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Roy J, Cheung E, Bhatti J, Muneem A, Lobo D. Curation and annotation of planarian gene expression patterns with segmented reference morphologies. Bioinformatics 2020; 36:2881-2887. [DOI: 10.1093/bioinformatics/btaa023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/07/2019] [Accepted: 01/14/2020] [Indexed: 12/30/2022] Open
Abstract
Abstract
Motivation
Morphological and genetic spatial data from functional experiments based on genetic, surgical and pharmacological perturbations are being produced at an extraordinary pace in developmental and regenerative biology. However, our ability to extract knowledge from these large datasets are hindered due to the lack of formalization methods and tools able to unambiguously describe, centralize and interpret them. Formalizing spatial phenotypes and gene expression patterns is especially challenging in organisms with highly variable morphologies such as planarian worms, which due to their extraordinary regenerative capability can experimentally result in phenotypes with almost any combination of body regions or parts.
Results
Here, we present a computational methodology and mathematical formalism to encode and curate the morphological outcomes and gene expression patterns in planaria. Worm morphologies are encoded with mathematical graphs based on anatomical ontology terms to automatically generate reference morphologies. Gene expression patterns are registered to these standard reference morphologies, which can then be annotated automatically with anatomical ontology terms by analyzing the spatial expression patterns and their textual descriptions. This methodology enables the curation and annotation of complex experimental morphologies together with their gene expression patterns in a centralized standardized dataset, paving the way for the extraction of knowledge and reverse-engineering of the much sought-after mechanistic models in planaria and other regenerative organisms.
Availability and implementation
We implemented this methodology in a user-friendly graphical software tool, PlanGexQ, freely available together with the data in the manuscript at https://lobolab.umbc.edu/plangexq.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Joy Roy
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Eric Cheung
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Junaid Bhatti
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Abraar Muneem
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Daniel Lobo
- Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
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2
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Chipman AD, Edgecombe GD. Developing an integrated understanding of the evolution of arthropod segmentation using fossils and evo-devo. Proc Biol Sci 2019; 286:20191881. [PMID: 31575373 DOI: 10.1098/rspb.2019.1881] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Segmentation is fundamental to the arthropod body plan. Understanding the evolutionary steps by which arthropods became segmented is being transformed by the integration of data from evolutionary developmental biology (evo-devo), Cambrian fossils that allow the stepwise acquisition of segmental characters to be traced in the arthropod stem-group, and the incorporation of fossils into an increasingly well-supported phylogenetic framework for extant arthropods based on genomic-scale datasets. Both evo-devo and palaeontology make novel predictions about the evolution of segmentation that serve as testable hypotheses for the other, complementary data source. Fossils underpin such hypotheses as arthropodization originating in a frontal appendage and then being co-opted into other segments, and segmentation of the endodermal midgut in the arthropod stem-group. Insights from development, such as tagmatization being associated with different modes of segment generation in different body regions, and a distinct patterning of the anterior head segments, are complemented by palaeontological evidence for the pattern of tagmatization during ontogeny of exceptionally preserved fossils. Fossil and developmental data together provide evidence for a short head in stem-group arthropods and the mechanism of its formation and retention. Future breakthroughs are expected from identification of molecular signatures of developmental innovations within a phylogenetic framework, and from a focus on later developmental stages to identify the differentiation of repeated units of different systems within segmental precursors.
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Affiliation(s)
- Ariel D Chipman
- Department of Ecology, Evolution and Behavior, The Silberman Institute of Life Sciences, Edmond J. Safra Campus - Givat Ram, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Gregory D Edgecombe
- Department of Earth Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK
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3
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Schmidt-Ott U, Lynch JA. Emerging developmental genetic model systems in holometabolous insects. Curr Opin Genet Dev 2016; 39:116-128. [PMID: 27399647 DOI: 10.1016/j.gde.2016.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 05/25/2016] [Accepted: 06/08/2016] [Indexed: 01/08/2023]
Abstract
The number of insect species that are amenable to functional genetic studies is growing rapidly and provides many new research opportunities in developmental and evolutionary biology. The holometabolous insects represent a disproportionate percentage of animal diversity and are thus well positioned to provide model species for a wide variety of developmental processes. Here we discuss emerging holometabolous models, and review some recent breakthroughs. For example, flies and midges were found to use structurally unrelated long-range pattern organizers, butterflies and moths revealed extensive pattern formation during oogenesis, new imaging possibilities in the flour beetle Tribolium castaneum showed how embryos break free of their extraembryonic membranes, and the complex genetics governing interspecies difference in head shape were revealed in Nasonia wasps.
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Affiliation(s)
- Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, United States.
| | - Jeremy A Lynch
- Department of Biological Sciences, University of Illinois at Chicago, United States.
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Crombach A, Wotton KR, Jiménez-Guri E, Jaeger J. Gap Gene Regulatory Dynamics Evolve along a Genotype Network. Mol Biol Evol 2016; 33:1293-307. [PMID: 26796549 PMCID: PMC4839219 DOI: 10.1093/molbev/msw013] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift.” System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).
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Affiliation(s)
- Anton Crombach
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karl R Wotton
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
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5
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Kozlov K, Gursky VV, Kulakovskiy IV, Dymova A, Samsonova M. Analysis of functional importance of binding sites in the Drosophila gap gene network model. BMC Genomics 2015; 16 Suppl 13:S7. [PMID: 26694511 PMCID: PMC4686791 DOI: 10.1186/1471-2164-16-s13-s7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND The statistical thermodynamics based approach provides a promising framework for construction of the genotype-phenotype map in many biological systems. Among important aspects of a good model connecting the DNA sequence information with that of a molecular phenotype (gene expression) is the selection of regulatory interactions and relevant transcription factor bindings sites. As the model may predict different levels of the functional importance of specific binding sites in different genomic and regulatory contexts, it is essential to formulate and study such models under different modeling assumptions. RESULTS We elaborate a two-layer model for the Drosophila gap gene network and include in the model a combined set of transcription factor binding sites and concentration dependent regulatory interaction between gap genes hunchback and Kruppel. We show that the new variants of the model are more consistent in terms of gene expression predictions for various genetic constructs in comparison to previous work. We quantify the functional importance of binding sites by calculating their impact on gene expression in the model and calculate how these impacts correlate across all sites under different modeling assumptions. CONCLUSIONS The assumption about the dual interaction between hb and Kr leads to the most consistent modeling results, but, on the other hand, may obscure existence of indirect interactions between binding sites in regulatory regions of distinct genes. The analysis confirms the previously formulated regulation concept of many weak binding sites working in concert. The model predicts a more or less uniform distribution of functionally important binding sites over the sets of experimentally characterized regulatory modules and other open chromatin domains.
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Affiliation(s)
- Konstantin Kozlov
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
| | - Vitaly V Gursky
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
- Ioffe Institute, 26 Polytechnicheskaya, 194021 St.Petersburg, Russia
| | - Ivan V Kulakovskiy
- Engelhardt Institute of Molecular Biology, 32 Vavilova, 119991 Moscow, Russia
| | - Arina Dymova
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
| | - Maria Samsonova
- Peter the Great St. Petersburg Polytechnic University, 29 Polytechnicheskaya, 195251 St.Petersburg, Russia
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Martínez-Abadías N, Mateu R, Niksic M, Russo L, Sharpe J. Geometric Morphometrics on Gene Expression Patterns Within Phenotypes: A Case Example on Limb Development. Syst Biol 2015; 65:194-211. [PMID: 26377442 PMCID: PMC4748747 DOI: 10.1093/sysbio/syv067] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/11/2015] [Indexed: 01/12/2023] Open
Abstract
How the genotype translates into the phenotype through development is critical to fully understand the evolution of phenotypes. We propose a novel approach to directly assess how changes in gene expression patterns are associated with changes in morphology using the limb as a case example. Our method combines molecular biology techniques, such as whole-mount in situ hybridization, with image and shape analysis, extending the use of Geometric Morphometrics to the analysis of nonanatomical shapes, such as gene expression domains. Elliptical Fourier and Procrustes-based semilandmark analyses were used to analyze the variation and covariation patterns of the limb bud shape with the expression patterns of two relevant genes for limb morphogenesis, Hoxa11 and Hoxa13. We devised a multiple thresholding method to semiautomatically segment gene domains at several expression levels in large samples of limb buds from C57Bl6 mouse embryos between 10 and 12 postfertilization days. Besides providing an accurate phenotyping tool to quantify the spatiotemporal dynamics of gene expression patterns within developing structures, our morphometric analyses revealed high, non-random, and gene-specific variation undergoing canalization during limb development. Our results demonstrate that Hoxa11 and Hoxa13, despite being paralogs with analogous functions in limb patterning, show clearly distinct dynamic patterns, both in shape and size, and are associated differently with the limb bud shape. The correspondence between our results and already well-established molecular processes underlying limb development confirms that this morphometric approach is a powerful tool to extract features of development regulating morphogenesis. Such multilevel analyses are promising in systems where not so much molecular information is available and will advance our understanding of the genotype–phenotype map. In systematics, this knowledge will increase our ability to infer how evolution modified a common developmental pattern to generate a wide diversity of morphologies, as in the vertebrate limb.
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Affiliation(s)
- Neus Martínez-Abadías
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Roger Mateu
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Martina Niksic
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lucia Russo
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- EMBL-CRG Systems Biology Program, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
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Caroti F, Urbansky S, Wosch M, Lemke S. Germ line transformation and in vivo labeling of nuclei in Diptera: report on Megaselia abdita (Phoridae) and Chironomus riparius (Chironomidae). Dev Genes Evol 2015; 225:179-86. [PMID: 26044750 PMCID: PMC4460289 DOI: 10.1007/s00427-015-0504-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 05/20/2015] [Indexed: 11/28/2022]
Abstract
To understand how and when developmental traits of the fruit fly Drosophila melanogaster originated during the course of insect evolution, similar traits are functionally studied in variably related satellite species. The experimental toolkit available for relevant fly models typically comprises gene expression and loss as well as gain-of-function analyses. Here, we extend the set of available molecular tools to piggyBac-based germ line transformation in two satellite fly models, Megaselia abdita and Chironomus riparius. As proof-of-concept application, we used a Gateway variant of the piggyBac transposon vector pBac{3xP3-eGFPafm} to generate a transgenic line that expresses His2Av-mCherry as fluorescent nuclear reporter ubiquitously in the gastrulating embryo of M. abdita. Our results open two phylogenetically important nodes of the insect order Diptera for advanced developmental evolutionary genetics.
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Affiliation(s)
- Francesca Caroti
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Silvia Urbansky
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Maike Wosch
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
| | - Steffen Lemke
- Centre for Organismal Studies, Universität Heidelberg, Im Neuenheimer Feld 230, 69120 Heidelberg, Germany
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Wotton KR, Jiménez-Guri E, Jaeger J. Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita. PLoS Genet 2015; 11:e1005042. [PMID: 25757102 PMCID: PMC4355411 DOI: 10.1371/journal.pgen.1005042] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 01/30/2015] [Indexed: 02/01/2023] Open
Abstract
Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution. Antero-posterior polarity of the embryo is established through systems of maternal morphogen gradients. In Drosophila melanogaster, the anterior system acts through opposing gradients of Bicoid (Bcd) and Caudal (Cad), while the posterior system involves Nanos (Nos) and Hunchback (Hb) protein. These systems act redundantly. Both Bcd and Hb need to be eliminated to cause a complete loss of polarity resulting in mirror-duplicated abdomens, so-called bicaudal phenotypes. In contrast, knock-down of bcd alone is sufficient to induce double abdomens in non-drosophilid cyclorrhaphan dipterans such as the hoverfly Episyrphus balteatus or the scuttle fly Megaselia abdita. We investigate conserved and divergent aspects of axis specification in the cyclorrhaphan lineage through a detailed study of the establishment and regulatory effect of maternal gradients in M. abdita. Our results show that the function of the anterior maternal system is highly conserved in this species, despite the loss of maternal cad expression. In contrast, hb does not activate gap genes in this species. The absence of this activatory role provides a precise genetic explanation for the loss of polarity upon bcd knock-down in M. abdita, and suggests a general scenario in which the posterior maternal system is increasingly replaced by the anterior one during the evolution of the cyclorrhaphan dipteran lineage. The basic head-to-tail polarity of an animal is established very early in development. In dipteran insects (flies, midges, and mosquitoes), polarity is established with the help of so-called morphogen gradients. Morphogens are regulatory proteins that are distributed as a concentration gradient, often involving diffusion from a localised source. This graded distribution then leads to the concentration-dependent activation of different target genes along the embryo’s axis. We examine this process, which differs to a surprising extent between dipteran species, in the scuttle fly Megaselia abdita, and compare our results to the model organism Drosophila melanogaster. In this way, we not only gain insights into how the mechanisms that establish polarity function differently in different species, but also how the system has evolved since these two flies shared a common ancestor. Specifically, we pin down the main difference between Drosophila and Megaselia in the altered function of the maternal Hunchback morphogen gradient, which activates target genes in the former, but not the latter species, where it has been completely replaced by the Bicoid morphogen during evolution.
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Affiliation(s)
- Karl R. Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- * E-mail: (KW); (JJ)
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Wotton KR, Jiménez-Guri E, Crombach A, Cicin-Sain D, Jaeger J. High-resolution gene expression data from blastoderm embryos of the scuttle fly Megaselia abdita. Sci Data 2015; 2:150005. [PMID: 25977812 PMCID: PMC4423355 DOI: 10.1038/sdata.2015.5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 02/03/2015] [Indexed: 12/21/2022] Open
Abstract
Gap genes are involved in segment determination during early development in dipteran insects (flies, midges, and mosquitoes). We carried out a systematic quantitative comparative analysis of the gap gene network across different dipteran species. Our work provides mechanistic insights into the evolution of this pattern-forming network. As a central component of our project, we created a high-resolution quantitative spatio-temporal data set of gap and maternal co-ordinate gene expression in the blastoderm embryo of the non-drosophilid scuttle fly, Megaselia abdita. Our data include expression patterns in both wild-type and RNAi-treated embryos. The data-covering 10 genes, 10 time points, and over 1,000 individual embryos-consist of original embryo images, quantified expression profiles, extracted positions of expression boundaries, and integrated expression patterns, plus metadata and intermediate processing steps. These data provide a valuable resource for researchers interested in the comparative study of gene regulatory networks and pattern formation, an essential step towards a more quantitative and mechanistic understanding of developmental evolution.
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Affiliation(s)
- Karl R Wotton
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Anton Crombach
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Damjan Cicin-Sain
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08002 Barcelona, Spain
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10
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Wotton KR, Jiménez-Guri E, Crombach A, Janssens H, Alcaine-Colet A, Lemke S, Schmidt-Ott U, Jaeger J. Quantitative system drift compensates for altered maternal inputs to the gap gene network of the scuttle fly Megaselia abdita. eLife 2015; 4:e04785. [PMID: 25560971 PMCID: PMC4337606 DOI: 10.7554/elife.04785] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 01/02/2015] [Indexed: 12/20/2022] Open
Abstract
The segmentation gene network in insects can produce equivalent phenotypic outputs despite differences in upstream regulatory inputs between species. We investigate the mechanistic basis of this phenomenon through a systems-level analysis of the gap gene network in the scuttle fly Megaselia abdita (Phoridae). It combines quantification of gene expression at high spatio-temporal resolution with systematic knock-downs by RNA interference (RNAi). Initiation and dynamics of gap gene expression differ markedly between M. abdita and Drosophila melanogaster, while the output of the system converges to equivalent patterns at the end of the blastoderm stage. Although the qualitative structure of the gap gene network is conserved, there are differences in the strength of regulatory interactions between species. We term such network rewiring 'quantitative system drift'. It provides a mechanistic explanation for the developmental hourglass model in the dipteran lineage. Quantitative system drift is likely to be a widespread mechanism for developmental evolution.
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Affiliation(s)
- Karl R Wotton
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Eva Jiménez-Guri
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anton Crombach
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Hilde Janssens
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
| | - Anna Alcaine-Colet
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
- Universitat de Barcelona, Barcelona, Spain
| | - Steffen Lemke
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Urs Schmidt-Ott
- Department of Organismal Biology and Anatomy, University of Chicago, Chicago, United States
| | - Johannes Jaeger
- European Molecular Biology Laboratory, CRG Systems Biology Research Unit, Centre for Genomic Regulation, Barcelona, Spain
- Universitat Pompeu Fabra, Barcelona, Spain
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