How to make stripes: deciphering the transition from non-periodic to periodic patterns in Drosophila segmentation

No abstract is available for this paper.

• Publication year

  2011

• Venue

  Development

• Publication date

  2011-07-15

• Fields of study

  Biology, Medicine, Computer Science

• Identifiers
  DOI 10.1242/dev.062141PMID 21693522PMCID PMC3119311
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• A model of spatially restricted transcription in opposing gradients of activators and repressors

  2012cited by this paper
• lnteractions between the pair-rule genes runt, hairy, even-skipped and fushi tarazu and the establishment of periodic pattern in the Drosophila embryo

  2011influential reference
• The Developmental Transcriptome of Drosophila melanogaster

  2010cited by this paper
• Heads and tails: evolution of antero-posterior patterning in insects.

  2009cited by this paper
• Genomic Views of Distant-Acting Enhancers

  2009cited by this paper
• Stripy Ftz target genes are coordinately regulated by Ftz-F1.

  2009cited by this paper
• The Tribolium ortholog of knirps and knirps-related is crucial for head segmentation but plays a minor role during abdominal patterning.

  2008cited by this paper
• Conserved cluster organization of insect Runx genes

  2008cited by this paper
• Analysis of homeodomain specificities allows the family-wide prediction of preferred recognition sites.

  2008cited by this paper
• Characterization of the Drosophila segment determination morphome.

  2008cited by this paper
• Predicting expression patterns from regulatory sequence in Drosophila segmentation

  2008cited by this paper
• Evo‐Devo and an Expanding Evolutionary Synthesis

  2008cited by this paper
• Shadow Enhancers as a Source of Evolutionary Novelty

  2008cited by this paper
• Evolutionary origin and genomic organisation of runt-domain containing genes in arthropods

  2008cited by this paper
• Global analysis of patterns of gene expression during Drosophila embryogenesis

  2007cited by this paper
• On the dynamic nature of positional information.

  2006cited by this paper
• Complex Loci in Human and Mouse Genomes

  2006cited by this paper
• An eh1-Like Motif in Odd-skipped Mediates Recruitment of Groucho and Repression In Vivo

  2005cited by this paper
• The role of binding site cluster strength in Bicoid-dependent patterning in Drosophila.

  2005cited by this paper
• Arthropod Segmentation: beyond the Drosophila paradigm

  2005cited by this paper
• Cell signalling: Divided divisions

  2005cited by this paper
• A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors

  2005cited by this paper
• Drawing lines in the sand: even skipped et al. and parasegment boundaries.

  2004cited by this paper
• Segmentation.

  2004cited by this paper
• Transcriptional Control in the Segmentation Gene Network of Drosophila

  2004influential reference
• Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura

  2004cited by this paper
• Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila

  2004cited by this paper
• Groucho-dependent repression by sloppy-paired 1 differentially positions anterior pair-rule stripes in the Drosophila embryo.

  2004cited by this paper
• A self-organizing system of repressor gradients establishes segmental complexity in Drosophila

  2003cited by this paper
• Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell.

  2003cited by this paper
• A probabilistic method to detect regulatory modules

  2003influential reference
• Long-range enhancer–promoter interactions in the Scr-Antp interval of the Drosophila Antennapedia complex

  2003influential reference
• The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster.

  2003cited by this paper
• 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.

  2002cited by this paper
• Anterior-posterior patterning in the Drosophila embryo

  2002cited by this paper
• Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo

  2002influential reference
• Drumstick is a zinc finger protein that antagonizes Lines to control patterning and morphogenesis of the Drosophila hindgut.

  2002cited by this paper
• Transcriptional repression: the long and the short of it.

  2001cited by this paper
• Groucho augments the repression of multiple Even skipped target genes in establishing parasegment boundaries.

  2001cited by this paper
• Establishment and maintenance of parasegmental compartments.

  2001cited by this paper
• Registration of the expression patterns of Drosophila segmentation genes by two independent methods

  2001influential reference
• Mechanisms regulating target gene selection by the homeodomain-containing protein Fushi tarazu.

  2000influential reference
• Polarized Insertion of New Membrane from a Cytoplasmic Reservoir during Cleavage of the Drosophila Embryo

  2000influential reference
• Evidence for stabilizing selection in a eukaryotic enhancer element

  2000cited by this paper
• Kinetic analysis of segmentation gene interactions in Drosophila embryos.

  1999influential reference
• Transcriptional repression by the Drosophila giant protein: cis element positioning provides an alternative means of interpreting an effector gradient.

  1999cited by this paper
• 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.

  1999cited by this paper
• Dynamic changes in the functions of Odd-skipped during early Drosophila embryogenesis.

  1998influential reference
• dCtBP mediates transcriptional repression by Knirps, Krüppel and Snail in the Drosophila embryo

  1998cited by this paper
• The nuclear hormone receptor Ftz-F1 is a cofactor for the Drosophila homeodomain protein Ftz

  1997cited by this paper
• Ftz-F1 is a cofactor in Ftz activation of the Drosophila engrailed gene.

  1997cited by this paper
• Groucho-dependent and -independent repression activities of Runt domain proteins

  1997cited by this paper
• hairy mediates dominant repression in the Drosophila embryo

  1997cited by this paper
• Disperse versus compact elements for the regulation of runt stripes in Drosophila.

  1996cited by this paper
• Regulation of two pair-rule stripes by a single enhancer in the Drosophila embryo.

  1996cited by this paper
• The eve stripe 2 enhancer employs multiple modes of transcriptional synergy.

  1996cited by this paper
• Drosophila Paired regulates late even-skipped expression through a composite binding site for the paired domain and the homeodomain.

  1996influential reference
• Comparison of the structure and expression of odd-skipped and two related genes that encode a new family of zinc finger proteins in Drosophila.

  1996cited by this paper
• The gap protein knirps mediates both quenching and direct repression in the Drosophila embryo.

  1996cited by this paper
• Early even-skipped stripes act as morphogenetic gradients at the single cell level to establish engrailed expression.

  1995influential reference
• Non-periodic cues generate seven ftz stripes in the Drosophila embryo.

  1995influential reference
• Gap gene properties of the pair-rule gene runt during Drosophila segmentation.

  1994cited by this paper
• Positioning adjacent pair-rule stripes in the posterior Drosophila embryo.

  1994cited by this paper
• A two-step mode of stripe formation in the Drosophila blastoderm requires interactions among primary pair rule genes.

  1994cited by this paper
• Multiple regulatory elements direct the complex expression pattern of the Drosophila segmentation gene paired.

  1994cited by this paper
• Control of segmental asymmetry in Drosophila embryos.

  1993cited by this paper
• Analysis of a fushi tarazu autoregulatory element: multiple sequence elements contribute to enhancer activity.

  1993cited by this paper
• The Drosophila segmentation gene runt has an extended cis-regulatory region that is required for vital expression at other stages of development.

  1992cited by this paper
• Concentration-dependent activities of the even-skipped protein in Drosophila embryos.

  1992cited by this paper
• Regulation of even‐skipped stripe 2 in the Drosophila embryo.

  1992cited by this paper
• Direct homeodomain–DNA interaction in the autoregulation of the fushi tarazu gene

  1992cited by this paper
• Regulation of a segmentation stripe by overlapping activators and repressors in the Drosophila embryo.

  1991cited by this paper
• Individual stripe regulatory elements in the Drosophila hairy promoter respond to maternal, gap, and pair-rule genes.

  1991cited by this paper
• Decoding positional information: regulation of the pair-rule gene hairy.

  1990cited by this paper
• Making stripes in the Drosophila embryo.

  1990influential reference
• Gradients of Krüppel and knirps gene products direct pair-rule gene stripe patterning in the posterior region of the Drosophila embryo.

  1990cited by this paper
• Analysis of the ftz upstream element: germ layer-specific enhancers are independently autoregulated.

  1990cited by this paper
• Network of interactions among pair-rule genes regulating paired expression during primordial segmentation of Drosophila.

  1990cited by this paper
• Early and late periodic patterns of even skipped expression are controlled by distinct regulatory elements that respond to different spatial cues.

  1989influential reference
• Spatial control of hairy protein expression during embryogenesis.

  1989cited by this paper
• The zygotic control of Drosophila pair-rule gene expression. II. Spatial repression by gap and pair-rule gene products.

  1989influential reference
• The molecular genetics of embryonic pattern formation in Drosophila

  1988influential reference
• Accumulation of collagen III at the cleft points of developing mouse submandibular epithelium.

  1988cited by this paper
• Complementary patterns of even-skipped and fushi tarazu expression involve their differential regulation by a common set of segmentation genes in Drosophila.

  1987cited by this paper
• Regulation and function of the Drosophila segmentation gene fushi tarazu.

  1987cited by this paper
• The molecular basis for metameric pattern in the Drosophila embryo.

  1987cited by this paper
• Determination of anteroposterior polarity in Drosophila.

  1987cited by this paper
• Regulatory interactions between the segmentation genes fushi tarazu, hairy, and engrailed in the Drosophila blastoderm.

  1986cited by this paper
• Control elements of the Drosophila segmentation gene fushi tarazu.

  1985cited by this paper
• Mutations affecting segment number and polarity in Drosophila

  1980cited by this paper
• Molecular Systems Biology Peer Review Process File Accurate Measurements of Dynamics and Reproducibility in Small Genetic Networks Transaction Report

  year unknowncited by this paper
• eScholarship@UMassChan eScholarship@UMassChan

  year unknowncited by this paper

• Balancing precision with plasticity: Redefining the roles of transcription factors in early cell fate specification

  2025cites this paper
• Genome-wide quantitative dissection of an arthropod segmented body plan at single-cell resolution

  2025cites this paper
• Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms

  2025cites this paper
• Compensatory action of different types of cis-regulatory elements buffers the striped expression of Drosophila pair-rule genes

  2025influential citation
• The people behind the papers - Matthew Fischer and Leslie Pick.

  2025cites this paper
• Optogenetic dissection of transcriptional repression in a multicellular organism

  2024cites this paper
• From genes to patterns: a framework for modeling the emergence of embryonic development from transcriptional regulation

  2024cites this paper
• The Id protein Extramacrochaetae restrains the E protein Daughterless to regulate Notch, Rap1, and Sevenless within the R7 equivalence group of the Drosophila eye

  2024cites this paper
• Modelling and calibration of pair-rule protein patterns in Drosophila embryo: From Even-skipped and Fushi-tarazu to Wingless expression networks.

  2024cites this paper
• The ftz upstream element drives late ftz stripes but is not required for regulation of ftz target genes.

  2023cites this paper
• Functional analysis of the Drosophila eve locus in response to non-canonical combinations of gap gene expression levels.

  2023cites this paper
• Global repression by tailless during segmentation.

  2023cites this paper
• In-silico identification and comparison of transcription factor binding sites cluster in anterior-posterior patterning genes in Drosophila melanogaster and Tribolium castaneum

  2023cites this paper
• A bistable autoregulatory module in the developing embryo commits cells to binary expression fates.

  2023cites this paper
• Multifaceted effects on even-skipped transcriptional dynamics upon Krüppel dosage changes

  2023cites this paper
• Precisely timed regulation of enhancer activity defines the binary expression pattern of Fushi tarazu in the Drosophila embryo

  2023cites this paper
• Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems

  2023cites this paper
• A bistable autoregulatory module in the developing embryo commits cells to binary fates

  2022cites this paper
• Regulating the timing of enhancer transitions is key to defining sharp boundaries of Fushi tarazu expression in the Drosophila embryo

  2022cites this paper
• How enhancers regulate wavelike gene expression patterns

  2022cites this paper
• An additive repression mechanism sets the anterior limits of anterior pair-rule stripes 1.

  2022cites this paper
• Transcriptional coupling of distant regulatory genes in living embryos

  2022cites this paper
• The Nasonia pair-rule gene regulatory network retains its function over 300 million years of evolution

  2022cites this paper
• A timer gene network is spatially regulated by the terminal system in the Drosophila embryo

  2022cites this paper
• Drosophila embryo as experimental model: lessons learnt from genes in axis formation

  2022cites this paper
• Dynamic modulation of enhancer responsiveness by core promoter elements in living Drosophila embryos

  2021cites this paper
• Mechanistic Gene Networks Inferred from Single-Cell Data are Better Predictors than Neural Networks

  2021influential citation
• Nasonia segmentation is regulated by an ancestral insect segmentation regulatory network also present in flies

  2021cites this paper
• Regulation of transcriptional bursting by core promoter elements in the Drosophila embryo

  2021cites this paper
• Anterior-posterior patterning of segments in Anopheles stephensi offers insights into the transition from sequential to simultaneous segmentation in holometabolous insects.

  2021cites this paper
• Mechanistic gene networks inferred from single-cell data with an outlier-insensitive method.

  2021cites this paper
• Patterning with clocks and genetic cascades: Segmentation and regionalization of vertebrate versus insect body plans

  2021cites this paper
• The fushi tarazu zebra element is not required for Drosophila viability or fertility

  2021cites this paper
• Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network

  2020cites this paper
• A Mutation in the Drosophila melanogaster eve Stripe 2 Minimal Enhancer Is Buffered by Flanking Sequences

  2020cites this paper
• Transcriptional Enhancers in Drosophila

  2020cites this paper
• Evolution of the Bicoid homeodomain required amino acid substitutions in three subdomains and epistatic interactions between them

  2020cites this paper
• Cell sorting and morphogenesis in early Drosophila embryos.

  2020cites this paper
• Visualizing the Role of Boundary Elements in Enhancer-Promoter Communication.

  2020cites this paper
• Suboptimal Intermediates Underlie Evolution of the Bicoid Homeodomain

  2020cites this paper
• Comparing gastrulation in flies: Links between cell biology and the evolution of embryonic morphogenesis

  2020cites this paper
• On the problem of biological form

  2020cites this paper
• Periodic subcellular structures undergo long-range synchronized reorganization during C. elegans epidermal development

  2020cites this paper
• Identifying Key Genetic Regions for Cell Sheet Morphogenesis on Chromosome 2L Using a Drosophila Deficiency Screen in Dorsal Closure

  2020cites this paper
• The evolution of the gene regulatory networks patterning the Drosophila Blastoderm.

  2020cites this paper
• Time and space in segmentation

  2020influential citation
• Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing the Drosophila Segmentation Network

  2019cites this paper
• Dynamic expression of Drosophila segmental cell surface-encoding genes and their pair-rule regulators.

  2019cites this paper
• The multicellular incoherent feedforward loop motif generates spatial patterns

  2019cites this paper
• ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

  2019cites this paper
• Arthropod segmentation

  2019influential citation
• The 3D genome shapes the regulatory code of developmental genes.

  2019cites this paper
• Arthropod segmentation 1

  2019influential citation
• A quantitative study of the diversity of stripe-forming processes in an arthropod cell-based field undergoing axis formation and growth.

  2018cites this paper
• Modeling of gap gene regulatory networks in Drosophila with the account of the gene modular structure (in Russian)

  2018cites this paper
• Hunchback is counter-repressed to regulate even-skipped stripe 2 expression in Drosophila embryos

  2018cites this paper
• Temporal dynamics of pair-rule stripes in living Drosophila embryos

  2018cites this paper
• No significant regulation of bicoid mRNA by Pumilio or Nanos in the early Drosophila embryo

  2018cites this paper
• Evidence for the temporal regulation of insect segmentation by a conserved sequence of transcription factors

  2018influential citation
• Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species

  2018cites this paper
• Odd-Paired: The Drosophila Zic Gene.

  2018cites this paper
• Dynamic patterning by the Drosophila pair-rule network reconciles long-germ and short-germ segmentation

  2017influential citation
• Germ line–inherited H3K27me3 restricts enhancer function during maternal-to-zygotic transition

  2017cites this paper
• Supplementary Text 1: Regulatory interactions between the primary pair-rule genes during cellularisation

  2017influential citation
• Speed regulation of genetic cascades allows for evolvability in the body plan specification of insects

  2017cites this paper
• Caudal counter-represses Hunchback to regulate even-skipped stripe 2 expression in Drosophila embryos

  2017cites this paper
• Deep Homology?: Uncanny Similarities of Humans and Flies Uncovered by Evo-Devo

  2017cites this paper
• An efficient gene regulatory network inference algorithm for early Drosophila melanogaster embryogenesis

  2017cites this paper
• Evidence for the temporal regulation of insect segmentation by a conserved set of developmental transcription factors

  2017influential citation
• Ancient role of ten-m/odz in segmentation and the transition from sequential to syncytial segmentation

  2017cites this paper
• Sequential construction of a model for modular gene expression control, applied to spatial patterning of the Drosophila gene hunchback

  2016cites this paper
• Predicting Ancestral Segmentation Phenotypes from Drosophila to Anopheles Using In Silico Evolution

  2016cites this paper
• The Heidelberg Screen for Pattern Mutants of Drosophila: A Personal Account.

  2016cites this paper
• Odd-paired controls frequency doubling in Drosophila segmentation by altering the pair-rule gene regulatory network

  2016influential citation
• Analyses of interactions among pair-rule genes and the gap gene Krüppel in Bombyx segmentation.

  2015cites this paper
• Quantitative Modeling of a Gene's Expression from Its Intergenic Sequence

  2014cites this paper
• A gene expression atlas of a bicoid-depleted Drosophila embryo reveals early canalization of cell fate

  2014cites this paper
• determinants reveals a multitude of novel recognition motifs and binding zinc finger proteins 2-His 2 Cys Drosophila Global analysis of Material Supplemental

  2014cites this paper
• In silico evolution of the hunchback gene indicates redundancy in cis-regulatory organization and spatial gene expression

  2014cites this paper
• Dual mode of embryonic development is highlighted by expression and function of Nasonia pair-rule genes

  2014cites this paper
• Enhancer biology and enhanceropathies

  2014cites this paper
• Establishment of spatial pattern

  2014cites this paper
• Evolution of the pair rule gene network: Insights from a centipede

  2013cites this paper
• Mechanisms and constraints shaping the evolution of body plan segmentation

  2013cites this paper
• Deciphering the onychophoran 'segmentation gene cascade': Gene expression reveals limited involvement of pair rule gene orthologs in segmentation, but a highly conserved segment polarity gene network.

  2013cites this paper
• The function of Notch signalling in segment formation in the crustacean Daphnia magna (Branchiopoda).

  2013influential citation
• P-value-based regulatory motif discovery using positional weight matrices

  2013cites this paper
• Mechanisms and constraints shaping the evolution of body plan segmentation

  2013cites this paper
• Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants

  2013cites this paper
• Quantitative dynamics and increased variability of segmentation gene expression in the Drosophila Krüppel and knirps mutants.

  2013cites this paper
• Cellular resolution models for even skipped regulation in the entire Drosophila embryo

  2013cites this paper
• Regulation of a duplicated locus: Drosophila sloppy paired is replete with functionally overlapping enhancers.

  2012cites this paper
• Evolution in silico of genes with multiple regulatory modules on the example of the Drosophila segmentation gene hunchback

  2012cites this paper
• Expression of pair rule gene orthologs in the blastoderm of a myriapod: evidence for pair rule-like mechanisms?

  2012cites this paper
• Regulatory motif discovery using PWMs and the architecture of eukaryotic core promoters

  2012cites this paper
• A Conserved Developmental Patterning Network Produces Quantitatively Different Output in Multiple Species of Drosophila

  2011cites this paper