. Riddihough G, Ish Horowicz D. Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes. Genes Dev. 1991;5:840-54 pubmed
    ..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. ..
  20. Hengenius J, Gribskov M, Rundell A, Fowlkes C, Umulis D. Analysis of gap gene regulation in a 3D organism-scale model of the Drosophila melanogaster embryo. PLoS ONE. 2011;6:e26797 pubmed publisher
    ..Finally, we find that incorporation of 3D data in simulation and optimization does not constrain the search space or improve optimization results. ..
  21. He X, Samee M, Blatti C, Sinha S. Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression. PLoS Comput Biol. 2010;6: pubmed publisher
    ..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. Jaeger J, Reinitz J. On the dynamic nature of positional information. Bioessays. 2006;28:1102-11 pubmed
    ..Based on this analysis, we propose a revised French Flag, which incorporates the dynamic, feedback-driven nature of pattern formation in the Drosophila blastoderm. ..
  23. Hoch M, Gerwin N, Taubert H, Jackle H. Competition for overlapping sites in the regulatory region of the Drosophila gene Krüppel. Science. 1992;256:94-7 pubmed
    ..Two hormone receptor-like proteins, encoded by the genes knirps (kni) and tailless (tll), bind specifically to the element...
  24. Rothe M, Nauber U, Jackle H. Three hormone receptor-like Drosophila genes encode an identical DNA-binding finger. EMBO J. 1989;8:3087-94 pubmed
    The putative finger domain of knirps (kni), a member of the gap class of segmentation genes, was used to isolate two sequence-related genes of Drosophila melanogaster under reduced stringency hybridization conditions...
  25. Nauber U, Pankratz M, Kienlin A, Seifert E, Klemm U, Jackle H. Abdominal segmentation of the Drosophila embryo requires a hormone receptor-like protein encoded by the gap gene knirps. Nature. 1988;336:489-92 pubmed
    ..for organizing the posterior segment pattern is a group of at least seven maternal genes and the zygotic gap gene knirps (kni). Their mutant phenotype has adjacent segments in the abdominal region of the embryo deleted...
  26. Goodwin B, Kauffman S. Spatial harmonics and pattern specification in early Drosophila development. Part I. Bifurcation sequences and gene expression. J Theor Biol. 1990;144:303-19 pubmed
    ..This model has implications for the general stability properties of evolving epigenetic systems. ..
  27. La Rosée A, Hader T, Taubert H, Rivera Pomar R, Jackle H. Mechanism and Bicoid-dependent control of hairy stripe 7 expression in the posterior region of the Drosophila embryo. EMBO J. 1997;16:4403-11 pubmed
    ..The results suggest that the gradients of Bicoid and Caudal combine their activities to activate segmentation genes along the entire axis of the embryo. ..
  28. Kim Y, Andreu M, Lim B, Chung K, Terayama M, Jiménez G, et al. Gene regulation by MAPK substrate competition. Dev Cell. 2011;20:880-7 pubmed publisher
    ..A mathematical model of this interaction can explain gene expression patterns with both anteroposterior and dorsoventral polarities. ..
  29. Ochoa Espinosa A, Yu D, Tsirigos A, Struffi P, Small S. Anterior-posterior positional information in the absence of a strong Bicoid gradient. Proc Natl Acad Sci U S A. 2009;106:3823-8 pubmed publisher
  30. Papatsenko D, Levine M. The Drosophila gap gene network is composed of two parallel toggle switches. PLoS ONE. 2011;6:e21145 pubmed publisher
    ..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. ..
  31. Kaplan T, Li X, Sabo P, Thomas S, Stamatoyannopoulos J, Biggin M, et al. Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet. 2011;7:e1001290 pubmed publisher
  32. Rothe M, Pehl M, Taubert H, Jackle H. Loss of gene function through rapid mitotic cycles in the Drosophila embryo. Nature. 1992;359:156-9 pubmed
    ..During this process localized expression of the gap gene knirps (kni) is required to establish abdomen segmentation...
  33. Perkins T, Jaeger J, Reinitz J, Glass L. Reverse engineering the gap gene network of Drosophila melanogaster. PLoS Comput Biol. 2006;2:e51 pubmed
    ..Interestingly, some relationships in standard textbook models of gap gene regulation appear to be unnecessary for or even inconsistent with the details of gap gene expression during wild-type development. ..
  34. Kraut R, Levine M. Mutually repressive interactions between the gap genes giant and Krüppel define middle body regions of the Drosophila embryo. Development. 1991;111:611-21 pubmed
    ..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 of gene expression...
  35. Ribeiro C, Neumann M, Affolter M. Genetic control of cell intercalation during tracheal morphogenesis in Drosophila. Curr Biol. 2004;14:2197-207 pubmed
    ..Only the combined action of these signaling systems allows efficient branch elongation and the formation of morphologically distinct branches. ..
  36. Ashyraliyev M, Siggens K, Janssens H, Blom J, Akam M, Jaeger J. Gene circuit analysis of the terminal gap gene huckebein. PLoS Comput Biol. 2009;5:e1000548 pubmed publisher
    ..This is an important step towards a better, quantitative understanding of the developmental and evolutionary dynamics of the gap gene network. ..
  37. Reinitz J, Kosman D, Vanario Alonso C, Sharp D. Stripe forming architecture of the gap gene system. Dev Genet. 1998;23:11-27 pubmed
    ..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. ..
  38. Fakhouri W, Ay A, Sayal R, Dresch J, Dayringer E, Arnosti D. Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo. Mol Syst Biol. 2010;6:341 pubmed publisher
    ..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...
  39. Capovilla M, Eldon E, Pirrotta V. The giant gene of Drosophila encodes a b-ZIP DNA-binding protein that regulates the expression of other segmentation gap genes. Development. 1992;114:99-112 pubmed
    ..shows that giant, ectopically expressed from the hsp70 promoter, represses the expression of both the Krüppel and knirps segmentation gap genes...
  40. Azevedo R, Lohaus R, Srinivasan S, Dang K, Burch C. Sexual reproduction selects for robustness and negative epistasis in artificial gene networks. Nature. 2006;440:87-90 pubmed
    ..Our results suggest that sexual reproduction selects for conditions that favour its own maintenance, a case of evolution forging its own path. ..
  41. Hallikas O, Palin K, Sinjushina N, Rautiainen R, Partanen J, Ukkonen E, et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell. 2006;124:47-59 pubmed
  42. Ho M, Johnsen H, Goetz S, Schiller B, Bae E, Tran D, et al. Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PLoS Genet. 2009;5:e1000709 pubmed publisher
    ..These results have implications for understanding mechanisms of gene expression during embryonic development, enhancer function, and the molecular evolution of eukaryotic regulatory modules...
  43. Pisarev A, Poustelnikova E, Samsonova M, Reinitz J. FlyEx, the quantitative atlas on segmentation gene expression at cellular resolution. Nucleic Acids Res. 2009;37:D560-6 pubmed publisher
    ..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. ..
  44. Lehmann R, Frohnhofer H. Segmental polarity and identity in the abdomen of Drosophila is controlled by the relative position of gap gene expression. Development. 1989;107 Suppl:21-9 pubmed
    ..The function of the maternal gene products becomes dispensable once the position of the zygotically expressed gap genes is determined. Subsequently the gap genes will control the pattern of the pair-rule and segment polarity genes. ..
  45. Kulkarni M, Arnosti D. cis-regulatory logic of short-range transcriptional repression in Drosophila melanogaster. Mol Cell Biol. 2005;25:3411-20 pubmed
    ..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. ..
  46. Dubuis J, Samanta R, Gregor T. Accurate measurements of dynamics and reproducibility in small genetic networks. Mol Syst Biol. 2013;9:639 pubmed publisher
  47. Jennings B, Wainwright S, Ish Horowicz D. Differential in vivo requirements for oligomerization during Groucho-mediated repression. EMBO Rep. 2008;9:76-83 pubmed
    ..Our results show that homo-oligomerization of Gro is not obligatory for its action in vivo, and that Gro represses transcription through more than one molecular mechanism. ..
  48. Zinzen R, Papatsenko D. Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput Biol. 2007;3:e84 pubmed
    ..The described mechanisms are sufficient to explain the formation of the anterior and the posterior knirps expression, the posterior hunchback expression domain, and the lateral stripes of rhomboid expression and of other ..
  49. Hunding A, Kauffman S, Goodwin B. Drosophila segmentation: supercomputer simulation of prepattern hierarchy. J Theor Biol. 1990;145:369-84 pubmed
    ..The study thus suggests that the crucial organizing principle in early Drosophila embryogenesis is based on global field mechanisms, not on particular local interactions. ..
  50. Mannervik M, Nibu Y, Zhang H, Levine M. Transcriptional coregulators in development. Science. 1999;284:606-9 pubmed
    ..Recent studies suggest that a growing set of coactivators and corepressors mediate communication between diverse upstream regulatory proteins and the core RNA polymerase II transcription complex. ..
  51. Pankratz M, Hoch M, Seifert E, Jackle H. Krüppel requirement for knirps enhancement reflects overlapping gap gene activities in the Drosophila embryo. Nature. 1989;341:337-40 pubmed
    ..Here we describe the interactions between the gap genes Krüppel (Kr), knirps (kni) and tailless (tll)...
  52. Wu X, Vasisht V, Kosman D, Reinitz J, Small S. Thoracic patterning by the Drosophila gap gene hunchback. Dev Biol. 2001;237:79-92 pubmed
    ..gradient is critical for establishing the positions of several target genes, including the gap genes Kruppel (Kr), knirps (kni), and giant (gt), and the homeotic gene Ultrabithorax (Ubx)...
  53. Reinitz J, Sharp D. Mechanism of eve stripe formation. Mech Dev. 1995;49:133-58 pubmed
    ..Third is the use of least squares fits to gene expression data to measure phenomenological parameters occurring in the gene circuit. ..
  54. Lehmann R, Nusslein Volhard C. hunchback, a gene required for segmentation of an anterior and posterior region of the Drosophila embryo. Dev Biol. 1987;119:402-17 pubmed
    ..Heterozygous mutant embryos derived from a homozygous mutant germ line develop normally, indicating that maternal gene expression is not required for normal development. ..
  55. Berman B, Nibu Y, Pfeiffer B, Tomancak P, Celniker S, Levine M, et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A. 2002;99:757-62 pubmed
    ..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. ..
  56. Laudet V, Hanni C, Coll J, Catzeflis F, Stehelin D. Evolution of the nuclear receptor gene superfamily. EMBO J. 1992;11:1003-13 pubmed
    ..but two groups of receptors are in a different position from that in the C domain tree: (i) the Drosophila knirps family genes have acquired very different E domains during evolution, and (ii) the vitamin D and ecdysone ..
  57. Ashyraliyev M, Jaeger J, Blom J. Parameter estimation and determinability analysis applied to Drosophila gap gene circuits. BMC Syst Biol. 2008;2:83 pubmed publisher
    ..Moreover, it improves previous analyses of the same model by allowing us to identify those interactions for which qualitative conclusions are reliable, and those for which they are ambiguous. ..
  58. Löhr U, Chung H, Beller M, Jackle H. Antagonistic action of Bicoid and the repressor Capicua determines the spatial limits of Drosophila head gene expression domains. Proc Natl Acad Sci U S A. 2009;106:21695-700 pubmed publisher
    ..We conclude that the spatial domains of head gene expression are determined by Bcd in concert with Tor-dependent repressors. ..
  59. Gonzalez Gaitan M, Rothe M, Wimmer E, Taubert H, Jackle H. Redundant functions of the genes knirps and knirps-related for the establishment of anterior Drosophila head structures. Proc Natl Acad Sci U S A. 1994;91:8567-71 pubmed
    ..We found that the evolutionarily related genes knirps (kni) and knirps-related (knrl) contribute to a similar phenomenon in Drosophila...
  60. Small S, Blair A, Levine M. Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo. Dev Biol. 1996;175:314-24 pubmed
    ..b>knirps, a member of the nuclear receptor family of transcription factors, appears to establish the posterior border of ..
  61. Clyde D, Corado M, Wu X, Pare A, Papatsenko D, Small S. A self-organizing system of repressor gradients establishes segmental complexity in Drosophila. Nature. 2003;426:849-53 pubmed
    ..Here we show that opposing gradients of two Drosophila transcriptional repressors, Hunchback (Hb) and Knirps (Kni), position several segments by differentially repressing two distinct regulatory regions (enhancers) of the ..
  62. Wimmer E, Carleton A, Harjes P, Turner T, Desplan C. Bicoid-independent formation of thoracic segments in Drosophila. Science. 2000;287:2476-9 pubmed
    ..By reestablishing a proposed ancient regulatory circuitry in which maternal Hb controls zygotic hunchback expression, we show that Hb is able to form thoracic segments in the absence of Bcd. ..
  63. Li X, MacArthur S, Bourgon R, Nix D, Pollard D, Iyer V, et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008;6:e27 pubmed publisher
  64. Hulskamp M, Pfeifle C, Tautz D. A morphogenetic gradient of hunchback protein organizes the expression of the gap genes Krüppel and knirps in the early Drosophila embryo. Nature. 1990;346:577-80 pubmed
    ..anterior and posterior borders of expression of the gap gene Krüppel (Kr) and the anterior border of the gap gene knirps (kni), thus defining three positional values...
  65. Pritchard D, Schubiger G. Activation of transcription in Drosophila embryos is a gradual process mediated by the nucleocytoplasmic ratio. Genes Dev. 1996;10:1131-42 pubmed
  66. Kraut R, Levine M. Spatial regulation of the gap gene giant during Drosophila development. Development. 1991;111:601-9 pubmed
    ..studies show that the gt patterns overlap with protein gradients specified by the gap genes hunchback (hb) and knirps (kni)...
  67. Fowlkes C, Eckenrode K, Bragdon M, Meyer M, Wunderlich Z, Simirenko L, et al. A conserved developmental patterning network produces quantitatively different output in multiple species of Drosophila. PLoS Genet. 2011;7:e1002346 pubmed publisher
    ..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. ..
  68. Tsai C, Gergen J. Gap gene properties of the pair-rule gene runt during Drosophila segmentation. Development. 1994;120:1671-83 pubmed
    ..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. ..
  69. Lifanov A, Makeev V, Nazina A, Papatsenko D. Homotypic regulatory clusters in Drosophila. Genome Res. 2003;13:579-88 pubmed
    ..We also discuss the potential of the clustering method in interpreting the differential response of genes to various levels of transcriptional regulators. ..
  70. Payankaulam S, Arnosti D. Groucho corepressor functions as a cofactor for the Knirps short-range transcriptional repressor. Proc Natl Acad Sci U S A. 2009;106:17314-9 pubmed publisher
    ..b>Knirps has essential roles in patterning the Drosophila embryo by means of short-range repression, an activity that is ..
  71. Kim J, He X, Sinha S. Evolution of regulatory sequences in 12 Drosophila species. PLoS Genet. 2009;5:e1000330 pubmed publisher
  72. Niessing D, Rivera Pomar R, La Rosée A, Hader T, Schock F, Purnell B, et al. A cascade of transcriptional control leading to axis determination in Drosophila. J Cell Physiol. 1997;173:162-7 pubmed
  73. Tautz D, Pfeifle C. A non-radioactive in situ hybridization method for the localization of specific RNAs in Drosophila embryos reveals translational control of the segmentation gene hunchback. Chromosoma. 1989;98:81-5 pubmed
    ..The non-radioactive in situ hybridization method is as sensitive as conventional methods, but is faster and easier to perform. This may make it a useful tool for a variety of other systems. ..
  74. Frasch M, Levine M. Complementary patterns of even-skipped and fushi tarazu expression involve their differential regulation by a common set of segmentation genes in Drosophila. Genes Dev. 1987;1:981-95 pubmed
  75. Struhl G, Johnston P, Lawrence P. Control of Drosophila body pattern by the hunchback morphogen gradient. Cell. 1992;69:237-249 pubmed
    ..of Drosophila are specified early in embryogenesis by the overlapping activities of the hunchback (hb), Krüppel, knirps, and giant gap genes...
  76. Glazer L, Shilo B. Hedgehog signaling patterns the tracheal branches. Development. 2001;128:1599-606 pubmed
    ..Signaling by several pathways, including the Hh pathway, thus serves to subdivide the uniform population of tracheal cells into distinct cell types that will subsequently be recruited into the different branches. ..
  77. Russell S, Sanchez Soriano N, Wright C, Ashburner M. The Dichaete gene of Drosophila melanogaster encodes a SOX-domain protein required for embryonic segmentation. Development. 1996;122:3669-76 pubmed
  78. Perry M, Boettiger A, Levine M. Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo. Proc Natl Acad Sci U S A. 2011;108:13570-5 pubmed publisher
    ..The combination of intronic and 5' knirps (kni) enhancers produces a faithful expression pattern, even though the intronic enhancer alone directs an ..
  79. Rothe M, Wimmer E, Pankratz M, Gonzalez Gaitan M, Jackle H. Identical transacting factor requirement for knirps and knirps-related Gene expression in the anterior but not in the posterior region of the Drosophila embryo. Mech Dev. 1994;46:169-81 pubmed
    The Drosophila genes knirps (kni) and knirps-related (knrl) are located within the 77E1,2 region on the left arm of the third chromosome...
  80. Dubuis J, Tkacik G, Wieschaus E, Gregor T, Bialek W. Positional information, in bits. Proc Natl Acad Sci U S A. 2013;110:16301-8 pubmed publisher
    ..We argue that this constancy is a signature of optimality in the transmission of information from primary morphogen inputs to the output of the gap gene network. ..
  81. Steingrimsson E, Pignoni F, Liaw G, Lengyel J. Dual role of the Drosophila pattern gene tailless in embryonic termini. Science. 1991;254:418-21 pubmed
    ..Ectopic expression of the tll gene also represses segmentation by repressing the gap genes Krüppel and knirps and probably also pair rule genes.
  82. Luengo Hendriks C, Keränen S, Fowlkes C, Simirenko L, Weber G, DePace A, et al. Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol. 2006;7:R123 pubmed
    ..The application of these quantitative methods to other developmental systems will likely reveal many other previously unknown features and provide a more rigorous understanding of developmental regulatory networks. ..
  83. Jennings B, Pickles L, Wainwright S, Roe S, Pearl L, Ish Horowicz D. Molecular recognition of transcriptional repressor motifs by the WD domain of the Groucho/TLE corepressor. Mol Cell. 2006;22:645-55 pubmed
    ..Our structural and functional analysis explains the rigid conservation of the WRPW motif, the sequence flexibility of eh1 motifs, and other aspects of repressor recognition by Gro in vivo. ..
  84. Llimargas M. Wingless and its signalling pathway have common and separable functions during tracheal development. Development. 2000;127:4407-17 pubmed
    ..The results suggest that another gene product, possibly a WNT, could help to trigger the wingless cascade in the developing tracheae. ..
  85. Klingler M, Soong J, Butler B, Gergen J. Disperse versus compact elements for the regulation of runt stripes in Drosophila. Dev Biol. 1996;177:73-84 pubmed
    ..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. ..
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