Genomes and Genes
Gene Symbol: slp2
Description: sloppy paired 2
Alias: CG2939, Dmel\CG2939, Dmslp2, FD7, FoxG, SLP, Slp, Slp2, slp, sloppy paired 2, CG2939-PA, Sloppy-paired, sloppy pair, sloppy paired, sloppy-paired 2, slp2-PA
Species: fruit fly
- Ingolia N. Topology and robustness in the Drosophila segment polarity network. PLoS Biol. 2004;2:e123 pubmed..I discuss how this topological property of networks provides robust pattern formation and how large changes in parameters can change the specific pattern produced by a network. ..
- Jaynes J, Fujioka M. Drawing lines in the sand: even skipped et al. and parasegment boundaries. Dev Biol. 2004;269:609-22 pubmed..We present a new model of pair-rule gene function that explains the response of these boundaries to the relative levels of Eve and Fushi Tarazu. ..
- Andrioli L, Oberstein A, Corado M, Yu D, Small S. Groucho-dependent repression by sloppy-paired 1 differentially positions anterior pair-rule stripes in the Drosophila embryo. Dev Biol. 2004;276:541-51 pubmed..The sloppy-paired (slp) locus contains two genes (slp1 and slp2) that are expressed in overlapping striped patterns in the presumptive thorax and abdomen...
- Peng P, Hassan Samee M, Sinha S. Incorporating chromatin accessibility data into sequence-to-expression modeling. Biophys J. 2015;108:1257-67 pubmed publisher..It also calls for future advances in modeling accessibility levels from sequence and the transregulatory context, so as to predict accurately the effect of cis and trans perturbations on gene expression. ..
- Lee H, Frasch M. Survey of forkhead domain encoding genes in the Drosophila genome: Classification and embryonic expression patterns. Dev Dyn. 2004;229:357-66 pubmed..Furthermore, the expression patterns of two of these genes, fd19B and fd102C, suggest a role for them as gap genes during early embryonic head segmentation. ..
- Wilson R. Competent steps in determination of cell fate. Bioessays. 1999;21:455-8 pubmed..A recent paper by Carmena et al. has revealed how several signalling mechanisms are used sequentially and in specific combinations to specify two mesodermal lineages in Drosophila. ..
- Crozatier M, Valle D, Dubois L, Ibnsouda S, Vincent A. Collier, a novel regulator of Drosophila head development, is expressed in a single mitotic domain. Curr Biol. 1996;6:707-18 pubmed..The structural conservation of Col during evolution raises the questions of its conservation of function in head specification and its interactions with other factors conserved between insects and vertebrates. ..
- Kaufmann E, Knochel W. Five years on the wings of fork head. Mech Dev. 1996;57:3-20 pubmed..The purpose of this review is to summarize the accumulating amount of data on structure, expression and function of fork head/HNF-3-related transcription factors. ..
- Hartmann B, Reichert H. The genetics of embryonic brain development in Drosophila. Mol Cell Neurosci. 1998;12:194-205 pubmed
- Fujioka M, Jaynes J. Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers. Dev Biol. 2012;362:309-19 pubmed publisherIn order to investigate regulation and redundancy within the sloppy paired (slp) locus, we analyzed 30 kilobases of DNA encompassing the tandem, coordinately regulated slp1 and slp2 transcription units...
- 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. ..
- WATSON J, Crews S. Formation and specification of a Drosophila dopaminergic precursor cell. Development. 2012;139:3316-25 pubmed publisher..a midline anterior domain by activating expression of the forkhead transcription factors sloppy paired 1 and sloppy paired 2. This is followed by hedgehog signaling that activates gsb/gsb-n expression in a subgroup of anterior cells...
- Nusslein Volhard C. Of flies and fishes. Science. 1994;266:572-4 pubmed
- Miskiewicz P, Morrissey D, Lan Y, Raj L, Kessler S, Fujioka M, et al. Both the paired domain and homeodomain are required for in vivo function of Drosophila Paired. Development. 1996;122:2709-18 pubmed..Quantitation of this effect shows that the paired domain mutant has a dominant-negative effect consistent with the observations that Paired protein can bind DNA as a dimer. ..
- Stoll G, Bischofberger M, Rougemont J, Naef F. Stabilizing patterning in the Drosophila segment polarity network by selecting models in silico. Biosystems. 2010;102:3-10 pubmed publisher..Here we demonstrate that simple dynamical considerations and in silico evolution can enhance the model to robustly express the expected pattern, helping to elucidate the role of further interactions. ..
- Cadigan K, Grossniklaus U, Gehring W. Localized expression of sloppy paired protein maintains the polarity of Drosophila parasegments. Genes Dev. 1994;8:899-913 pubmed..The sloppy paired (slp) locus contains two transcription units, both encoding proteins containing a forkhead domain, a DNA-..
- 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. ..
- Fujioka M, Gebelein B, COFER Z, Mann R, Jaynes J. Engrailed cooperates directly with Extradenticle and Homothorax on a distinct class of homeodomain binding sites to repress sloppy paired. Dev Biol. 2012;366:382-92 pubmed publisher..The sloppy-paired (slp) locus is a target of repression by both Eve and En...
- Halfon M, Arnosti D. New tools, resources for gene regulatory analysis in Drosophila. Fly (Austin). 2007;1:123-4 pubmed
- Buescher M, Svendsen P, Tio M, Miskolczi McCallum C, Tear G, Brook W, et al. Drosophila T box proteins break the symmetry of hedgehog-dependent activation of wingless. Curr Biol. 2004;14:1694-702 pubmed..In odd-numbered abdominal segments, Mid/H15 activity plays an important role in restricting the expression of Wg to a single domain. ..
- 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/. ..
- Gates A, Rocha L. Control of complex networks requires both structure and dynamics. Sci Rep. 2016;6:24456 pubmed publisher..Our analysis further shows that the logic of automata transition functions, namely how canalizing they are, plays an important role in the extent to which structure predicts dynamics. ..
- Noordermeer J, Klingensmith J, Nusse R. Differential requirements for segment polarity genes in wingless signaling. Mech Dev. 1995;51:145-55 pubmed..Signaling from engrailed cells to this novel wingless expression domain is dependent on hedgehog but also on porcupine. We further demonstrate a novel requirement for hedgehog in maintenance of expression of engrailed itself. ..
- Kobayashi M, Fujioka M, Tolkunova E, Deka D, Abu Shaar M, Mann R, et al. Engrailed cooperates with extradenticle and homothorax to repress target genes in Drosophila. Development. 2003;130:741-51 pubmed..These studies expand the functional requirements for extradenticle and homothorax beyond the Hox proteins to a larger family of non-Hox homeodomain proteins. ..
- Wheeler J, VanderZwan C, Xu X, Swantek D, Tracey W, Gergen J. Distinct in vivo requirements for establishment versus maintenance of transcriptional repression. Nat Genet. 2002;32:206-10 pubmed..Other transcription factors can also establish repression in Rpd3-deficient embryos, which indicates that the distinction between establishment and maintenance may be a general feature of eukaryotic transcriptional repression. ..
- Nasiadka A, Grill A, Krause H. Mechanisms regulating target gene selection by the homeodomain-containing protein Fushi tarazu. Development. 2000;127:2965-76 pubmed..Activity regulation then fine-tunes the temporal and spatial domains of promoter responses, the magnitude of these responses, and whether they are positive or negative. ..
- Clark K, Halay E, Lai E, Burley S. Co-crystal structure of the HNF-3/fork head DNA-recognition motif resembles histone H5. Nature. 1993;364:412-20 pubmed..The remainder of the protein includes a twisted, antiparallel beta-structure and random coil that interacts with the minor groove. ..
- Sanchez L, Thieffry D. Segmenting the fly embryo: a logical analysis of the pair-rule cross-regulatory module. J Theor Biol. 2003;224:517-37 pubmed..Finally, it provides new insights into the roles and evolutionary origins of the apparent redundancies in the regulatory architecture of the pair-rule module. ..
- Kobayashi M, Goldstein R, Fujioka M, Paroush Z, Jaynes J. Groucho augments the repression of multiple Even skipped target genes in establishing parasegment boundaries. Development. 2001;128:1805-15 pubmed..active on two target genes that are normally repressed by Even skipped at different concentrations, paired and sloppy paired. When the Groucho interaction motif is mutated, repression of each target gene is reduced to a similar extent, ..
- Gebelein B, Mann R. Compartmental modulation of abdominal Hox expression by engrailed and sloppy-paired patterns the fly ectoderm. Dev Biol. 2007;308:593-605 pubmed..we show that en is essential for high Abd-A levels and low Ubx levels in the P compartment, whereas sloppy-paired (slp) is required for high Ubx levels in the A compartment...
- Andrioli L, Vasisht V, Theodosopoulou E, Oberstein A, Small S. Anterior repression of a Drosophila stripe enhancer requires three position-specific mechanisms. Development. 2002;129:4931-40 pubmed..These results suggest a common mechanism for preventing anterior activation of three different eve enhancers. ..
- Nikulova A, Favorov A, Sutormin R, Makeev V, Mironov A. CORECLUST: identification of the conserved CRM grammar together with prediction of gene regulation. Nucleic Acids Res. 2012;40:e93 pubmed publisher..Compared with related methods, CORECLUST shows better performance at identification of CRMs conferring muscle-specific gene expression in vertebrates and early-developmental CRMs in Drosophila. ..
- Kozlov K, Myasnikova E, Samsonova A, Surkova S, Reinitz J, Samsonova M. GCPReg package for registration of the segmentation gene expression data in Drosophila. Fly (Austin). 2009;3:151-6 pubmed..GCPReg has been designed to operate ona UNIX platform and is freely available via the Internet at http://urchin.spbcas.ru/downloads/GCPReg/GCPReg.htm. ..
- Chaves M, Albert R. Studying the effect of cell division on expression patterns of the segment polarity genes. J R Soc Interface. 2008;5 Suppl 1:S71-84 pubmed publisher..Two of these questions are analysed here: the dependence of the signalling protein sloppy paired on the segment polarity genes and the effect of cell division on the segment polarity genes' expression ..
- Fujioka M, Yusibova G, Patel N, Brown S, Jaynes J. The repressor activity of Even-skipped is highly conserved, and is sufficient to activate engrailed and to regulate both the spacing and stability of parasegment boundaries. Development. 2002;129:4411-21 pubmed
- Martinez C, Rest J, Kim A, Ludwig M, Kreitman M, White K, et al. Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Mol Biol Evol. 2014;31:903-16 pubmed publisher..A multiplicity of mechanisms for binding site turnover exemplified by Bicoid, Giant, and Krüppel sites, explains how rapid sequence change may occur while maintaining the function of the cis-regulatory element...
- Park M, Wu X, Golden K, Axelrod J, Bodmer R. The wingless signaling pathway is directly involved in Drosophila heart development. Dev Biol. 1996;177:104-16 pubmed..In particular, overexpression of dsh can restore heart formation in the absence of wg function. We discuss the possibility that Wg signaling is part of a combinatorial mechanism to specify the cardiac mesoderm. ..
- Piepenburg O, Vorbrüggen G, Jackle H. Drosophila segment borders result from unilateral repression of hedgehog activity by wingless signaling. Mol Cell. 2000;6:203-9 pubmed..The nuclear mediators of the two signaling pathways, Cubitus interruptus and Pangolin, function as activator and symmetry-breaking repressor of stripe expression, respectively. ..
- 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. ..
- Cadigan K, Grossniklaus U, Gehring W. Functional redundancy: the respective roles of the two sloppy paired genes in Drosophila segmentation. Proc Natl Acad Sci U S A. 1994;91:6324-8 pubmedThe sloppy paired (slp) locus consists of two genes, slp1 and slp2, both of which encode proteins containing a forkhead domain (a DNA-binding motif)...
- Lindner J, Hillman P, Barrett A, Jackson M, Perry T, Park Y, et al. The Drosophila Perlecan gene trol regulates multiple signaling pathways in different developmental contexts. BMC Dev Biol. 2007;7:121 pubmed..These studies also highlight the fact that Trol function is not dedicated to a single molecular mechanism, but is capable of regulating different growth factor pathways depending on the cell-type and event underway. ..
- 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. ..
- Goldstein R, Cook O, Dinur T, Pisanté A, Karandikar U, Bidwai A, et al. An eh1-like motif in odd-skipped mediates recruitment of Groucho and repression in vivo. Mol Cell Biol. 2005;25:10711-20 pubmed..Our data suggest that phosphorylation of these phosphomeric residues, if it occurs, will down-regulate Groucho binding and therefore repression, providing a mechanism for posttranslational control of Groucho-mediated repression. ..
- Skeath J, Panganiban G, Selegue J, Carroll S. Gene regulation in two dimensions: the proneural achaete and scute genes are controlled by combinations of axis-patterning genes through a common intergenic control region. Genes Dev. 1992;6:2606-19 pubmed
- Quan J, Saaem I, Tang N, Ma S, Negre N, Gong H, et al. Parallel on-chip gene synthesis and application to optimization of protein expression. Nat Biotechnol. 2011;29:449-52 pubmed publisher..This technology may facilitate systematic investigation of the molecular mechanisms of protein translation and the design, construction and evolution of macromolecular machines, metabolic networks and synthetic cells. ..
- 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..In addition, we show that the early eve gradient is sufficient, at its posterior edge, for subdividing the ftz domain into engrailed expressing and non-expressing cells. ..
- Gutierrez Aviño F, Ferres Marco D, Dominguez M. The position and function of the Notch-mediated eye growth organizer: the roles of JAK/STAT and four-jointed. EMBO Rep. 2009;10:1051-8 pubmed publisher..These findings redefine the process of organizer formation and function, and they identify four-jointed as a regulatory node, integrating multiple growth-control pathways. ..
- Riechmann V, Irion U, Wilson R, Grosskortenhaus R, Leptin M. Control of cell fates and segmentation in the Drosophila mesoderm. Development. 1997;124:2915-22 pubmed..Both the domain of even-skipped function and the level of twist expression are regulated by sloppy-paired. sloppy-paired thus controls segmental allocation of mesodermal cells to different fates. ..
- Goriely A, Stella M, Coffinier C, Kessler D, Mailhos C, Dessain S, et al. A functional homologue of goosecoid in Drosophila. Development. 1996;122:1641-50 pubmed..The identification of gsc target genes and/or other genes involved in similar developmental processes will allow the definition of the precise phylogenetic relationship among Gsc proteins. ..
- Nakachi Y, Hayakawa T, Oota H, Sumiyama K, Wang L, Ueda S. Nucleotide compositional constraints on genomes generate alanine-, glycine-, and proline-rich structures in transcription factors. Mol Biol Evol. 1997;14:1042-9 pubmed publisher..Furthermore, reptile class III POU sequences revealed no evolutionary directionality increasing the GC contents from cold- to warm-blooded vertebrates...
- 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. ..
- Crozatier M, Valle D, Dubois L, Ibnsouda S, Vincent A. Head versus trunk patterning in the Drosophila embryo; collier requirement for formation of the intercalary segment. Development. 1999;126:4385-94 pubmed
- Hacker U, Grossniklaus U, Gehring W, Jackle H. Developmentally regulated Drosophila gene family encoding the fork head domain. Proc Natl Acad Sci U S A. 1992;89:8754-8 pubmed..Two of these fkh-domain-encoding genes ("FD genes") map to the sloppy paired locus (slp), which exerts segmentation gene function...
- Jennings B. Stopping transcription in its tracks. Nat Genet. 2002;32:87-8 pubmed
- 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..A model fully accounting for these results proposes that metameric slp1 expression is achieved through the Runt-dependent regulation of interactions between these two pair-rule response elements and the slp1 promoter...
- Carroll S, Scott M. Zygotically active genes that affect the spatial expression of the fushi tarazu segmentation gene during early Drosophila embryogenesis. Cell. 1986;45:113-26 pubmed..No simple regulatory relationships can be deduced. Rather, expression of the ftz gene depends upon the interactions among the different segmentation genes active at each position along the anterior-posterior axis of the early embryo. ..
- Li X, Erclik T, Bertet C, Chen Z, Voutev R, Venkatesh S, et al. Temporal patterning of Drosophila medulla neuroblasts controls neural fates. Nature. 2013;498:456-62 pubmed publisher..Five transcription factors-Homothorax, Eyeless, Sloppy paired, Dichaete and Tailless-are sequentially expressed in a temporal cascade in each of the medulla neuroblasts as ..
- Ruiz Gomez M. Muscle patterning and specification in Drosophila. Int J Dev Biol. 1998;42:283-90 pubmed