Gene Symbol: run
Description: runt
Alias: AA33, CG1849, Dmel\CG1849, LB5, P235, RUN, Rnt, Run, Runt, l(1)19Ea, l(1)AA33, l(1)B2/13.1, l(1)LB9, lLB5, leg, runt, CG1849-PA, CG1849-PB, CG1849-PC, legless, run-PA, run-PB, run-PC, section 1, section 2
Species: fruit fly
Products:     run

Top Publications

  1. Duffy J, Gergen J. The Drosophila segmentation gene runt acts as a position-specific numerator element necessary for the uniform expression of the sex-determining gene Sex-lethal. Genes Dev. 1991;5:2176-87 pubmed
    ..We demonstrate that the X-linked segmentation gene runt is required for this process and has genetic and molecular properties of a numerator element...
  2. Dormand E, Brand A. Runt determines cell fates in the Drosophila embryonic CNS. Development. 1998;125:1659-67 pubmed
    The segmentation gene, runt, is expressed by a subset of the 30 neuroblasts that give rise to each neuromere of the Drosophila embryo. Runt activity in the neuroblasts is necessary for expression of even-skipped in the EL neurons...
  3. Li L, Gergen J. Differential interactions between Brother proteins and Runt domain proteins in the Drosophila embryo and eye. Development. 1999;126:3313-22 pubmed
    Brother and Big brother were isolated as Runt-interacting proteins and are homologous to CBF(beta), which interacts with the mammalian CBF(alpha) Runt-domain proteins...
  4. 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
    ..genes and is required for the appropriate expression of the primary pair-rule genes even skipped, hairy and runt. The molecular nature of Dichaete and its expression pattern during early embryogenesis suggest that the gene plays ..
  5. Kaminker J, Canon J, Salecker I, Banerjee U. Control of photoreceptor axon target choice by transcriptional repression of Runt. Nat Neurosci. 2002;5:746-50 pubmed
    ..The transcription factor Runt (Run) is normally expressed in the two inner R cells (R7 and R8) that project their axons to the medulla...
  6. Jackson Behan K, Fair J, Singh S, Bogwitz M, Perry T, Grubor V, et al. Alternative splicing removes an Ets interaction domain from Lozenge during Drosophila eye development. Dev Genes Evol. 2005;215:423-35 pubmed
    ..The runt-homology domain responsible for DNA binding and also the C-terminus are both nearly identical between the two ..
  7. Vander Zwan C, Wheeler J, Li L, Tracey W, Gergen J. A DNA-binding-independent pathway of repression by the Drosophila Runt protein. Blood Cells Mol Dis. 2003;30:207-22 pubmed
    ..analysis of gene function in the Drosophila embryo, we have discovered a DNA-binding-independent activity of Runt, the founding member of the RUNX family of transcriptional regulators...
  8. Aronson B, Fisher A, Blechman K, Caudy M, Gergen J. Groucho-dependent and -independent repression activities of Runt domain proteins. Mol Cell Biol. 1997;17:5581-7 pubmed
    b>Runt domain proteins are transcriptional regulators that specify cell fates for processes extending from pattern formation in insects to leukemogenesis in humans...
  9. Smith E, Allis C, Lucchesi J. Linking global histone acetylation to the transcription enhancement of X-chromosomal genes in Drosophila males. J Biol Chem. 2001;276:31483-6 pubmed
    ..This study represents the first biochemical interpretation of the very large body of cytological observations on the chromosomal distribution of the MSL complex. ..

More Information


  1. Tsai C, Gergen J. Gap gene properties of the pair-rule gene runt during Drosophila segmentation. Development. 1994;120:1671-83 pubmed
    The Drosophila Runt protein is a member of a new family of transcriptional regulators that have important roles in processes extending from pattern formation in insect embryos to leukemogenesis in humans...
  2. 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. ..
  3. Markstein M, Markstein P, Markstein V, Levine M. Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. Proc Natl Acad Sci U S A. 2002;99:763-8 pubmed
    ..These results suggest that bioinformatics can be used to identify novel target genes and associated regulatory DNAs in a gene network. ..
  4. Pepling M, Gergen J. Conservation and function of the transcriptional regulatory protein Runt. Proc Natl Acad Sci U S A. 1995;92:9087-91 pubmed
    A phylogenetic approach was used to identify conserved regions of the transcriptional regulator Runt. Alignment of the deduced protein sequences from Drosophila melanogaster, Drosophila pseudoobscura, and Drosophila virilis revealed eight ..
  5. WATSON J, Wheeler S, Stagg S, Crews S. Drosophila hedgehog signaling and engrailed-runt mutual repression direct midline glia to alternative ensheathing and non-ensheathing fates. Development. 2011;138:1285-95 pubmed publisher
    ..Two transcription factor genes, runt and engrailed, play important roles in AMG and PMG development...
  6. Gergen J. Dosage Compensation in Drosophila: Evidence That daughterless and Sex-lethal Control X Chromosome Activity at the Blastoderm Stage of Embryogenesis. Genetics. 1987;117:477-85 pubmed
  7. Schroeder M, Greer C, Gaul U. How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation. Development. 2011;138:3067-78 pubmed publisher
    ..We find that runt (run), fushi tarazu (ftz) and odd skipped (odd) establish most of their pattern through stripe-specific elements, ..
  8. Edwards T, Meinertzhagen I. Photoreceptor neurons find new synaptic targets when misdirected by overexpressing runt in Drosophila. J Neurosci. 2009;29:828-41 pubmed publisher
    ..melanogaster, we used the yeast GAL4/UAS system to drive exogenous expression of the transcription factor Runt in subsets of photoreceptors, resulting in aberrant axonal pathfinding and, ultimately, incorrect targeting of R1-..
  9. 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
    ..We discuss the role of the hierarchy in understanding transcriptional regulation and in detection of transcription regulatory regions in genomes. ..
  10. Golling G, Li L, Pepling M, Stebbins M, Gergen J. Drosophila homologs of the proto-oncogene product PEBP2/CBF beta regulate the DNA-binding properties of Runt. Mol Cell Biol. 1996;16:932-42 pubmed
    The Drosophila runt gene is the founding member of the Runt domain family of transcriptional regulators. Mammalian Runt domain genes encode the alpha subunit of the heterometric DNA-binding factor PEBP2/CBF...
  11. Wolff C, Pepling M, Gergen P, Klingler M. Structure and evolution of a pair-rule interaction element: runt regulatory sequences in D. melanogaster and D. virilis. Mech Dev. 1999;80:87-99 pubmed
    ..Previously, we described a pair-rule input region of the runt gene...
  12. 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. ..
  13. Domingos P, Brown S, Barrio R, Ratnakumar K, Frankfort B, Mardon G, et al. Regulation of R7 and R8 differentiation by the spalt genes. Dev Biol. 2004;273:121-33 pubmed
    ..5, and runt) is lost in spalt mutant clones...
  14. Brown J, Wu C. Repression of Drosophila pair-rule segmentation genes by ectopic expression of tramtrack. Development. 1993;117:45-58 pubmed
    ..endogenous ftz gene, as well as significant repression of the pair-rule genes even skipped, odd skipped, hairy and runt. These findings suggest that specific repression by ttk (or by undiscovered repressors) may be more than an ..
  15. 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. ..
  16. Gergen J, Wieschaus E. The localized requirements for a gene affecting segmentation in Drosophila: analysis of larvae mosaic for runt. Dev Biol. 1985;109:321-35 pubmed
    The runt gene is required in a developing Drosophila embryo for proper segmentation. Mutant embryos fail to hatch but secrete a larval cuticle in which pattern defects are apparent...
  17. 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
  18. Behan K, Nichols C, Cheung T, Farlow A, Hogan B, Batterham P, et al. Yan regulates Lozenge during Drosophila eye development. Dev Genes Evol. 2002;212:267-76 pubmed
    ..We propose that upregulated Lozenge acts as a cofactor to alter Pointed affinity, by a mechanism that is recapitulated in mammalian development. ..
  19. Kania M, Bonner A, Duffy J, Gergen J. The Drosophila segmentation gene runt encodes a novel nuclear regulatory protein that is also expressed in the developing nervous system. Genes Dev. 1990;4:1701-13 pubmed
    ..The segmentation gene runt has been classified as one of the primary pair-rule genes because of the pivotal role it plays in regulating the ..
  20. Kosman D, Small S, Reinitz J. Rapid preparation of a panel of polyclonal antibodies to Drosophila segmentation proteins. Dev Genes Evol. 1998;208:290-4 pubmed
    ..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. ..
  21. Pick L. Segmentation: painting stripes from flies to vertebrates. Dev Genet. 1998;23:1-10 pubmed
  22. 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. ..
  23. Tracey W, Ning X, Klingler M, Kramer S, Gergen J. Quantitative analysis of gene function in the Drosophila embryo. Genetics. 2000;154:273-84 pubmed
    ..Analysis of the response to overexpression of runt provides evidence that this pair-rule segmentation gene has a direct role in repressing transcription of the ..
  24. Prazak L, Fujioka M, Gergen J. Non-additive interactions involving two distinct elements mediate sloppy-paired regulation by pair-rule transcription factors. Dev Biol. 2010;344:1048-59 pubmed publisher
    ..expresses only even-numbered stripes and mediates repression by Even-skipped (Eve) as well as by the combination of Runt and Fushi-tarazu (Ftz)...
  25. Surkova S, Myasnikova E, Janssens H, Kozlov K, Samsonova A, Reinitz J, et al. Pipeline for acquisition of quantitative data on segmentation gene expression from confocal images. Fly (Austin). 2008;2:58-66 pubmed
    ..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. ..
  26. Pomiankowski A, Nöthiger R, Wilkins A. The evolution of the Drosophila sex-determination pathway. Genetics. 2004;166:1761-73 pubmed
    ..Our hypothesis is built on the available data from Drosophila and other insect species, and we point out where it is amenable to further experimental and comparative tests. ..
  27. Kind J, Vaquerizas J, Gebhardt P, Gentzel M, Luscombe N, Bertone P, et al. Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell. 2008;133:813-28 pubmed publisher
    ..Therefore, MOF is not only involved in the onset of dosage compensation, but also acts as a regulator of gene expression in the Drosophila genome. ..
  28. Nasiadka A, Krause H. Kinetic analysis of segmentation gene interactions in Drosophila embryos. Development. 1999;126:1515-26 pubmed
    ..In total, 11 putative Ftz target genes are analyzed, and the data provide a substantially revised view of Ftz roles and activities within the segmentation hierarchy. ..
  29. Cline T, Meyer B. Vive la différence: males vs females in flies vs worms. Annu Rev Genet. 1996;30:637-702 pubmed
    ..Although no overlap has been found among the molecules used by flies and worms to achieve sex determination, striking similarities have been found in the genetic strategies used by these two species to differentiate their sexes. ..
  30. 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...
  31. Younger Shepherd S, Vaessin H, Bier E, Jan L, Jan Y. deadpan, an essential pan-neural gene encoding an HLH protein, acts as a denominator in Drosophila sex determination. Cell. 1992;70:911-22 pubmed
  32. 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. ..
  33. 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
  34. Fujioka M, Jaynes J, Goto T. Early even-skipped stripes act as morphogenetic gradients at the single cell level to establish engrailed expression. Development. 1995;121:4371-82 pubmed
    ..Within this zone, single cell rows express either engrailed, where runt and sloppy-paired are repressed, or wingless, where they are not...
  35. Nusslein Volhard C, Wieschaus E. Mutations affecting segment number and polarity in Drosophila. Nature. 1980;287:795-801 pubmed
  36. Cohen S, Jurgens G. Drosophila headlines. Trends Genet. 1991;7:267-72 pubmed
    ..Organization of the cephalic segments uses a mechanism distinct from the familiar bierarchical cascade of segmentation genes that subdivides the trunk of the embryo. ..
  37. Kind J, Akhtar A. Cotranscriptional recruitment of the dosage compensation complex to X-linked target genes. Genes Dev. 2007;21:2030-40 pubmed
    ..We propose a model of dynamic MSL complex binding to active genes based on exposed DNA target elements. ..
  38. Swantek D, Gergen J. Ftz modulates Runt-dependent activation and repression of segment-polarity gene transcription. Development. 2004;131:2281-90 pubmed
    ..for quantitative manipulation of expression levels to probe the role of the primary pair-rule transcription factor Runt in segment-polarity gene regulation...
  39. Carroll S. Zebra patterns in fly embryos: activation of stripes or repression of interstripes?. Cell. 1990;60:9-16 pubmed
    ..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. ..
  40. Saulier Le Dréan B, Nasiadka A, Dong J, Krause H. Dynamic changes in the functions of Odd-skipped during early Drosophila embryogenesis. Development. 1998;125:4851-61 pubmed
    ..Based on these results, and the segmental phenotypes generated by ectopic Odd, we suggest a number of new roles for Odd in the patterning of embryonic segments. These include gap-, pair-rule- and segment polarity-type functions. ..
  41. de Renzis S, Elemento O, Tavazoie S, Wieschaus E. Unmasking activation of the zygotic genome using chromosomal deletions in the Drosophila embryo. PLoS Biol. 2007;5:e117 pubmed
    ..We propose that this regulatory mode links morphogen gradients with temporal regulation during the maternal-to-zygotic transition. ..
  42. Tsai C, Kramer S, Gergen J. Pair-rule gene runt restricts orthodenticle expression to the presumptive head of the Drosophila embryo. Dev Genet. 1998;23:35-44 pubmed
    Ectopic expression of the pair-rule gene runt in the anterior end of the Drosophila embryo antagonizes transcriptional activation of the head gap gene orthodenticle (otd) by the anterior morphogen bicoid...
  43. Kaminker J, Singh R, Lebestky T, Yan H, Banerjee U. Redundant function of Runt Domain binding partners, Big brother and Brother, during Drosophila development. Development. 2001;128:2639-48 pubmed
    ..The alpha-subunit is encoded by members of the Runt Domain family of proteins and the beta-subunit is encoded by the CBF beta gene...
  44. Walrad P, Hang S, Joseph G, Salas J, Gergen J. Distinct contributions of conserved modules to Runt transcription factor activity. Mol Biol Cell. 2010;21:2315-26 pubmed publisher
    ..Two Runx protein hallmarks are the DNA-binding Runt domain and a C-terminal VWRPY motif that mediates interaction with TLE/Gro corepressor proteins...
  45. 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
    ..Here we describe the cis-regulatory region of the runt gene...
  46. Butler B, Soong J, Gergen J. The Drosophila segmentation gene runt has an extended cis-regulatory region that is required for vital expression at other stages of development. Mech Dev. 1992;39:17-28 pubmed
    The Drosophila runt gene functions in several developmental pathways during embryogenesis...
  47. 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. ..
  48. 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
  49. Duffy J, Kania M, Gergen J. Expression and function of the Drosophila gene runt in early stages of neural development. Development. 1991;113:1223-30 pubmed
    The Drosophila gene runt was initially identified on the basis of its role during segmentation...
  50. Little S, Tikhonov M, Gregor T. Precise developmental gene expression arises from globally stochastic transcriptional activity. Cell. 2013;154:789-800 pubmed publisher
    ..The findings shed light on how the apparent paradox between stochastic transcription and developmental precision is resolved. ..
  51. Rennert J, Coffman J, Mushegian A, Robertson A. The evolution of Runx genes I. A comparative study of sequences from phylogenetically diverse model organisms. BMC Evol Biol. 2003;3:4 pubmed
    Runx genes encode proteins defined by the highly conserved Runt DNA-binding domain. Studies of Runx genes and proteins in model organisms indicate that they are key transcriptional regulators of animal development...
  52. Tayler T, Garrity P. Axon targeting in the Drosophila visual system. Curr Opin Neurobiol. 2003;13:90-5 pubmed
    ..of the R1-R6 subset of photoreceptor axons have been found to be influenced by the nuclear factors Brakeless and Runt, and target selection decisions of the R7 subset of axons have been found to require the cell-surface proteins ..
  53. Bhat K, van Beers E, Bhat P. Sloppy paired acts as the downstream target of wingless in the Drosophila CNS and interaction between sloppy paired and gooseberry inhibits sloppy paired during neurogenesis. Development. 2000;127:655-65 pubmed
    ..This mechanism appears to be responsible for specifying NB5-3 identity to a row 5 neuroblast and preventing Wg from specifying NB4-2 identity to that cell. ..
  54. Sackerson C, Fujioka M, Goto T. The even-skipped locus is contained in a 16-kb chromatin domain. Dev Biol. 1999;211:39-52 pubmed
    ..4) Expression in different sites in the central nervous system is driven by separable elements widely dispersed throughout 8 kb 3' of the gene. ..
  55. Goto T, MacDonald P, Maniatis T. Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues. Cell. 1989;57:413-22 pubmed
    ..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. ..
  56. Manoukian A, Krause H. Concentration-dependent activities of the even-skipped protein in Drosophila embryos. Genes Dev. 1992;6:1740-51 pubmed
    ..of response times appeared to distinguish between genes that were direct [fushi tarazu (ftz), odd-skipped (odd), runt (run), paired, and wingless] and indirect [eve, hairy, and engrailed (en)] targets of Eve...
  57. Wang X, Lee C, Gilmour D, Gergen J. Transcription elongation controls cell fate specification in the Drosophila embryo. Genes Dev. 2007;21:1031-6 pubmed
    ..We find that the initial repression of slp1 in response to Runt and Fushi-tarazu (Ftz) does not involve chromatin remodeling, or histone modification...
  58. MacArthur S, Li X, Li J, Brown J, Chu H, Zeng L, et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009;10:R80 pubmed publisher
  59. Kramer S, Jinks T, Schedl P, Gergen J. Direct activation of Sex-lethal transcription by the Drosophila runt protein. Development. 1999;126:191-200 pubmed
    b>Runt functions as a transcriptional regulator in multiple developmental pathways in Drosophila melanogaster. Recent evidence indicates that Runt represses the transcription of several downstream target genes in the segmentation pathway...
  60. Gergen J, Butler B. Isolation of the Drosophila segmentation gene runt and analysis of its expression during embryogenesis. Genes Dev. 1988;2:1179-93 pubmed
    b>runt is one of the genes required for establishment of the segmented body pattern of the Drosophila embryo. We have isolated DNA sequences containing this gene using P-element transposon tagging...
  61. 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. ..
  62. Jennings B, Shah S, Yamaguchi Y, Seki M, Phillips R, Handa H, et al. Locus-specific requirements for Spt5 in transcriptional activation and repression in Drosophila. Curr Biol. 2004;14:1680-4 pubmed
    ..expression of gap genes remains wild-type, but striped patterning of the primary pair-rule genes even-skipped and runt is disrupted...
  63. Fujioka M, Emi Sarker Y, Yusibova G, Goto T, Jaynes J. 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. Development. 1999;126:2527-38 pubmed
    ..Additionally, a strong pairing-sensitive repression element was localized to the 3' end of the locus, but was not found to contribute to efficient functional rescue. ..
  64. Daga A, Karlovich C, Dumstrei K, Banerjee U. Patterning of cells in the Drosophila eye by Lozenge, which shares homologous domains with AML1. Genes Dev. 1996;10:1194-205 pubmed homologous to AML1, a transcription factor associated with human leukemias, and to the Drosophila protein Runt. We show here that Lz plays a crucial role in governing the fate of two groups of cells that are born in a single ..
  65. Torres M, Sanchez L. The segmentation gene runt is needed to activate Sex-lethal, a gene that controls sex determination and dosage compensation in Drosophila. Genet Res. 1992;59:189-98 pubmed
    ..Here we find that the X-linked segmentation gene runt plays a role in this process...