Genomes and Genes
Gene Symbol: cad
Alias: 38E.19, CAD, CG1759, Cad, Dmel\CG1759, S67, anon-WO2004063362.83, caudal, CG1759-PA, CG1759-PB, CG1759-PC, cad-PA, cad-PB, cad-PC
Species: fruit fly
- Mlodzik M, Gibson G, Gehring W. Effects of ectopic expression of caudal during Drosophila development. Development. 1990;109:271-7 pubmedThe effects of heat-shock-induced ectopic expression of the homeobox gene caudal (cad) at all stages of Drosophila development have been examined...
- Surkova S, Golubkova E, Manu -, Panok L, Mamon L, Reinitz J, et al. Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants. Dev Biol. 2013;376:99-112 pubmed publisher..This is a surprising result in view of the role that mutual repression is thought to play in the gap gene system. ..
- 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. ..
- 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. ..
- Papatsenko D, Goltsev Y, Levine M. Organization of developmental enhancers in the Drosophila embryo. Nucleic Acids Res. 2009;37:5665-77 pubmed publisher..for particular combinations of binding motifs, including Bicoid-Bicoid, Hunchback-Hunchback, Bicoid-Dorsal, Bicoid-Caudal and Dorsal-Twist...
- 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. ..
- Ochoa Espinosa A, Yucel G, Kaplan L, Pare A, Pura N, Oberstein A, et al. The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila. Proc Natl Acad Sci U S A. 2005;102:4960-5 pubmed..Rather, we find that binding sites for other activators, including Hunchback and Caudal correlate with CRM expression in middle and posterior body regions...
- 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..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 proteins...
- Nekrasov M, Klymenko T, Fraterman S, Papp B, Oktaba K, Kocher T, et al. Pcl-PRC2 is needed to generate high levels of H3-K27 trimethylation at Polycomb target genes. EMBO J. 2007;26:4078-88 pubmed..Pcl-PRC2 is thus the HMTase that generates the high levels of H3-K27 trimethylation in Polycomb target genes that are needed to maintain a Polycomb-repressed chromatin state. ..
- 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...
- Holmqvist P, Boija A, Philip P, Crona F, Stenberg P, Mannervik M. Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos. PLoS Genet. 2012;8:e1002769 pubmed publisher..We conclude that CBP occupancy in Drosophila embryos preferentially overlaps factors controlling dorso-ventral patterning and that CBP binds silent genes without causing histone hyperacetylation. ..
- 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. ..
- 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. ..
- 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..of gap gene expression patterns in Kr mutants can be explained by the dynamic decrease of activating effect of Cad on a target gene and exclusion of Kr gene from the complex network of gap gene interactions, that makes it possible ..
- McGinnis W, Krumlauf R. Homeobox genes and axial patterning. Cell. 1992;68:283-302 pubmed
- 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. ..
- Beuchle D, Struhl G, Muller J. Polycomb group proteins and heritable silencing of Drosophila Hox genes. Development. 2001;128:993-1004 pubmed..Some PcG proteins may be required to define and propagate this mark; others may function to repress the transcription of Hox genes that bear the mark. ..
- 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. ..
- Rivera Pomar R, Niessing D, Schmidt Ott U, Gehring W, Jackle H. RNA binding and translational suppression by bicoid. Nature. 1996;379:746-9 pubmed..Its posterior counterpart, the homeodomain transcription factor caudal (cad), forms a concentration gradient in the opposite direction, emanating from evenly distributed messenger RNA ..
- 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. ..
- Zamparo L, Perkins T. Statistical lower bounds on protein copy number from fluorescence expression images. Bioinformatics. 2009;25:2670-6 pubmed publisher..The data are all drawn from FlyEx (explained within), and is available at http://flyex.ams.sunysb.edu/FlyEx/. ..
- Mlodzik M, Gehring W. Expression of the caudal gene in the germ line of Drosophila: formation of an RNA and protein gradient during early embryogenesis. Cell. 1987;48:465-78 pubmedThe caudal (cad) gene of Drosophila encodes a maternal and a zygotic transcript which have different promoters. Both mRNAs contain the same open reading frame, including a homeo box...
- 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. ..
- Gursky V, Panok L, Myasnikova E, Manu -, Samsonova M, Reinitz J, et al. Mechanisms of gap gene expression canalization in the Drosophila blastoderm. BMC Syst Biol. 2011;5:118 pubmed publisher..The canalization of gap gene expression can be understood as arising from the actions of attractors in the gap gene dynamical system...
- 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..region-specific combinations and concentrations of both the maternal homeodomain transcriptional activators, Caudal and Bicoid, and of transcriptional repressors encoded by locally expressed zygotic gap genes...
- Megason S, Fraser S. Imaging in systems biology. Cell. 2007;130:784-95 pubmed..Here, we discuss the power of integrating imaging tools with more conventional -omic approaches to analyze the biological circuits of microorganisms, plants, and animals. ..
- Harrison M, Li X, Kaplan T, Botchan M, Eisen M. Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet. 2011;7:e1002266 pubmed publisher..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. ..
- Dubnau J, Struhl G. RNA recognition and translational regulation by a homeodomain protein. Nature. 1996;379:694-9 pubmed..also binds RNA and acts as a translational repressor to generate an opposing gradient of the homeodomain protein caudal (cad)...
- Gaul U, Weigel D. Regulation of Krüppel expression in the anlage of the Malpighian tubules in the Drosophila embryo. Mech Dev. 1990;33:57-67 pubmed..In addition, Krüppel activates different genes in the Malpighian tubules than in the central domain. Thus, both the regulation and the function of Krüppel in the Malpighian tubules differ strikingly from its role in segmentation. ..
- 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. ..
- Hwang M, Kim Y, Choi N, Park J, Oh E, Kwon E, et al. The caudal homeodomain protein activates Drosophila E2F gene expression. Nucleic Acids Res. 2002;30:5029-35 pubmedThe Drosophila caudal homeobox gene is required for definition of the anteroposterior axis and for gut development, and CDX1 and CDX2, human homologs, play crucial roles in the regulation of cell proliferation and differentiation in the ..
- Janssens H, Crombach A, Wotton K, Cicin Sain D, Surkova S, Lim C, et al. Lack of tailless leads to an increase in expression variability in Drosophila embryos. Dev Biol. 2013;377:305-17 pubmed publisher..Our analysis provides evidence that loss of canalisation in mutants could be more widespread than previously thought. ..
- Macdonald P, Struhl G. A molecular gradient in early Drosophila embryos and its role in specifying the body pattern. Nature. 1986;324:537-45 pubmedAfter fertilization, the protein products of the Drosophila homeobox gene caudal (cad) accumulate in a concentration gradient spanning the anteroposterior axis of the developing embryo...
- Manu -, Surkova S, Spirov A, Gursky V, Janssens H, Kim A, et al. Canalization of gene expression in the Drosophila blastoderm by gap gene cross regulation. PLoS Biol. 2009;7:e1000049 pubmed publisher..More generally, we show that the complex multigenic phenomenon of canalization can be understood at a quantitative and predictive level by the application of a precise dynamical model...
- Lewis E, Knafels J, Mathog D, Celniker S. Sequence analysis of the cis-regulatory regions of the bithorax complex of Drosophila. Proc Natl Acad Sci U S A. 1995;92:8403-7 pubmed..5 case is expected. Expected values are based on a third-order Markov chain, which is the optimal order for representing the BXCALL sequence. ..
- Schulz C, Tautz D. Zygotic caudal regulation by hunchback and its role in abdominal segment formation of the Drosophila embryo. Development. 1995;121:1023-8 pubmedb>caudal (cad) is a maternally and zygotically expressed gene in Drosophila whereby the two phases of expression can functionally replace each other...
- Kuhn D, Turenchalk G, Mack J, Packert G, Kornberg T. Analysis of the genes involved in organizing the tail segments of the Drosophila melanogaster embryo. Mech Dev. 1995;53:3-13 pubmed..We documented the domains of engrailed (en), Abdominal-B (Abd-B) and caudal (cad) expression in the tail region...
- Crombach A, Wotton K, Cicin Sain D, Ashyraliyev M, Jaeger J. Efficient reverse-engineering of a developmental gene regulatory network. PLoS Comput Biol. 2012;8:e1002589 pubmed publisher..Only the quantitative investigation of a large number of developmental gene regulatory networks will allow us to discover whether there are rules or regularities governing development and evolution of complex multi-cellular organisms. ..
- 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..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)...
- Kühnlein R, Bronner G, Taubert H, Schuh R. Regulation of Drosophila spalt gene expression. Mech Dev. 1997;66:107-18 pubmed..In addition, we provide evidence that a zygotic gene product of the terminal system, Tailless, cooperates with the maternal gene product Caudal and thereby activates gene expression in the terminal region of the embryo.
- Sanchez L, Thieffry D. A logical analysis of the Drosophila gap-gene system. J Theor Biol. 2001;211:115-41 pubmed..qualitative, functional levels associated with each of the key regulatory factors (the three maternal Bcd, Hb and Cad products, and the four gap Gt, Hb, Kr and Kni products); (2) the most crucial interactions and regulatory circuits ..
- Reinitz J, Levine M. Control of the initiation of homeotic gene expression by the gap genes giant and tailless in Drosophila. Dev Biol. 1990;140:57-72 pubmed..giant also regulates the establishment of the expression patterns of Antennapedia and Abdominal-B. In particular, giant is the factor that controls the anterior limit of early Antennapedia expression. ..
- He X, Ling X, Sinha S. Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution. PLoS Comput Biol. 2009;5:e1000299 pubmed publisher..Our approach is implemented as software, EMMA (Evolutionary Model-based cis-regulatory Module Analysis), ready to be applied in a broad biological context...
- Rivera Pomar R, Jackle H. From gradients to stripes in Drosophila embryogenesis: filling in the gaps. Trends Genet. 1996;12:478-83 pubmed..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. ..
- Rivera Pomar R, Lu X, Perrimon N, Taubert H, Jackle H. Activation of posterior gap gene expression in the Drosophila blastoderm. Nature. 1995;376:253-6 pubmed..Here we show that caudal, a conserved homeodomain protein that forms a posterior-to-anterior concentration gradient, and the anterior ..
- Dearolf C, Topol J, Parker C. The caudal gene product is a direct activator of fushi tarazu transcription during Drosophila embryogenesis. Nature. 1989;341:340-3 pubmed..Here we report that the homoeodomain-containing protein encoded by caudal (cad) is one such regulator...
- Ryu J, Nam K, Oh C, Nam H, Kim S, Yoon J, et al. The homeobox gene Caudal regulates constitutive local expression of antimicrobial peptide genes in Drosophila epithelia. Mol Cell Biol. 2004;24:172-85 pubmed..Here, we show that the Drosophila homeobox gene product Caudal functions as the innate immune transcription modulator that is responsible for the constitutive local expression ..
- Jaeger J, Blagov M, Kosman D, Kozlov K, Manu -, Myasnikova E, et al. Dynamical analysis of regulatory interactions in the gap gene system of Drosophila melanogaster. Genetics. 2004;167:1721-37 pubmed..Our models predict activation of Kr by Cad and clarify several other regulatory interactions...
- 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. ..
- 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. ..
- Sokolowski T, Erdmann T, ten Wolde P. Mutual repression enhances the steepness and precision of gene expression boundaries. PLoS Comput Biol. 2012;8:e1002654 pubmed publisher..and cooperative activation of hb by the anterior morphogen Bicoid (Bcd) and of kni by the posterior morphogen Caudal (Cad), as well as the diffusion of Hb and Kni between neighboring nuclei...
- 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. ..
- 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
- Zinzen R, Papatsenko D. Enhancer responses to similarly distributed antagonistic gradients in development. PLoS Comput Biol. 2007;3:e84 pubmed