1
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Petrosky SJ, Williams TM, Rebeiz M. A genetic screen of transcription factors in the Drosophila melanogaster abdomen identifies novel pigmentation genes. G3 (BETHESDA, MD.) 2024; 14:jkae097. [PMID: 38820091 PMCID: PMC11373662 DOI: 10.1093/g3journal/jkae097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 06/02/2024]
Abstract
Gene regulatory networks specify the gene expression patterns needed for traits to develop. Differences in these networks can result in phenotypic differences between organisms. Although loss-of-function genetic screens can identify genes necessary for trait formation, gain-of-function screens can overcome genetic redundancy and identify loci whose expression is sufficient to alter trait formation. Here, we leveraged transgenic lines from the Transgenic RNAi Project at Harvard Medical School to perform both gain- and loss-of-function CRISPR/Cas9 screens for abdominal pigmentation phenotypes. We identified measurable effects on pigmentation patterns in the Drosophila melanogaster abdomen for 21 of 55 transcription factors in gain-of-function experiments and 7 of 16 tested by loss-of-function experiments. These included well-characterized pigmentation genes, such as bab1 and dsx, and transcription factors that had no known role in pigmentation, such as slp2. Finally, this screen was partially conducted by undergraduate students in a Genetics Laboratory course during the spring semesters of 2021 and 2022. We found this screen to be a successful model for student engagement in research in an undergraduate laboratory course that can be readily adapted to evaluate the effect of hundreds of genes on many different Drosophila traits, with minimal resources.
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Affiliation(s)
- Sarah J Petrosky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | | | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, USA
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2
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Berardi S, Rhodes JA, Berner MC, Greenblum SI, Bitter MC, Behrman EL, Betancourt NJ, Bergland AO, Petrov DA, Rajpurohit S, Schmidt P. Drosophila melanogaster pigmentation demonstrates adaptive phenotypic parallelism but genomic unpredictability over multiple timescales. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.09.607378. [PMID: 39211235 PMCID: PMC11361081 DOI: 10.1101/2024.08.09.607378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Populations are capable of responding to environmental change over ecological timescales via adaptive tracking. However, the translation from patterns of allele frequency change to rapid adaptation of complex traits remains unresolved. We used abdominal pigmentation in Drosophila melanogaster as a model phenotype to address the nature, genetic architecture, and repeatability of rapid adaptation in the field. We show that D. melanogaster pigmentation evolves as a highly parallel and deterministic response to shared environmental gradients across latitude and season in natural North American populations. We then experimentally evolved replicate, genetically diverse fly populations in field mesocosms to remove any confounding effects of demography and/or cryptic structure that may drive patterns in wild populations; we show that pigmentation rapidly responds, in parallel, in fewer than ten generations. Thus, pigmentation evolves concordantly in response to spatial and temporal climatic gradients. We next examined whether phenotypic differentiation was associated with allele frequency change at loci with established links to genetic variance in pigmentation in natural populations. We found that across all spatial and temporal scales, phenotypic patterns were associated with variation at pigmentation-related loci, and the sets of genes we identified in each context were largely nonoverlapping. Therefore, our findings suggest that parallel phenotypic evolution is associated with an unpredictable genomic response, with distinct components of the polygenic architecture shifting across each environmental gradient to produce redundant adaptive patterns. Significance Statement Shifts in global climate conditions have heightened our need to understand the dynamics and pace of adaptation in natural populations. In order to anticipate the population-level response to rapidly changing environmental conditions, we need to understand whether trait evolution is predictable over short timescales, and whether the genetic basis of adaptation is shared or distinct across multiple timescales. Here, we explored parallelism in the adaptive response of a complex phenotype, D. melanogaster pigmentation, to shared conditions that varied over multiple spatiotemporal scales. Our results demonstrate that while phenotypic adaptation proceeds as a predictable response to environmental gradients, even over short timescales, the genetic basis of the adaptive response is variable and nuanced across spatial and temporal contexts.
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3
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Lafuente E, Duneau D, Beldade P. Genetic basis of variation in thermal developmental plasticity for Drosophila melanogaster body pigmentation. Mol Ecol 2024; 33:e17294. [PMID: 38366327 DOI: 10.1111/mec.17294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/30/2024] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Seasonal differences in insect pigmentation are attributed to the influence of ambient temperature on pigmentation development. This thermal plasticity is adaptive and heritable, and thereby capable of evolving. However, the specific genes contributing to the variation in plasticity that can drive its evolution remain largely unknown. To address this, we analysed pigmentation and pigmentation plasticity in Drosophila melanogaster. We measured two components of pigmentation in the thorax and abdomen: overall darkness and the proportion of length covered by darker pattern elements (a trident in the thorax and bands in the abdomen) in females from two developmental temperatures (17 or 28°C) and 191 genotypes. Using a GWAS approach to identify the genetic basis of variation in pigmentation and its response to temperature, we identified numerous dispersed QTLs, including some mapping to melanogenesis genes (yellow, ebony, and tan). Remarkably, we observed limited overlap between QTLs for variation within specific temperatures and those influencing thermal plasticity, as well as minimal overlap between plasticity QTLs across pigmentation components and across body parts. For most traits, consistent with selection favouring the retention of plasticity, we found that lower plasticity alleles were often at lower frequencies. The functional analysis of selected candidate QTLs and pigmentation genes largely confirmed their contributions to variation in pigmentation and/or pigmentation plasticity. Overall, our study reveals the existence and underlying basis of extensive and trait-specific genetic variation for pigmentation and pigmentation plasticity, offering a rich reservoir of raw material for natural selection to shape the evolution of these traits independently.
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Affiliation(s)
- E Lafuente
- Instituto Gulbenkian de Ciência, Oeiras, Portugal
| | - D Duneau
- UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
- Queen's Medical Research Institute, University of Edinburgh, Edinburgh, UK
| | - P Beldade
- cE3c (Center for Ecology, Evolution and Environmental Changes) & CHANGE (Global Change and Sustainability Institute), FCUL, Lisboa, Portugal
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4
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Thayer RC, Patel NH. A meta-analysis of butterfly structural colors: their color range, distribution and biological production. J Exp Biol 2023; 226:jeb245940. [PMID: 37937662 DOI: 10.1242/jeb.245940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2023]
Abstract
Butterfly scales are among the richest natural sources of optical nanostructures, which produce structural color and iridescence. Several recurring nanostructure types have been described, such as ridge multilayers, gyroids and lower lamina thin films. While the optical mechanisms of these nanostructure classes are known, their phylogenetic distributions and functional ranges have not been described in detail. In this Review, we examine a century of research on the biological production of structural colors, including their evolution, development and genetic regulation. We have also created a database of more than 300 optical nanostructures in butterflies and conducted a meta-analysis of the color range, abundance and phylogenetic distribution of each nanostructure class. Butterfly structural colors are ubiquitous in short wavelengths but extremely rare in long wavelengths, especially red. In particular, blue wavelengths (around 450 nm) occur in more clades and are produced by more kinds of nanostructures than other hues. Nanostructure categories differ in prevalence, phylogenetic distribution, color range and brightness. For example, lamina thin films are the least bright; perforated lumen multilayers occur most often but are almost entirely restricted to the family Lycaenidae; and 3D photonic crystals, including gyroids, have the narrowest wavelength range (from about 450 to 550 nm). We discuss the implications of these patterns in terms of nanostructure evolution, physical constraint and relationships to pigmentary color. Finally, we highlight opportunities for future research, such as analyses of subadult and Hesperid structural colors and the identification of genes that directly build the nanostructures, with relevance for biomimetic engineering.
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Affiliation(s)
- Rachel C Thayer
- Department of Evolution and Ecology, University of California, Davis, Davis, CA 95616, USA
| | - Nipam H Patel
- Marine Biological Laboratory, Woods Hole, MA 02543, USA
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5
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Levo M, Raimundo J, Bing XY, Sisco Z, Batut PJ, Ryabichko S, Gregor T, Levine MS. Transcriptional coupling of distant regulatory genes in living embryos. Nature 2022; 605:754-760. [PMID: 35508662 PMCID: PMC9886134 DOI: 10.1038/s41586-022-04680-7] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 03/23/2022] [Indexed: 02/01/2023]
Abstract
The prevailing view of metazoan gene regulation is that individual genes are independently regulated by their own dedicated sets of transcriptional enhancers. Past studies have reported long-range gene-gene associations1-3, but their functional importance in regulating transcription remains unclear. Here we used quantitative single-cell live imaging methods to provide a demonstration of co-dependent transcriptional dynamics of genes separated by large genomic distances in living Drosophila embryos. We find extensive physical and functional associations of distant paralogous genes, including co-regulation by shared enhancers and co-transcriptional initiation over distances of nearly 250 kilobases. Regulatory interconnectivity depends on promoter-proximal tethering elements, and perturbations in these elements uncouple transcription and alter the bursting dynamics of distant genes, suggesting a role of genome topology in the formation and stability of co-transcriptional hubs. Transcriptional coupling is detected throughout the fly genome and encompasses a broad spectrum of conserved developmental processes, suggesting a general strategy for long-range integration of gene activity.
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Affiliation(s)
- Michal Levo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - João Raimundo
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Xin Yang Bing
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Zachary Sisco
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Philippe J. Batut
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Sergey Ryabichko
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Joseph Henry Laboratories of Physics, Princeton University, Princeton, NJ, USA,Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, Paris, France,Corresponding authors
| | - Michael S. Levine
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA,Corresponding authors
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6
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Bourbon HMG, Benetah MH, Guillou E, Mojica-Vazquez LH, Baanannou A, Bernat-Fabre S, Loubiere V, Bantignies F, Cavalli G, Boube M. A shared ancient enhancer element differentially regulates the bric-a-brac tandem gene duplicates in the developing Drosophila leg. PLoS Genet 2022; 18:e1010083. [PMID: 35294439 PMCID: PMC8959175 DOI: 10.1371/journal.pgen.1010083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/28/2022] [Accepted: 02/07/2022] [Indexed: 11/18/2022] Open
Abstract
Gene duplications and transcriptional enhancer emergence/modifications are thought having greatly contributed to phenotypic innovations during animal evolution. Nevertheless, little is known about how enhancers evolve after gene duplication and how regulatory information is rewired between duplicated genes. The Drosophila melanogaster bric-a-brac (bab) complex, comprising the tandem paralogous genes bab1 and bab2, provides a paradigm to address these issues. We previously characterized an intergenic enhancer (named LAE) regulating bab2 expression in the developing legs. We show here that bab2 regulators binding directly the LAE also govern bab1 expression in tarsal cells. LAE excision by CRISPR/Cas9-mediated genome editing reveals that this enhancer appears involved but not strictly required for bab1 and bab2 co-expression in leg tissues. Instead, the LAE enhancer is critical for paralog-specific bab2 expression along the proximo-distal leg axis. Chromatin features and phenotypic rescue experiments indicate that LAE functions partly redundantly with leg-specific regulatory information overlapping the bab1 transcription unit. Phylogenomics analyses indicate that (i) the bab complex originates from duplication of an ancestral singleton gene early on within the Cyclorrhapha dipteran sublineage, and (ii) LAE sequences have been evolutionarily-fixed early on within the Brachycera suborder thus predating the gene duplication event. This work provides new insights on enhancers, particularly about their emergence, maintenance and functional diversification during evolution.
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Affiliation(s)
- Henri-Marc G. Bourbon
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Mikhail H. Benetah
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Emmanuelle Guillou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Luis Humberto Mojica-Vazquez
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Aissette Baanannou
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Sandra Bernat-Fabre
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
| | - Vincent Loubiere
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Frédéric Bantignies
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, University of Montpellier, CNRS Montpellier, France
| | - Muriel Boube
- Center for Integrative Biology, Molecular Cellular and Developmental (MCD) Biology Unit, Federal University of Toulouse, Toulouse, France
- * E-mail:
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7
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Ficarrotta V, Hanly JJ, Loh LS, Francescutti CM, Ren A, Tunström K, Wheat CW, Porter AH, Counterman BA, Martin A. A genetic switch for male UV iridescence in an incipient species pair of sulphur butterflies. Proc Natl Acad Sci U S A 2022; 119:e2109255118. [PMID: 35012980 PMCID: PMC8784150 DOI: 10.1073/pnas.2109255118] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 11/19/2021] [Indexed: 11/18/2022] Open
Abstract
Mating cues evolve rapidly and can contribute to species formation and maintenance. However, little is known about how sexual signals diverge and how this variation integrates with other barrier loci to shape the genomic landscape of reproductive isolation. Here, we elucidate the genetic basis of ultraviolet (UV) iridescence, a courtship signal that differentiates the males of Colias eurytheme butterflies from a sister species, allowing females to avoid costly heterospecific matings. Anthropogenic range expansion of the two incipient species established a large zone of secondary contact across the eastern United States with strong signatures of genomic admixtures spanning all autosomes. In contrast, Z chromosomes are highly differentiated between the two species, supporting a disproportionate role of sex chromosomes in speciation known as the large-X (or large-Z) effect. Within this chromosome-wide reproductive barrier, linkage mapping indicates that cis-regulatory variation of bric a brac (bab) underlies the male UV-iridescence polymorphism between the two species. Bab is expressed in all non-UV scales, and butterflies of either species or sex acquire widespread ectopic iridescence following its CRISPR knockout, demonstrating that Bab functions as a suppressor of UV-scale differentiation that potentiates mating cue divergence. These results highlight how a genetic switch can regulate a premating signal and integrate with other reproductive barriers during intermediate phases of speciation.
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Affiliation(s)
- Vincent Ficarrotta
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Joseph J Hanly
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Ling S Loh
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | | | - Anna Ren
- Department of Biological Sciences, The George Washington University, Washington, DC 20052
| | - Kalle Tunström
- Department of Zoology, Stockholm University, Stockholm S-10691, Sweden
| | | | - Adam H Porter
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003
| | | | - Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052;
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8
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Tarikere S, Ylla G, Extavour CG. Distinct gene expression dynamics in germ line and somatic tissue during ovariole morphogenesis in Drosophila melanogaster. G3 (BETHESDA, MD.) 2021; 12:6364899. [PMID: 34849771 PMCID: PMC9210308 DOI: 10.1093/g3journal/jkab305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022]
Abstract
The survival and evolution of a species is a function of the number of offspring it can produce. In insects, the number of eggs that an ovary can produce is a major determinant of reproductive capacity. Insect ovaries are made up of tubular egg-producing subunits called ovarioles, whose number largely determines the number of eggs that can be potentially laid. Ovariole number in Drosophila is directly determined by the number of cellular structures called terminal filaments, which are stacks of cells that assemble in the larval ovary. Elucidating the developmental and regulatory mechanisms of terminal filament formation is thus key to understanding the regulation of insect reproduction through ovariole number regulation. We systematically measured mRNA expression of all cells in the larval ovary at the beginning, middle, and end of terminal filament formation. We also separated somatic and germ line cells during these stages and assessed their tissue-specific gene expression during larval ovary development. We found that the number of differentially expressed somatic genes is highest during the late stages of terminal filament formation and includes many signaling pathways that govern ovary development. We also show that germ line tissue, in contrast, shows greater differential expression during early stages of terminal filament formation, and highly expressed germ line genes at these stages largely control cell division and DNA repair. We provide a tissue-specific and temporal transcriptomic dataset of gene expression in the developing larval ovary as a resource to study insect reproduction.
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Affiliation(s)
- Shreeharsha Tarikere
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Guillem Ylla
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cassandra G Extavour
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA,Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA,Corresponding author:
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9
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Ruiz-Losada M, Pérez-Reyes C, Estella C. Role of the Forkhead Transcription Factors Fd4 and Fd5 During Drosophila Leg Development. Front Cell Dev Biol 2021; 9:723927. [PMID: 34409041 PMCID: PMC8365472 DOI: 10.3389/fcell.2021.723927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022] Open
Abstract
Appendage development requires the coordinated function of signaling pathways and transcription factors to pattern the leg along the three main axes: the antero-posterior (AP), proximo-distal (PD), and dorso-ventral (DV). The Drosophila leg DV axis is organized by two morphogens, Decapentaplegic (Dpp), and Wingless (Wg), which direct dorsal and ventral cell fates, respectively. However, how these signals regulate the differential expression of its target genes is mostly unknown. In this work, we found that two members of the Drosophila forkhead family of transcription factors, Fd4 and Fd5 (also known as fd96Ca and fd96Cb), are identically expressed in the ventro-lateral domain of the leg imaginal disc in response to Dpp signaling. Here, we analyze the expression regulation and function of these genes during leg development. We have generated specific mutant alleles for each gene and a double fd4/fd5 mutant chromosome to study their function during development. We highlight the redundant role of the fd4/fd5 genes during the formation of the sex comb, a male specific structure that appears in the ventro-lateral domain of the prothoracic leg.
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Affiliation(s)
- Mireya Ruiz-Losada
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
| | - Cristian Pérez-Reyes
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
| | - Carlos Estella
- Centro de Biología Molecular Severo Ochoa (C.S.I.C.-U.A.M.), Universidad Autónoma de Madrid, Madrid, Spain
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10
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Banisch TU, Slaidina M, Gupta S, Ho M, Gilboa L, Lehmann R. A transitory signaling center controls timing of primordial germ cell differentiation. Dev Cell 2021; 56:1742-1755.e4. [PMID: 34081907 PMCID: PMC8330407 DOI: 10.1016/j.devcel.2021.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 03/07/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
Organogenesis requires exquisite spatiotemporal coordination of cell morphogenesis, migration, proliferation, and differentiation of multiple cell types. For gonads, this involves complex interactions between somatic and germline tissues. During Drosophila ovary morphogenesis, primordial germ cells (PGCs) either are sequestered in stem cell niches and are maintained in an undifferentiated germline stem cell state or transition directly toward differentiation. Here, we identify a mechanism that links hormonal triggers of somatic tissue morphogenesis with PGC differentiation. An early ecdysone pulse initiates somatic swarm cell (SwC) migration, positioning these cells close to PGCs. A second hormone peak activates Torso-like signal in SwCs, which stimulates the Torso receptor tyrosine kinase (RTK) signaling pathway in PGCs promoting their differentiation by de-repression of the differentiation gene, bag of marbles. Thus, systemic temporal cues generate a transitory signaling center that coordinates ovarian morphogenesis with stem cell self-renewal and differentiation programs, highlighting a more general role for such centers in reproductive and developmental biology.
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Affiliation(s)
- Torsten U Banisch
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA.
| | - Maija Slaidina
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Selena Gupta
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Megan Ho
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA
| | - Lilach Gilboa
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ruth Lehmann
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY 10016, USA.
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11
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Postika N, Schedl P, Georgiev P, Kyrchanova O. Redundant enhancers in the iab-5 domain cooperatively activate Abd-B in the A5 and A6 abdominal segments of Drosophila.. [DOI: 10.1101/2021.05.22.445252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractThe homeotic Abdominal-B (Abd-B) gene belongs to Bithorax complex and is regulated by four regulatory domains named iab-5, iab-6, iab-7 and iab-8, each of which is thought to be responsible for directing the expression of Abd-B in one of the abdominal segments from A5 to A8. It is assumed that male specific features of the adult cuticle in A5 is solely dependent on regulatory elements located in iab-5, while the regulatory elements in the iab-6 are both necessary and sufficient for the proper differentiation of the A6 cuticle. Unexpectedly, we found that this long held assumption is not correct. Instead, redundant tissue-specific enhancers located in the iab-5 domain are required for the proper activation of Abd-B not only in A5 but also in A6. Our study of deletions shows that the iab-5 initiator is essential for the functioning of the iab-5 enhancers in A5, as well as for the correct differentiation of A6. This requirement is circumvented by deletions that remove the initiator and most of the iab-5 regulatory domain sequences. While the remaining iab-5 enhancers are inactive in A5, they are activated in A6 and contribute to the differentiation of this segment. In this case, Abd-B stimulation by the iab-5 enhancers in A6 depends on the initiators in the iab-4 and iab-6 domains.Summary StatementIn Drosophila, the segmental-specific expression of the homeotic gene Abdominal-B in the abdominal segments is regulated by autonomous regulatory domains. We demonstrated cooperation between these domains in activation of Abdominal-B.
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12
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Unbehend M, Kozak GM, Koutroumpa F, Coates BS, Dekker T, Groot AT, Heckel DG, Dopman EB. bric à brac controls sex pheromone choice by male European corn borer moths. Nat Commun 2021; 12:2818. [PMID: 33990556 PMCID: PMC8121916 DOI: 10.1038/s41467-021-23026-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 03/28/2021] [Indexed: 02/03/2023] Open
Abstract
The sex pheromone system of ~160,000 moth species acts as a powerful form of assortative mating whereby females attract conspecific males with a species-specific blend of volatile compounds. Understanding how female pheromone production and male preference coevolve to produce this diversity requires knowledge of the genes underlying change in both traits. In the European corn borer moth, pheromone blend variation is controlled by two alleles of an autosomal fatty-acyl reductase gene expressed in the female pheromone gland (pgFAR). Here we show that asymmetric male preference is controlled by cis-acting variation in a sex-linked transcription factor expressed in the developing male antenna, bric à brac (bab). A genome-wide association study of preference using pheromone-trapped males implicates variation in the 293 kb bab intron 1, rather than the coding sequence. Linkage disequilibrium between bab intron 1 and pgFAR further validates bab as the preference locus, and demonstrates that the two genes interact to contribute to assortative mating. Thus, lack of physical linkage is not a constraint for coevolutionary divergence of female pheromone production and male behavioral response genes, in contrast to what is often predicted by evolutionary theory.
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Affiliation(s)
- Melanie Unbehend
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Genevieve M Kozak
- Department of Biology, Tufts University, Medford, MA, USA
- Department of Biology, University of Massachusetts Dartmouth, Dartmouth, MA, USA
| | - Fotini Koutroumpa
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, XH, the Netherlands
- INRAE, Sorbonne Université, CNRS, IRD, UPEC, Université Paris Diderot, Institute of Ecology and Environmental Sciences of Paris, Versailles, Cedex, France
| | - Brad S Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA, USA
| | - Teun Dekker
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Astrid T Groot
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, XH, the Netherlands
| | - David G Heckel
- Department of Entomology, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Erik B Dopman
- Department of Biology, Tufts University, Medford, MA, USA.
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13
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Distant activation of Notch signaling induces stem cell niche assembly. PLoS Genet 2021; 17:e1009489. [PMID: 33780456 PMCID: PMC8031783 DOI: 10.1371/journal.pgen.1009489] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/08/2021] [Accepted: 03/15/2021] [Indexed: 11/26/2022] Open
Abstract
Here we show that multiple modes of Notch signaling activation specify the complexity of spatial cellular interactions necessary for stem cell niche assembly. In particular, we studied the formation of the germline stem cell niche in Drosophila ovaries, which is a two-step process whereby terminal filaments are formed first. Then, terminal filaments signal to the adjacent cap cell precursors, resulting in Notch signaling activation, which is necessary for the lifelong acquisition of stem cell niche cell fate. The genetic data suggest that in order to initiate the process of stem cell niche assembly, Notch signaling is activated among non-equipotent cells via distant induction, where germline Delta is delivered to somatic cells located several diameters away via cellular projections generated by primordial germ cells. At the same time, to ensure the robustness of niche formation, terminal filament cell fate can also be induced by somatic Delta via cis- or trans-inhibition. This exemplifies a double security mechanism that guarantees that the germline stem cell niche is formed, since it is indispensable for the adjacent germline precursor cells to acquire and maintain stemness necessary for successful reproduction. These findings contribute to our understanding of the formation of stem cell niches in their natural environment, which is important for stem cell biology and regenerative medicine. Adult organs often contain a stem cell niche that maintains stem cells necessary for the replenishment of different types of terminally differentiated cells that are continuously lost. This study reveals that various modes of Notch signaling activation induce the formation of the germline stem cell niche in Drosophila. We show for the first time that even among non-equipotent cells, Notch signaling can be trans-activated via distant induction mode, where the ligand Delta is delivered via cellular protrusions to the somatic stem cell niche precursors located several cell diameters away. Moreover, there is a second security mechanism controlled by the soma that additionally ensures that the stem cell niche is formed. In the stem cell niche precursors, Notch signaling can be locally inhibited by the somatic Delta. While Notch signaling trans-inhibition has been proposed via mathematical modelling, our findings show that a group of cells that have high Delta can be seen in a living organism, confirming that this mode of Notch signaling inhibition by trans-Delta exists in vivo. This work provides significant advances in the understanding of Notch signaling and the stem cell niche formation, which is important for the fields of stem cell biology and regenerative medicine.
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14
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Slaidina M, Banisch TU, Gupta S, Lehmann R. A single-cell atlas of the developing Drosophila ovary identifies follicle stem cell progenitors. Genes Dev 2020; 34:239-249. [PMID: 31919193 PMCID: PMC7000915 DOI: 10.1101/gad.330464.119] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/02/2019] [Indexed: 12/16/2022]
Abstract
Addressing the complexity of organogenesis at a system-wide level requires a complete understanding of adult cell types, their origin, and precursor relationships. The Drosophila ovary has been a model to study how coordinated stem cell units, germline, and somatic follicle stem cells maintain and renew an organ. However, lack of cell type-specific tools have limited our ability to study the origin of individual cell types and stem cell units. Here, we used a single-cell RNA sequencing approach to uncover all known cell types of the developing ovary, reveal transcriptional signatures, and identify cell type-specific markers for lineage tracing. Our study identifies a novel cell type corresponding to the elusive follicle stem cell precursors and predicts subtypes of known cell types. Altogether, we reveal a previously unanticipated complexity of the developing ovary and provide a comprehensive resource for the systematic analysis of ovary morphogenesis.
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Affiliation(s)
- Maija Slaidina
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York 10016, USA
| | - Torsten U Banisch
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York 10016, USA
| | - Selena Gupta
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York 10016, USA
| | - Ruth Lehmann
- Department of Cell Biology, Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York 10016, USA
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15
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Natori K, Kojima T. Subdivision of the Tarsal Region into Five Tarsal Segments by the Combination of Region-Specific Transcription Factors. CYTOLOGIA 2019. [DOI: 10.1508/cytologia.84.105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Kohei Natori
- Graduate School of Frontier Sciences, The University of Tokyo
| | - Tetsuya Kojima
- Graduate School of Frontier Sciences, The University of Tokyo
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16
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Camara N, Whitworth C, Dove A, Van Doren M. Doublesex controls specification and maintenance of the gonad stem cell niches in Drosophila. Development 2019; 146:dev.170001. [PMID: 31043421 DOI: 10.1242/dev.170001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 04/23/2019] [Indexed: 11/20/2022]
Abstract
Sex-specific development of the gonads is a key aspect of sexual dimorphism that is regulated by Doublesex/Mab3-related transcription factors (DMRTs) in diverse animal species. We find that in mutants for Drosophila dsx, important components of the male and female gonad stem cell niches (hubs and terminal filaments/cap cells, respectively) still form. Initially, gonads in all dsx mutants (both XX and XY) initiate the male program of development, but later half of these gonads switch to form female stem cell niche structures. One individual can have both male-type and female-type gonad niches; however, male and female niches are usually not observed in the same gonad, indicating that cells make a 'group decision' about which program to follow. We conclude that dsx does not act in an instructive manner to regulate male versus female niche formation, as these structures form in the absence of dsx function. Instead, dsx acts to 'tip the balance' between the male or female programs, which are then executed independently of dsx We show that bric a brac acts downstream of dsx to control the male versus female niche decision. These results indicate that, in both flies and mammals, the sexual fate of the somatic gonad is remarkably plastic and is controlled by a combination of autonomous and non-autonomous cues.
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Affiliation(s)
- Nicole Camara
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Cale Whitworth
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Abigail Dove
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Mark Van Doren
- Department of Biology, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA
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17
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Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
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Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
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18
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De Castro S, Peronnet F, Gilles JF, Mouchel-Vielh E, Gibert JM. bric à brac (bab), a central player in the gene regulatory network that mediates thermal plasticity of pigmentation in Drosophila melanogaster. PLoS Genet 2018; 14:e1007573. [PMID: 30067846 PMCID: PMC6089454 DOI: 10.1371/journal.pgen.1007573] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 08/13/2018] [Accepted: 07/19/2018] [Indexed: 01/28/2023] Open
Abstract
Drosophila body pigmentation has emerged as a major Evo-Devo model. Using two Drosophila melanogaster lines, Dark and Pale, selected from a natural population, we analyse here the interaction between genetic variation and environmental factors to produce this complex trait. Indeed, pigmentation varies with genotype in natural populations and is sensitive to temperature during development. We demonstrate that the bric à brac (bab) genes, that are differentially expressed between the two lines and whose expression levels vary with temperature, participate in the pigmentation difference between the Dark and Pale lines. The two lines differ in a bab regulatory sequence, the dimorphic element (called here bDE). Both bDE alleles are temperature-sensitive, but the activity of the bDE allele from the Dark line is lower than that of the bDE allele from the Pale line. Our results suggest that this difference could partly be due to differential regulation by AbdB. bab has been previously reported to be a repressor of abdominal pigmentation. We show here that one of its targets in this process is the pigmentation gene tan (t), regulated via the tan abdominal enhancer (t_MSE). Furthermore, t expression is strongly modulated by temperature in the two lines. Thus, temperature sensitivity of t expression is at least partly a consequence of bab thermal transcriptional plasticity. We therefore propose that a gene regulatory network integrating both genetic variation and temperature sensitivity modulates female abdominal pigmentation. Interestingly, both bDE and t_MSE were previously shown to have been recurrently involved in abdominal pigmentation evolution in drosophilids. We propose that the environmental sensitivity of these enhancers has turned them into evolutionary hotspots. Complex traits such as size or disease susceptibility are typically modulated by both genetic variation and environmental conditions. Model organisms such as fruit flies (Drosophila) are particularly appropriate to analyse the interactions between genetic variation and environmental factors during the development of complex phenotypes. Natural populations carry high genetic variation and can be grown in controlled conditions in the laboratory. Here, we use Drosophila melanogaster female abdominal pigmentation, which is both genetically variable and modulated by the environment (temperature) to dissect this kind of interaction. We show that the pigmentation difference between two inbred fly lines is caused by genetic variation in an enhancer of the bab locus, which encodes two transcription factors controlling abdominal pigmentation. Indeed, this enhancer drives differential expression between the two lines. Interestingly, this enhancer is sensitive to temperature in both lines. We show that the effect of bab on pigmentation is mediated by the pigmentation gene tan (t) that is repressed by bab. Thus, the previously reported temperature-sensitive expression of t is a direct consequence of bab transcriptional plasticity.
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Affiliation(s)
- Sandra De Castro
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
| | - Frédérique Peronnet
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
| | - Jean-François Gilles
- Sorbonne Université, CNRS, Core facility, Institut de Biologie Paris Seine (IBPS), Paris, France
| | - Emmanuèle Mouchel-Vielh
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
- * E-mail: (EM-V); (J-MG)
| | - Jean-Michel Gibert
- Sorbonne Université, CNRS, Laboratoire de Biologie du Développement -Institut de Biologie Paris Seine (LBD-IBPS), Team “Epigenetic control of developmental homeostasis and plasticity”, Paris, France
- * E-mail: (EM-V); (J-MG)
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19
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Bao R, Dia SE, Issa HA, Alhusein D, Friedrich M. Comparative Evidence of an Exceptional Impact of Gene Duplication on the Developmental Evolution of Drosophila and the Higher Diptera. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00063] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
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20
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Allbee AW, Rincon-Limas DE, Biteau B. Lmx1a is required for the development of the ovarian stem cell niche in Drosophila. Development 2018; 145:dev.163394. [PMID: 29615466 DOI: 10.1242/dev.163394] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 03/26/2018] [Indexed: 01/02/2023]
Abstract
The Drosophila ovary serves as a model for pioneering studies of stem cell niches, with defined cell types and signaling pathways supporting both germline and somatic stem cells. The establishment of the niche units begins during larval stages with the formation of terminal filament-cap structures; however, the genetics underlying their development remains largely unknown. Here, we show that the transcription factor Lmx1a is required for ovary morphogenesis. We found that Lmx1a is expressed in early ovarian somatic lineages and becomes progressively restricted to terminal filaments and cap cells. We show that Lmx1a is required for the formation of terminal filaments, during the larval-pupal transition. Finally, our data demonstrate that Lmx1a functions genetically downstream of Bric-à-Brac, and is crucial for the expression of key components of several conserved pathways essential to ovarian stem cell niche development. Importantly, expression of chicken Lmx1b is sufficient to rescue the null Lmx1a phenotype, indicating functional conservation across the animal kingdom. These results significantly expand our understanding of the mechanisms controlling stem cell niche development in the fly ovary.
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Affiliation(s)
- Andrew W Allbee
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Diego E Rincon-Limas
- Department of Neurology, McKnight Brain Institute, University of Florida, 1149 Newell Drive, FL 32611, USA
| | - Benoît Biteau
- Department of Biomedical Genetics, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY 14642, USA
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21
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Roeske MJ, Camino EM, Grover S, Rebeiz M, Williams TM. Cis-regulatory evolution integrated the Bric-à-brac transcription factors into a novel fruit fly gene regulatory network. eLife 2018; 7. [PMID: 29297463 PMCID: PMC5752203 DOI: 10.7554/elife.32273] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 12/19/2017] [Indexed: 11/13/2022] Open
Abstract
Gene expression evolution through gene regulatory network (GRN) changes has gained appreciation as a driver of morphological evolution. However, understanding how GRNs evolve is hampered by finding relevant cis-regulatory element (CRE) mutations, and interpreting the protein-DNA interactions they alter. We investigated evolutionary changes in the duplicated Bric-à-brac (Bab) transcription factors and a key Bab target gene in a GRN underlying the novel dimorphic pigmentation of D. melanogaster and its relatives. It has remained uncertain how Bab was integrated within the pigmentation GRN. Here, we show that the ancestral transcription factor activity of Bab gained a role in sculpting sex-specific pigmentation through the evolution of binding sites in a CRE of the pigment-promoting yellow gene. This work demonstrates how a new trait can evolve by incorporating existing transcription factors into a GRN through CRE evolution, an evolutionary path likely to predominate newly evolved functions of transcription factors.
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Affiliation(s)
- Maxwell J Roeske
- Department of Biology, University of Dayton, Dayton, United States
| | - Eric M Camino
- Department of Biology, University of Dayton, Dayton, United States
| | - Sumant Grover
- Department of Biology, University of Dayton, Dayton, United States
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, United States
| | - Thomas Michael Williams
- Department of Biology, University of Dayton, Dayton, United States.,Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, United States
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22
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Pan JW, Li Q, Barish S, Okuwa S, Zhao S, Soeder C, Kanke M, Jones CD, Volkan PC. Patterns of transcriptional parallelism and variation in the developing olfactory system of Drosophila species. Sci Rep 2017; 7:8804. [PMID: 28821769 PMCID: PMC5562767 DOI: 10.1038/s41598-017-08563-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/13/2017] [Indexed: 11/09/2022] Open
Abstract
Organisms have evolved strikingly parallel phenotypes in response to similar selection pressures suggesting that there may be shared constraints limiting the possible evolutionary trajectories. For example, the behavioral adaptation of specialist Drosophila species to specific host plants can exhibit parallel changes in their adult olfactory neuroanatomy. We investigated the genetic basis of these parallel changes by comparing gene expression during the development of the olfactory system of two specialist Drosophila species to that of four other generalist species. Our results suggest that the parallelism observed in the adult olfactory neuroanatomy of ecological specialists extends more broadly to their developmental antennal expression profiles, and to the transcription factor combinations specifying olfactory receptor neuron (ORN) fates. Additionally, comparing general patterns of variation for the antennal transcriptional profiles in the adult and developing olfactory system of the six species suggest the possibility that specific, non-random components of the developmental programs underlying the Drosophila olfactory system harbor a disproportionate amount of interspecies variation. Further examination of these developmental components may be able to inform a deeper understanding of how traits evolve.
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Affiliation(s)
- Jia Wern Pan
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Qingyun Li
- Department of Biology, Stanford University, Stanford, California, USA
| | - Scott Barish
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Sumie Okuwa
- Pratt School of Engineering, Duke University, Durham, North Carolina, USA
| | - Songhui Zhao
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Charles Soeder
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Matthew Kanke
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Corbin D Jones
- Department of Biology and Integrative Program for Biological & Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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23
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Lobell AS, Kaspari RR, Serrano Negron YL, Harbison ST. The Genetic Architecture of Ovariole Number in Drosophila melanogaster: Genes with Major, Quantitative, and Pleiotropic Effects. G3 (BETHESDA, MD.) 2017; 7:2391-2403. [PMID: 28550012 PMCID: PMC5499145 DOI: 10.1534/g3.117.042390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 05/24/2017] [Indexed: 01/03/2023]
Abstract
Ovariole number has a direct role in the number of eggs produced by an insect, suggesting that it is a key morphological fitness trait. Many studies have documented the variability of ovariole number and its relationship to other fitness and life-history traits in natural populations of Drosophila However, the genes contributing to this variability are largely unknown. Here, we conducted a genome-wide association study of ovariole number in a natural population of flies. Using mutations and RNAi-mediated knockdown, we confirmed the effects of 24 candidate genes on ovariole number, including a novel gene, anneboleyn (formerly CG32000), that impacts both ovariole morphology and numbers of offspring produced. We also identified pleiotropic genes between ovariole number traits and sleep and activity behavior. While few polymorphisms overlapped between sleep parameters and ovariole number, 39 candidate genes were nevertheless in common. We verified the effects of seven genes on both ovariole number and sleep: bin3, blot, CG42389, kirre, slim, VAChT, and zfh1 Linkage disequilibrium among the polymorphisms in these common genes was low, suggesting that these polymorphisms may evolve independently.
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Affiliation(s)
- Amanda S Lobell
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Rachel R Kaspari
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Yazmin L Serrano Negron
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Susan T Harbison
- Laboratory of Systems Genetics, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
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24
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A comparison of nucleosome organization in Drosophila cell lines. PLoS One 2017; 12:e0178590. [PMID: 28570602 PMCID: PMC5453549 DOI: 10.1371/journal.pone.0178590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 05/16/2017] [Indexed: 01/25/2023] Open
Abstract
Changes in the distribution of nucleosomes along the genome influence chromatin structure and impact gene expression by modulating the accessibility of DNA to transcriptional machinery. However, the role of genome-wide nucleosome positioning in gene expression and in maintaining differentiated cell states remains poorly understood. Drosophila melanogaster cell lines represent distinct tissue types and exhibit cell-type specific gene expression profiles. They thus could provide a useful tool for investigating cell-type specific nucleosome organization of an organism's genome. To evaluate this possibility, we compared genome-wide nucleosome positioning and occupancy in five different Drosophila tissue-specific cell lines, and in reconstituted chromatin, and then tested for correlations between nucleosome positioning, transcription factor binding motifs, and gene expression. Nucleosomes in all cell lines were positioned in accordance with previously known DNA-nucleosome interactions, with helically repeating A/T di-nucleotide pairs arranged within nucleosomal DNAs and AT-rich pentamers generally excluded from nucleosomal DNA. Nucleosome organization in all cell lines differed markedly from in vitro reconstituted chromatin, with highly expressed genes showing strong nucleosome organization around transcriptional start sites. Importantly, comparative analysis identified genomic regions that exhibited cell line-specific nucleosome enrichment or depletion. Further analysis of these regions identified 91 out of 16,384 possible heptamer sequences that showed differential nucleosomal occupation between cell lines, and 49 of the heptamers matched one or more known transcription factor binding sites. These results demonstrate that there is differential nucleosome positioning between these Drosophila cell lines and therefore identify a system that could be used to investigate the functional significance of differential nucleosomal positioning in cell type specification.
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25
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Tissue-specific enhancer repression through molecular integration of cell signaling inputs. PLoS Genet 2017; 13:e1006718. [PMID: 28394894 PMCID: PMC5402979 DOI: 10.1371/journal.pgen.1006718] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 04/24/2017] [Accepted: 03/27/2017] [Indexed: 11/19/2022] Open
Abstract
Drosophila leg morphogenesis occurs under the control of a relatively well-known genetic cascade, which mobilizes both cell signaling pathways and tissue-specific transcription factors. However, their cross-regulatory interactions, deployed to refine leg patterning, remain poorly characterized at the gene expression level. Within the genetically interacting landscape that governs limb development, the bric-à-brac2 (bab2) gene is required for distal leg segmentation. We have previously shown that the Distal-less (Dll) homeodomain and Rotund (Rn) zinc-finger activating transcription factors control limb-specific bab2 expression by binding directly a single critical leg/antennal enhancer (LAE) within the bric-à-brac locus. By genetic and molecular analyses, we show here that the EGFR-responsive C15 homeodomain and the Notch-regulated Bowl zinc-finger transcription factors also interact directly with the LAE enhancer as a repressive duo. The appendage patterning gene bab2 is the first identified direct target of the Bowl repressor, an Odd-skipped/Osr family member. Moreover, we show that C15 acts on LAE activity independently of its regular partner, the Aristaless homeoprotein. Instead, we find that C15 interacts physically with the Dll activator through contacts between their homeodomain and binds competitively with Dll to adjacent cognate sites on LAE, adding potential new layers of regulation by C15. Lastly, we show that C15 and Bowl activities regulate also rn expression. Our findings shed light on how the concerted action of two transcriptional repressors, in response to cell signaling inputs, shapes and refines gene expression along the limb proximo-distal axis in a timely manner. Limb morphogenesis is controlled by a well-known genetic cascade, mobilizing both cell signaling and tissue-specific transcription factors (TFs). However, how their concerted action refines gene expression remains to be deciphered. It is thus crucial to understand how cell signaling inputs are integrated by transcriptional “enhancers”. The Drosophila leg provides a good paradigm to dissect the molecular mechanisms underlying gene regulation. Here, we used the bric-a-brac2 (bab2) gene as a model to study the integrated regulation of patterning genes implicated in tarsal segmentation. bab2 expression in the leg primordium is dynamic and complex, going from initial broad distal expression to precisely positioned tarsal rings. By genetic and molecular analyses, we show here that the cell signaling-responding TFs C15 and Bowl interact directly with the limb-specific bab2 enhancer as a repressive duo. Moreover, C15 acts independently of its partner Aristaless through physical interaction with the Dll activator. We propose that Dll induces early circular bab2 expression pattern, then EGFR signaling-induced C15 in the distalmost cells competes with Dll for LAE binding and resolves bab2 pattern as a ring. Taken together our data shed light on how the concerted action of a quartet of transcription factors reshapes gene expression during limb proximo-distal axis development.
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Kojima T. Developmental mechanism of the tarsus in insect legs. CURRENT OPINION IN INSECT SCIENCE 2017; 19:36-42. [PMID: 28521941 DOI: 10.1016/j.cois.2016.11.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Revised: 11/16/2016] [Accepted: 11/22/2016] [Indexed: 06/07/2023]
Abstract
Insects show a tremendous morphological variety and have been a subject of studying morphological evolution. In legs, the tarsus is especially variable in the number of subsegments (tarsal segments) and their proportion unlike other leg segments. Recent studies in Drosophila melanogaster have revealed details of the tarsal development: regionalization of the tarsal region through integration of regulatory network and its growth, determination of the joint-forming region in each segment through strict regulation of Notch activity, changes in tissue morphology through regulation of RhoGTPases regulators and localized cell death, and finally, the morphogenetic mechanism of the ball-and-socket joint between tarsal segments. The substantial knowledge of the tarsal development makes it a suitable model for studying mechanisms of morphological evolution and diversification.
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Affiliation(s)
- Tetsuya Kojima
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8562, Japan.
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27
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Quijano JC, Wisotzkey RG, Tran NL, Huang Y, Stinchfield MJ, Haerry TE, Shimmi O, Newfeld SJ. lolal Is an Evolutionarily New Epigenetic Regulator of dpp Transcription during Dorsal-Ventral Axis Formation. Mol Biol Evol 2016; 33:2621-32. [PMID: 27401231 PMCID: PMC5026256 DOI: 10.1093/molbev/msw132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Secreted ligands in the Dpp/BMP family drive dorsal–ventral (D/V) axis formation in all Bilaterian species. However, maternal factors regulating Dpp/BMP transcription in this process are largely unknown. We identified the BTB domain protein longitudinals lacking-like (lolal) as a modifier of decapentaplegic (dpp) mutations. We show that Lolal is evolutionarily related to the Trithorax group of chromatin regulators and that lolal interacts genetically with the epigenetic factor Trithorax-like during Dpp D/V signaling. Maternally driven LolalHA is found in oocytes and translocates to zygotic nuclei prior to the point at which dpp transcription begins. lolal maternal and zygotic mutant embryos display significant reductions in dpp, pMad, and zerknullt expression, but they are never absent. The data suggest that lolal is required to maintain dpp transcription during D/V patterning. Phylogenetic data revealed that lolal is an evolutionarily new gene present only in insects and crustaceans. We conclude that Lolal is the first maternal protein identified with a role in dpp D/V transcriptional maintenance, that Lolal and the epigenetic protein Trithorax-like are essential for Dpp D/V signaling and that the architecture of the Dpp D/V pathway evolved in the arthropod lineage after the separation from vertebrates via the incorporation of new genes such as lolal.
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Affiliation(s)
| | | | | | - Yunxian Huang
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | | | - Theodor E Haerry
- Center for Molecular Biology and Biotechnology, Florida Atlantic University
| | - Osamu Shimmi
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
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Tan D, Tong XL, Hu H, Wu SY, Li CL, Xiong G, Xiang ZH, Dai FY, Lu C. Morphological characterization and molecular mapping of an irradiation-induced Speckled mutant in the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2016; 25:93-104. [PMID: 26661290 DOI: 10.1111/imb.12205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Speckled (Spc), an X-ray-induced lethal mutant of Bombyx mori, exhibits a mosaic dark-brown-spotted larval epidermis in both sexes and egg-laying problems only in females. Here, we report the morphological characterization and molecular mapping of the Spc mutant. Morphological investigations revealed that the epidermal ultrastructure of the small, dark-brown spots was more dense than that of the white regions in both Spc/+ mutants and wild type, and that the lethality of the Spc/Spc mutants occurred during early embryogenesis. Furthermore, the ovarioles and ovipositor were disconnected in approximately 85.5% of Spc/+ females, a further 2.5% had a connection between the ovarioles and ovipositor that was too narrow to lay eggs. The remaining females showed a normal connection similar to that of the wild type. We successfully narrowed down the location of the Spc mutation to a region on chromosome 4 that was ∼1041 kb long. Gene-prediction analysis identified 25 candidate genes in this region. Chromosome structure analysis indicated that a ∼305 kb deletion was included in the mapping region. Temporal and spatial reverse transcription PCR (RT-PCR) analysis showed that several genes in the mapped region are associated with the Spc mutant. Although the genes responsible for the Spc mutation were not definitively identified, our results further the current understanding of the complex mechanism underlying the multiple morphological defects in Spc mutants.
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Affiliation(s)
- D Tan
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - X-L Tong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - H Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - S-Y Wu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - C-L Li
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - G Xiong
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - Z-H Xiang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - F-Y Dai
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China
- Key Laboratory for Sericulture Functional Genomics and Biotechnology of Agricultural Ministry, Southwest University, Chongqing, China
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29
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Sobotka JA, Daley M, Chandrasekaran S, Rubin BD, Thompson GJ. Structure and function of gene regulatory networks associated with worker sterility in honeybees. Ecol Evol 2016; 6:1692-701. [PMID: 26925214 PMCID: PMC4755009 DOI: 10.1002/ece3.1997] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 01/26/2023] Open
Abstract
A characteristic of eusocial bees is a reproductive division of labor in which one or a few queens monopolize reproduction, while her worker daughters take on reproductively altruistic roles within the colony. The evolution of worker reproductive altruism involves indirect selection for the coordinated expression of genes that regulate personal reproduction, but evidence for this type of selection remains elusive. In this study, we tested whether genes coexpressed under queen‐induced worker sterility show evidence of adaptive organization within a model brain transcriptional regulatory network (TRN). If so, this structured pattern would imply that indirect selection on nonreproductive workers has influenced the functional organization of genes within the network, specifically to regulate the expression of sterility. We found that literature‐curated sets of candidate genes for sterility, ranging in size from 18 to 267, show strong evidence of clustering within the three‐dimensional space of the TRN. This finding suggests that our candidate sets of genes for sterility form functional modules within the living bee brain's TRN. Moreover, these same gene sets colocate to a single, albeit large, region of the TRN's topology. This spatially organized and convergent pattern contrasts with a null expectation for functionally unrelated genes to be haphazardly distributed throughout the network. Our meta‐genomic analysis therefore provides first evidence for a truly “social transcriptome” that may regulate the conditional expression of honeybee worker sterility.
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Affiliation(s)
- Julia A Sobotka
- Biology Department Western University 1151 Richmond Street London ON N6A 5B7 Canada
| | - Mark Daley
- Biology Department Western University 1151 Richmond Street London ON N6A 5B7 Canada
| | - Sriram Chandrasekaran
- Harvard Society of Fellows Faculty of Arts and Sciences Harvard University 78 Mount Auburn Street Cambridge Massachusetts; The Broad Institute of MIT and Harvard 415 Main Street Cambridge Massachusetts
| | - Benjamin D Rubin
- Biology Department Western University 1151 Richmond Street London ON N6A 5B7 Canada
| | - Graham J Thompson
- Biology Department Western University 1151 Richmond Street London ON N6A 5B7 Canada
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30
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Li Q, Barish S, Okuwa S, Maciejewski A, Brandt AT, Reinhold D, Jones CD, Volkan PC. A Functionally Conserved Gene Regulatory Network Module Governing Olfactory Neuron Diversity. PLoS Genet 2016; 12:e1005780. [PMID: 26765103 PMCID: PMC4713227 DOI: 10.1371/journal.pgen.1005780] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 12/08/2015] [Indexed: 12/21/2022] Open
Abstract
Sensory neuron diversity is required for organisms to decipher complex environmental cues. In Drosophila, the olfactory environment is detected by 50 different olfactory receptor neuron (ORN) classes that are clustered in combinations within distinct sensilla subtypes. Each sensilla subtype houses stereotypically clustered 1-4 ORN identities that arise through asymmetric divisions from a single multipotent sensory organ precursor (SOP). How each class of SOPs acquires a unique differentiation potential that accounts for ORN diversity is unknown. Previously, we reported a critical component of SOP diversification program, Rotund (Rn), increases ORN diversity by generating novel developmental trajectories from existing precursors within each independent sensilla type lineages. Here, we show that Rn, along with BarH1/H2 (Bar), Bric-à-brac (Bab), Apterous (Ap) and Dachshund (Dac), constitutes a transcription factor (TF) network that patterns the developing olfactory tissue. This network was previously shown to pattern the segmentation of the leg, which suggests that this network is functionally conserved. In antennal imaginal discs, precursors with diverse ORN differentiation potentials are selected from concentric rings defined by unique combinations of these TFs along the proximodistal axis of the developing antennal disc. The combinatorial code that demarcates each precursor field is set up by cross-regulatory interactions among different factors within the network. Modifications of this network lead to predictable changes in the diversity of sensilla subtypes and ORN pools. In light of our data, we propose a molecular map that defines each unique SOP fate. Our results highlight the importance of the early prepatterning gene regulatory network as a modulator of SOP and terminally differentiated ORN diversity. Finally, our model illustrates how conserved developmental strategies are used to generate neuronal diversity.
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Affiliation(s)
- Qingyun Li
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Scott Barish
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Sumie Okuwa
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Abigail Maciejewski
- Department of Biology, Duke University, Durham, North Carolina, United States of America
| | - Alicia T. Brandt
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Dominik Reinhold
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Department of Mathematics and Computer Science, Clark University, Worcester, Massachusetts, United States of America
| | - Corbin D. Jones
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, United States of America
| | - Pelin Cayirlioglu Volkan
- Department of Biology, Duke University, Durham, North Carolina, United States of America
- Duke Institute for Brain Sciences, Duke University, Durham, North Carolina, United States of America
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31
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Wu K, Hoy MA. Cloning and Functional Characterization of Two BTB Genes in the Predatory Mite Metaseiulus occidentalis. PLoS One 2015; 10:e0144291. [PMID: 26640898 PMCID: PMC4671623 DOI: 10.1371/journal.pone.0144291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/16/2015] [Indexed: 12/12/2022] Open
Abstract
Proteins containing the BTB (Bric-à-brac, tramtrack, and Broad Complex) domain typically share low sequence similarities and are involved in a wide range of cellular functions. We previously identified two putative and closely related BTB genes, BTB1 and BTB2, in the genome of the predatory mite Metaseiulus occidentalis. In the current study, full-length BTB1 and BTB2 cDNAs were cloned and sequenced. BTB1 and BTB2 encode proteins of 380 and 401 amino acids, respectively. BTB1 and BTB2 proteins each contain an N-terminal BTB domain and no other identifiable domains. Thus, they belong to a large category of BTB-domain proteins that are widely distributed in eukaryotes, yet with largely unknown function(s). BTB1 and BTB2 gene knockdowns in M. occidentalis females using RNAi reduced their fecundity by approximately 40% and 73%, respectively, whereas knockdown had no impact on their survival or the development of their offspring. These findings suggest these two proteins may be involved in processes related to egg production in this predatory mite, expanding the list of functions attributed to these diverse proteins.
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Affiliation(s)
- Ke Wu
- Department of Entomology and Nematology, PO Box 11620, University of Florida, Gainesville, Florida, 32611, United States of America
- * E-mail:
| | - Marjorie A. Hoy
- Department of Entomology and Nematology, PO Box 11620, University of Florida, Gainesville, Florida, 32611, United States of America
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32
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The elimination of an adult segment by the Hox gene Abdominal-B. Mech Dev 2015; 138 Pt 2:210-217. [DOI: 10.1016/j.mod.2015.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 07/31/2015] [Accepted: 08/01/2015] [Indexed: 11/19/2022]
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Irizarry J, Stathopoulos A. FGF signaling supports Drosophila fertility by regulating development of ovarian muscle tissues. Dev Biol 2015; 404:1-13. [PMID: 25958090 DOI: 10.1016/j.ydbio.2015.04.023] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 04/28/2015] [Indexed: 12/29/2022]
Abstract
The thisbe (ths) gene encodes a Drosophila fibroblast growth factor (FGF), and mutant females are viable but sterile suggesting a link between FGF signaling and fertility. Ovaries exhibit abnormal morphology including lack of epithelial sheaths and muscle tissues that surround ovarioles. Here we investigated how FGF influences Drosophila ovary morphogenesis and identified several roles. Heartless (Htl) FGF receptor was found to be expressed within somatic cells at the larval and pupal stages, and phenotypes were uncovered using RNAi. Differentiation of terminal filament cells was affected, but this effect did not alter the ovariole number. In addition, proliferation of epithelial sheath progenitors, the apical cells, was decreased in both htl and ths mutants, while ectopic expression of the Ths ligand led to these cells' over-proliferation suggesting that FGF signaling supports ovarian muscle sheath formation by controlling apical cell number in the developing gonad. Additionally, live imaging of adult ovaries was used to show that htl RNAi mutants, hypomorphic mutants in which epithelial sheaths are present, exhibit abnormal muscle contractions. Collectively, our results demonstrate that proper formation of ovarian muscle tissues is regulated by FGF signaling in the larval and pupal stages through control of apical cell proliferation and is required to support fertility.
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Affiliation(s)
- Jihyun Irizarry
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States
| | - Angelike Stathopoulos
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, United States.
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34
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Ishimaru Y, Nakamura T, Bando T, Matsuoka Y, Ohuchi H, Noji S, Mito T. Involvement of dachshund and Distal-less in distal pattern formation of the cricket leg during regeneration. Sci Rep 2015; 5:8387. [PMID: 25669615 PMCID: PMC4323655 DOI: 10.1038/srep08387] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 01/19/2015] [Indexed: 12/02/2022] Open
Abstract
Cricket nymphs have the remarkable ability to regenerate a functional leg following amputation, indicating that the regenerating blastemal cells contain information for leg morphology. However, the molecular mechanisms that underlie regeneration of leg patterns remain poorly understood. Here, we analyzed phenotypes of the tibia and tarsus (three tarsomeres) obtained by knockdown with regeneration-dependent RNA interference (rdRNAi) against Gryllus dachshund (Gb'dac) and Distal-less (Gb'Dll). We found that depletion of Gb'Dll mRNA results in loss of the tarsal segments, while rdRNAi against Gb'dac shortens the tibia at the two most distal tarsomeres. These results indicate that Gb'Dll expression is indispensable for formation of the tarsus, while Gb'dac expression is necessary for elongation of the tibia and formation of the most proximal tarsomere. These findings demonstrate that mutual transcriptional regulation between the two is indispensable for formation of the tarsomeres, whereas Gb'dac is involved in determination of tibial size through interaction with Gb'ds/Gb'ft.
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Affiliation(s)
- Yoshiyasu Ishimaru
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Taro Nakamura
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Tetsuya Bando
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama City, Okayama, 700-8530, Japan
| | - Yuji Matsuoka
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
| | - Hideyo Ohuchi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, 2-5-1 Shikata-cho, Kita-ku, Okayama City, Okayama, 700-8530, Japan
| | - Sumihare Noji
- Center for Collaboration among Agriculture, Industry and Commerce, The University of Tokushima, 2-24 Shinkura-cho, Tokushima City, Tokushima 770-8501, Japan
| | - Taro Mito
- Department of Life Systems, Institute of Technology and Science, The University of Tokushima Graduate School, 2-1 Minami-Jyosanjima-cho, Tokushima City, Tokushima, 770-8506, Japan
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The bHLH-PAS transcription factor dysfusion regulates tarsal joint formation in response to Notch activity during drosophila leg development. PLoS Genet 2014; 10:e1004621. [PMID: 25329825 PMCID: PMC4199481 DOI: 10.1371/journal.pgen.1004621] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 07/19/2014] [Indexed: 01/22/2023] Open
Abstract
A characteristic of all arthropods is the presence of flexible structures called joints that connect all leg segments. Drosophila legs include two types of joints: the proximal or "true" joints that are motile due to the presence of muscle attachment and the distal joints that lack musculature. These joints are not only morphologically, functionally and evolutionarily different, but also the morphogenetic program that forms them is distinct. Development of both proximal and distal joints requires Notch activity; however, it is still unknown how this pathway can control the development of such homologous although distinct structures. Here we show that the bHLH-PAS transcription factor encoded by the gene dysfusion (dys), is expressed and absolutely required for tarsal joint development while it is dispensable for proximal joints. In the presumptive tarsal joints, Dys regulates the expression of the pro-apoptotic genes reaper and head involution defective and the expression of the RhoGTPases modulators, RhoGEf2 and RhoGap71E, thus directing key morphogenetic events required for tarsal joint development. When ectopically expressed, dys is able to induce some aspects of the morphogenetic program necessary for distal joint development such as fold formation and programmed cell death. This novel Dys function depends on its obligated partner Tango to activate the transcription of target genes. We also identified a dedicated dys cis-regulatory module that regulates dys expression in the tarsal presumptive leg joints through direct Su(H) binding. All these data place dys as a key player downstream of Notch, directing distal versus proximal joint morphogenesis.
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36
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Mondal BC, Shim J, Evans CJ, Banerjee U. Pvr expression regulators in equilibrium signal control and maintenance of Drosophila blood progenitors. eLife 2014; 3:e03626. [PMID: 25201876 PMCID: PMC4185420 DOI: 10.7554/elife.03626] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Accepted: 09/05/2014] [Indexed: 12/18/2022] Open
Abstract
Blood progenitors within the lymph gland, a larval organ that supports hematopoiesis in Drosophila melanogaster, are maintained by integrating signals emanating from niche-like cells and those from differentiating blood cells. We term the signal from differentiating cells the 'equilibrium signal' in order to distinguish it from the 'niche signal'. Earlier we showed that equilibrium signaling utilizes Pvr (the Drosophila PDGF/VEGF receptor), STAT92E, and adenosine deaminase-related growth factor A (ADGF-A) (Mondal et al., 2011). Little is known about how this signal initiates during hematopoietic development. To identify new genes involved in lymph gland blood progenitor maintenance, particularly those involved in equilibrium signaling, we performed a genetic screen that identified bip1 (bric à brac interacting protein 1) and Nucleoporin 98 (Nup98) as additional regulators of the equilibrium signal. We show that the products of these genes along with the Bip1-interacting protein RpS8 (Ribosomal protein S8) are required for the proper expression of Pvr.
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Affiliation(s)
- Bama Charan Mondal
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Jiwon Shim
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Life Science, Hanyang University, Seoul, Republic of Korea
| | - Cory J Evans
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
| | - Utpal Banerjee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, United States
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, United States
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, Los Angeles, United States
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37
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Atallah J, Vurens G, Mavong S, Mutti A, Hoang D, Kopp A. Sex-specific repression of dachshund is required for Drosophila sex comb development. Dev Biol 2014; 386:440-7. [DOI: 10.1016/j.ydbio.2013.12.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2013] [Revised: 12/07/2013] [Accepted: 12/11/2013] [Indexed: 02/06/2023]
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38
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Rogers WA, Grover S, Stringer SJ, Parks J, Rebeiz M, Williams TM. A survey of the trans-regulatory landscape for Drosophila melanogaster abdominal pigmentation. Dev Biol 2014; 385:417-32. [DOI: 10.1016/j.ydbio.2013.11.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/07/2013] [Accepted: 11/05/2013] [Indexed: 10/26/2022]
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39
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Salomone JR, Rogers WA, Rebeiz M, Williams TM. The evolution of Bab paralog expression and abdominal pigmentation amongSophophorafruit fly species. Evol Dev 2013; 15:442-57. [DOI: 10.1111/ede.12053] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joseph R. Salomone
- Department of Biology; University of Dayton; 300 College Park Dayton OH 45469 USA
| | - William A. Rogers
- Department of Biology; University of Dayton; 300 College Park Dayton OH 45469 USA
| | - Mark Rebeiz
- Department of Biological Sciences; University of Pittsburgh; Pittsburgh PA 15260 USA
| | - Thomas M. Williams
- Department of Biology; University of Dayton; 300 College Park Dayton OH 45469 USA
- Center for Tissue Regeneration and Engineering at Dayton; University of Dayton; 300 College Park Dayton OH 45469 USA
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The zinc finger homeodomain-2 gene of Drosophila controls Notch targets and regulates apoptosis in the tarsal segments. Dev Biol 2013; 385:350-65. [PMID: 24144920 DOI: 10.1016/j.ydbio.2013.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2013] [Revised: 10/06/2013] [Accepted: 10/12/2013] [Indexed: 12/19/2022]
Abstract
The development of the Drosophila leg is a good model to study processes of pattern formation, cell death and segmentation. Such processes require the coordinate activity of different genes and signaling pathways that progressively subdivide the leg territory into smaller domains. One of the main pathways needed for leg development is the Notch pathway, required for determining the proximo-distal axis of the leg and for the formation of the joints that separate different leg segments. The mechanisms required to coordinate such events are largely unknown. We describe here that the zinc finger homeodomain-2 (zfh-2) gene is highly expressed in cells that will form the leg joints and needed to establish a correct size and pattern in the distal leg. There is an early requirement of zfh-2 to establish the correct proximo-distal axis, but zfh-2 is also needed at late third instar to form the joint between the fourth and fifth tarsal segments. The expression of zfh-2 requires Notch activity but zfh-2 is necessary, in turn, to activate Notch targets such as Enhancer of split and big brain. zfh-2 is controlled by the Drosophila activator protein 2 gene and regulates the late expression of tarsal-less. In the absence of zfh-2 many cells ectopically express the pro-apoptotic gene head involution defective, activate caspase-3 and are positive for acridine orange, indicating they undergo apoptosis. Our results demonstrate the key role of zfh-2 in the control of cell death and Notch signaling during leg development.
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Rogers WA, Salomone JR, Tacy DJ, Camino EM, Davis KA, Rebeiz M, Williams TM. Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation diversity. PLoS Genet 2013; 9:e1003740. [PMID: 24009528 PMCID: PMC3757066 DOI: 10.1371/journal.pgen.1003740] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 07/09/2013] [Indexed: 11/18/2022] Open
Abstract
The development of morphological traits occurs through the collective action of networks of genes connected at the level of gene expression. As any node in a network may be a target of evolutionary change, the recurrent targeting of the same node would indicate that the path of evolution is biased for the relevant trait and network. Although examples of parallel evolution have implicated recurrent modification of the same gene and cis-regulatory element (CRE), little is known about the mutational and molecular paths of parallel CRE evolution. In Drosophila melanogaster fruit flies, the Bric-à-brac (Bab) transcription factors control the development of a suite of sexually dimorphic traits on the posterior abdomen. Female-specific Bab expression is regulated by the dimorphic element, a CRE that possesses direct inputs from body plan (ABD-B) and sex-determination (DSX) transcription factors. Here, we find that the recurrent evolutionary modification of this CRE underlies both intraspecific and interspecific variation in female pigmentation in the melanogaster species group. By reconstructing the sequence and regulatory activity of the ancestral Drosophila melanogaster dimorphic element, we demonstrate that a handful of mutations were sufficient to create independent CRE alleles with differing activities. Moreover, intraspecific and interspecific dimorphic element evolution proceeded with little to no alterations to the known body plan and sex-determination regulatory linkages. Collectively, our findings represent an example where the paths of evolution appear biased to a specific CRE, and drastic changes in function were accompanied by deep conservation of key regulatory linkages.
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Affiliation(s)
- William A. Rogers
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Joseph R. Salomone
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - David J. Tacy
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Eric M. Camino
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Kristen A. Davis
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
| | - Mark Rebeiz
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
| | - Thomas M. Williams
- Department of Biology, University of Dayton, Dayton, Ohio, United States of America
- Center for Tissue Regeneration and Engineering at Dayton, University of Dayton, Dayton, Ohio, United States of America
- * E-mail:
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Turkel N, Sahota VK, Bolden JE, Goulding KR, Doggett K, Willoughby LF, Blanco E, Martin-Blanco E, Corominas M, Ellul J, Aigaki T, Richardson HE, Brumby AM. The BTB-zinc finger transcription factor abrupt acts as an epithelial oncogene in Drosophila melanogaster through maintaining a progenitor-like cell state. PLoS Genet 2013; 9:e1003627. [PMID: 23874226 PMCID: PMC3715428 DOI: 10.1371/journal.pgen.1003627] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 05/30/2013] [Indexed: 01/07/2023] Open
Abstract
The capacity of tumour cells to maintain continual overgrowth potential has been linked to the commandeering of normal self-renewal pathways. Using an epithelial cancer model in Drosophila melanogaster, we carried out an overexpression screen for oncogenes capable of cooperating with the loss of the epithelial apico-basal cell polarity regulator, scribbled (scrib), and identified the cell fate regulator, Abrupt, a BTB-zinc finger protein. Abrupt overexpression alone is insufficient to transform cells, but in cooperation with scrib loss of function, Abrupt promotes the formation of massive tumours in the eye/antennal disc. The steroid hormone receptor coactivator, Taiman (a homologue of SRC3/AIB1), is known to associate with Abrupt, and Taiman overexpression also drives tumour formation in cooperation with the loss of Scrib. Expression arrays and ChIP-Seq indicates that Abrupt overexpression represses a large number of genes, including steroid hormone-response genes and multiple cell fate regulators, thereby maintaining cells within an epithelial progenitor-like state. The progenitor-like state is characterised by the failure to express the conserved Eyes absent/Dachshund regulatory complex in the eye disc, and in the antennal disc by the failure to express cell fate regulators that define the temporal elaboration of the appendage along the proximo-distal axis downstream of Distalless. Loss of scrib promotes cooperation with Abrupt through impaired Hippo signalling, which is required and sufficient for cooperative overgrowth with Abrupt, and JNK (Jun kinase) signalling, which is required for tumour cell migration/invasion but not overgrowth. These results thus identify a novel cooperating oncogene, identify mammalian family members of which are also known oncogenes, and demonstrate that epithelial tumours in Drosophila can be characterised by the maintenance of a progenitor-like state. Cancer is a multigenic process, involving cooperative interactions between oncogenes or tumour suppressors. In this study, in a genetic screen in the vinegar fly, Drosophila melanogaster, for genes that cooperate with a mutation in the cell polarity (shape) regulator, scribbled (scrib), we identify a novel cooperative oncogene, abrupt. Expression of abrupt in scrib mutant tissue in the developing eye/antennal epithelium results in overgrown invasive tumours. abrupt encodes a BTB-zinc finger transcription factor, which has homology to several cancer-causing proteins in humans, such as BCL6. Analysis of the Abrupt targets and misexpressed genes in abrupt expressing-tissue and abrupt-expressing scrib mutant tumours, revealed cell fate regulators as a major class of targets. Thus, our results reveal that deregulation of multiple cell fate factors by Abrupt expression in the context of polarity disruption is associated with a progenitor-like cell state and the formation of overgrown invasive tumours. Our findings suggest that defective polarity may also be a critical factor in BTB-zinc finger-driven human cancers, and warrants further investigation into this issue.
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Affiliation(s)
- Nezaket Turkel
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- Department of Anatomy and Cell Biology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Virender K. Sahota
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jessica E. Bolden
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Karen R. Goulding
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Karen Doggett
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Lee F. Willoughby
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Enrique Blanco
- Departament de Genètica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Enrique Martin-Blanco
- Instituto de Biología Molecular de Barcelona (CSIC), Parc Cientific de Barcelona, Barcelona, Spain
| | - Montserrat Corominas
- Departament de Genètica i Institut de Biomedicina (IBUB), Universitat de Barcelona, Barcelona, Spain
| | - Jason Ellul
- Bioinformatics Core Facility, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Toshiro Aigaki
- Department of Biological Sciences, Tokyo Metropolitan University, Hachioji, Tokyo, Japan
| | - Helena E. Richardson
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- Department of Anatomy and Cell Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne, Victoria, Australia
- * E-mail:
| | - Anthony M. Brumby
- Cell Cycle and Development Laboratory, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
- Department of Anatomy and Cell Biology, The University of Melbourne, Melbourne, Victoria, Australia
- Department of Genetics, The University of Melbourne, Melbourne, Victoria, Australia
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Drosophila distal-less and Rotund bind a single enhancer ensuring reliable and robust bric-a-brac2 expression in distinct limb morphogenetic fields. PLoS Genet 2013; 9:e1003581. [PMID: 23825964 PMCID: PMC3694829 DOI: 10.1371/journal.pgen.1003581] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/05/2013] [Indexed: 11/19/2022] Open
Abstract
Most identified Drosophila appendage-patterning genes encode DNA-binding proteins, whose cross-regulatory interactions remain to be better characterized at the molecular level, notably by studying their direct binding to tissue-specific transcriptional enhancers. A fine-tuned spatio-temporal expression of bric-a-brac2 (bab2) along concentric rings is essential for proper proximo-distal (P-D) differentiation of legs and antennae. However, within the genetic interaction landscape governing limb development, no transcription factor directly controlling bab2 expression has been identified to date. Using site-targeted GFP reporter assay and BAC recombineering, we show here that restricted bab2 expression in leg and antennal imaginal discs relies on a single 567-bp-long cis-regulatory module (CRM), termed LAE (for leg and antennal enhancer). We show that this CRM (i) is necessary and sufficient to ensure normal bab2 activity in developing leg and antenna, and (ii) is structurally and functionally conserved among Drosophilidae. Through deletion and site-directed mutagenesis approaches, we identified within the LAE essential sequence motifs required in both leg and antennal tissues. Using genetic and biochemical tests, we establish that in the LAE (i) a key TAAT-rich activator motif interacts with the homeodomain P-D protein Distal-less (Dll) and (ii) a single T-rich activator motif binds the C2H2 zinc-finger P-D protein Rotund (Rn), leading to bab2 up-regulation respectively in all or specifically in the proximal-most ring(s), both in leg and antenna. Joint ectopic expression of Dll and Rn is sufficient to cell-autonomously activate endogenous bab2 and LAE-driven reporter expression in wing and haltere cells. Our findings indicate that accuracy, reliability and robustness of developmental gene expression do not necessarily require cis-regulatory information redundancy. In insects, leg and antenna are homologous limbs, though derive from a single ancestral appendage. In Drosophila, leg and antennal development along the proximo-distal (P-D) axis relies on relatively-well known genetic cascades, in which most appendage-patterning genes encode transcription factors (TF). However, their cross-regulatory interactions remain to be better characterized at the molecular level. A fine-tuned expression of the bric-a-brac2 (bab2) gene is essential for normal leg and antennal segmentation. However, within the genetic cascades governing P-D limb development, no TF directly controlling bab2 expression has been identified to date. We show here that restricted bab2 expression in developing leg and antenna is governed by a single enhancer, termed LAE, which is necessary and sufficient in-vivo to ensure bab2 functions there. We show that leg and antennal cis-regulatory elements are closely associated and that essential LAE sites interact with Distal-less (Dll) and Rotund (Rn) TFs, leading to bab2 activation in all or specifically in the proximal-most expressing cells, respectively. Finally, joint ectopic expression of Dll and Rn is sufficient to instruct wing and haltere cells to up-regulate bab2. Taken together, our work indicates that a single enhancer is necessary and sufficient to reliably govern bab2 expression in distinct morphogenetic fields.
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Bastide H, Betancourt A, Nolte V, Tobler R, Stöbe P, Futschik A, Schlötterer C. A genome-wide, fine-scale map of natural pigmentation variation in Drosophila melanogaster. PLoS Genet 2013; 9:e1003534. [PMID: 23754958 PMCID: PMC3674992 DOI: 10.1371/journal.pgen.1003534] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/11/2013] [Indexed: 11/25/2022] Open
Abstract
Various approaches can be applied to uncover the genetic basis of natural phenotypic variation, each with their specific strengths and limitations. Here, we use a replicated genome-wide association approach (Pool-GWAS) to fine-scale map genomic regions contributing to natural variation in female abdominal pigmentation in Drosophila melanogaster, a trait that is highly variable in natural populations and highly heritable in the laboratory. We examined abdominal pigmentation phenotypes in approximately 8000 female European D. melanogaster, isolating 1000 individuals with extreme phenotypes. We then used whole-genome Illumina sequencing to identify single nucleotide polymorphisms (SNPs) segregating in our sample, and tested these for associations with pigmentation by contrasting allele frequencies between replicate pools of light and dark individuals. We identify two small regions near the pigmentation genes tan and bric-à-brac 1, both corresponding to known cis-regulatory regions, which contain SNPs showing significant associations with pigmentation variation. While the Pool-GWAS approach suffers some limitations, its cost advantage facilitates replication and it can be applied to any non-model system with an available reference genome. Phenotypic variation is abundant in natural populations, but its genetic basis is not always well-understood. Here, we examine the genetic basis of body pigmentation in Drosophila, a trait with a long history of study in Drosophila genetics and evolution. We conducted the first genome-wide scan for polymorphism associated with pigmentation variation in a large natural sample of D. melanogaster, and found SNPs near two genes, tan and bric-à-brac 1, affecting the trait. The SNPs associated with pigmentation variation in these genes appear to act by affecting the regulation of the pigmentation genes, rather than their protein coding sequence.
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Affiliation(s)
- Héloïse Bastide
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | | | - Viola Nolte
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Raymond Tobler
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
| | - Petra Stöbe
- Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria
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Lührig S, Kolb S, Mellies N, Nolte J. The novel BTB-kelch protein, KBTBD8, is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis. Cell Div 2013; 8:3. [PMID: 23578279 PMCID: PMC3639201 DOI: 10.1186/1747-1028-8-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 04/05/2013] [Indexed: 11/30/2022] Open
Abstract
Proteins of the BTB-kelch family are known to be involved in multiple biological processes such as migration, cytoskeleton arrangement, regulation of cell morphology, protein ubiquitination and gene expression. KBTBD8 is a new member of this family. The gene was found in a comparative transcriptome analysis of pluripotent stem cells and was therefore suggested to play a role in the regulation of pluripotency. Comparative analysis of the gene and protein sequences revealed a high conservation throughout evolution especially in the characteristic domains of BTB, BACK and kelch. We identified the Golgi apparatus as the subcellular localization of the KBTBD8 protein in non-dividing cells and could show that KBTBD8 co-localizes with α-tubulin on the spindle apparatus of mitotic cells suggesting a role in cell proliferation. In conclusion, KBTBD8 is a new member of the BTB-kelch superfamily that is located in the Golgi apparatus and translocates to the spindle apparatus during mitosis.
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Affiliation(s)
- Sandra Lührig
- Institute of Human Genetics, University of Göttingen, Göttingen, 37073, Germany.
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Abstract
The diversity of animal and plant forms is shaped by nested evolutionary innovations. Understanding the genetic and molecular changes responsible for these innovations is therefore one of the key goals of evolutionary biology. From the genetic point of view, the origin of novel traits implies the origin of new regulatory pathways to control their development. To understand how these new pathways are assembled in the course of evolution, we need model systems that combine relatively recent innovations with a powerful set of genetic and molecular tools. One such model is provided by the Drosophila sex comb-a male-specific morphological structure that evolved in a relatively small lineage related to the model species D. melanogaster. Our extensive knowledge of sex comb development in D. melanogaster provides the basis for investigating the genetic changes responsible for sex comb origin and diversification. At the same time, sex combs can change on microevolutionary timescales and differ spectacularly among closely related species, providing opportunities for direct genetic analysis and for integrating developmental and population-genetic approaches. Sex comb evolution is associated with the origin of novel interactions between Hox and sex determination genes. Activity of the sex determination pathway was brought under the control of the Hox code to become segment-specific, while Hox gene expression became sexually dimorphic. At the same time, both Hox and sex determination genes were integrated into the intrasegmental spatial patterning network, and acquired new joint downstream targets. Phylogenetic analysis shows that similar sex comb morphologies evolved independently in different lineages. Convergent evolution at the phenotypic level reflects convergent changes in the expression of Hox and sex determination genes, involving both independent gains and losses of regulatory interactions. However, the downstream cell-differentiation programs have diverged between species, and in some lineages, similar adult morphologies are produced by different morphogenetic mechanisms. These features make the sex comb an excellent model for examining not only the genetic changes responsible for its evolution, but also the cellular processes that translate DNA sequence changes into morphological diversity. The origin and diversification of sex combs provides insights into the roles of modularity, cooption, and regulatory changes in evolutionary innovations, and can serve as a model for understanding the origin of the more drastic novelties that define higher order taxa.
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Affiliation(s)
- Artyom Kopp
- Department of Evolution and Ecology, University of California - Davis, Davis, CA 95616, USA.
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Devi TR, Amruthavalli C, Shyamala B. Evolution of sex comb from the primitive bristle pattern indrosophilais associated with modification in the developmental regulatory protein dachshund. Genesis 2013. [DOI: 10.1002/dvg.22361] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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48
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Bartoletti M, Rubin T, Chalvet F, Netter S, Dos Santos N, Poisot E, Paces-Fessy M, Cumenal D, Peronnet F, Pret AM, Théodore L. Genetic basis for developmental homeostasis of germline stem cell niche number: a network of Tramtrack-Group nuclear BTB factors. PLoS One 2012. [PMID: 23185495 PMCID: PMC3503823 DOI: 10.1371/journal.pone.0049958] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The potential to produce new cells during adult life depends on the number of stem cell niches and the capacity of stem cells to divide, and is therefore under the control of programs ensuring developmental homeostasis. However, it remains generally unknown how the number of stem cell niches is controlled. In the insect ovary, each germline stem cell (GSC) niche is embedded in a functional unit called an ovariole. The number of ovarioles, and thus the number of GSC niches, varies widely among species. In Drosophila, morphogenesis of ovarioles starts in larvae with the formation of terminal filaments (TFs), each made of 8–10 cells that pile up and sort in stacks. TFs constitute organizers of individual germline stem cell niches during larval and early pupal development. In the Drosophila melanogaster subgroup, the number of ovarioles varies interspecifically from 8 to 20. Here we show that pipsqueak, Trithorax-like, batman and the bric-à-brac (bab) locus, all encoding nuclear BTB/POZ factors of the Tramtrack Group, are involved in limiting the number of ovarioles in D. melanogaster. At least two different processes are differentially perturbed by reducing the function of these genes. We found that when the bab dose is reduced, sorting of TF cells into TFs was affected such that each TF contains fewer cells and more TFs are formed. In contrast, psq mutants exhibited a greater number of TF cells per ovary, with a normal number of cells per TF, thereby leading to formation of more TFs per ovary than in the wild type. Our results indicate that two parallel genetic pathways under the control of a network of nuclear BTB factors are combined in order to negatively control the number of germline stem cell niches.
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Affiliation(s)
- Mathieu Bartoletti
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Thomas Rubin
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Fabienne Chalvet
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Departement de Biologie, University of Paris-Sud, Orsay, France
| | - Sophie Netter
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Nicolas Dos Santos
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Emilie Poisot
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
| | - Mélanie Paces-Fessy
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Delphine Cumenal
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Frédérique Peronnet
- Biologie du Développement Unité Mixte de Recherche 7622, Centre National de la Recherche Scientifique et Université Pierre et Marie Curie, Paris, France
| | - Anne-Marie Pret
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Departement de Biologie, University of Versailles St-Quentin, Versailles, France
| | - Laurent Théodore
- Centre de Génétique Moléculaire, Unité Propre de Recherche 3404 du Centre National de la Recherche Scientifique, Gif-sur-Yvette, France
- Laboratoire de Génétique et Biologie Cellulaire, Equipe Associée 4589, University of Versailles St-Quentin, Versailles, France
- Departement de Biologie, University of Paris-Sud, Orsay, France
- * E-mail:
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Green DA, Extavour CG. Convergent evolution of a reproductive trait through distinct developmental mechanisms in Drosophila. Dev Biol 2012; 372:120-30. [PMID: 23022298 DOI: 10.1016/j.ydbio.2012.09.014] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/08/2012] [Accepted: 09/16/2012] [Indexed: 11/18/2022]
Abstract
Convergent morphologies often arise due to similar selective pressures in independent lineages. It is poorly understood whether the same or different developmental genetic mechanisms underlie such convergence. Here we show that independent evolution of a reproductive trait, ovariole number, has resulted from changes in distinct developmental mechanisms, each of which may have a different underlying genetic basis in Drosophila. Ovariole number in Drosophila is species-specific, highly variable, and largely under genetic control. Convergent changes in Drosophila ovariole number have evolved independently within and between species. We previously showed that the number of a specific ovarian cell type, terminal filament (TF) cells, determines ovariole number. Here we examine TF cell development in different Drosophila lineages that independently evolved a significantly lower ovariole number than the D. melanogaster Oregon R strain. We show that in these Drosophila lineages, reduction in ovariole number occurs primarily through variations in one of two different developmental mechanisms: (1) reduced number of somatic gonad precursors (SGP cells) specified during embryogenesis; or (2) alterations of somatic gonad cell morphogenesis and differentiation in larval life. Mutations in the D. melanogaster Insulin Receptor (InR) alter SGP cell number but not ovarian morphogenesis, while targeted loss of function of bric-à-brac 2 (bab2) affects morphogenesis without changing SGP cell number. Thus, evolution can produce similar ovariole numbers through distinct developmental mechanisms, likely controlled by different genetic mechanisms.
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Affiliation(s)
- Delbert A Green
- Department of Molecular and Cellular Biology, Harvard University, 16 Divinity Avenue, Cambridge, MA 02138, USA
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50
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Kennell JA, Cadigan KM, Shakhmantsir I, Waldron EJ. The microRNA miR-8 is a positive regulator of pigmentation and eclosion in Drosophila. Dev Dyn 2012; 241:161-8. [PMID: 22174085 DOI: 10.1002/dvdy.23705] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are short, non-coding RNAs that post-transcriptionally silence gene expression by binding to target mRNAs. Previous studies have identified the miRNA miR-8 as a pleiotropic regulator of Drosophila development, controlling body size and neuronal survival by targeting multiple mRNAs. In this study we demonstrate that miR-8 is also required for proper spatial patterning of pigment on the adult abdominal cuticle in females but not males. RESULTS Female adult flies lacking miR-8 exhibit decreased pigmentation of the dorsal abdomen, with a pattern of pigmentation similar to wild type flies grown at higher temperatures. This pigmentation defect in miR-8 mutants is independent of the previously reported body size defect, and miR-8 acts directly in the developing cuticle to regulate pigmentation patterning. The decrease in pigmentation in miR-8 mutants was more pronounced in flies grown at higher temperatures. We also found that loss of miR-8 dramatically affected the ability to eclose at higher temperatures. CONCLUSION Loss of miR-8 increased the sensitivity of Drosophila to higher temperatures for both pigmentation patterning and the ability to eclose. Together, these data suggest that miR-8 acts as a buffer to stabilize gene expression patterns in the midst of environmental variation.
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Affiliation(s)
- Jennifer A Kennell
- Department of Biology, Vassar College, Poughkeepsie, New York 12604, USA.
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