1
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Lavin R, Rathore S, Bauer B, Disalvo J, Mosley N, Shearer E, Elia Z, Cook TA, Buschbeck EK. EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification. Front Cell Dev Biol 2022; 10:964746. [PMID: 36092740 PMCID: PMC9459020 DOI: 10.3389/fcell.2022.964746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program’s animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan.
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Affiliation(s)
- Ryan Lavin
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Shubham Rathore
- Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
| | - Brian Bauer
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Joe Disalvo
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Nick Mosley
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Evan Shearer
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Zachary Elia
- Electrical Engineering and Computer Science, University of Cincinnati, Cincinnati, OH, United States
| | - Tiffany A. Cook
- Center of Molecular Medicine and Genomics, Wayne State University School of Medicine, Detroit, MI, United States
| | - Elke K. Buschbeck
- Biological Sciences, University of Cincinnati, Cincinnati, OH, United States
- *Correspondence: Elke K. Buschbeck,
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2
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Hatleberg WL, Hinman VF. Modularity and hierarchy in biological systems: Using gene regulatory networks to understand evolutionary change. Curr Top Dev Biol 2021; 141:39-73. [DOI: 10.1016/bs.ctdb.2020.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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3
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Casares F, McGregor AP. The evolution and development of eye size in flies. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2020; 10:e380. [PMID: 32400100 DOI: 10.1002/wdev.380] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Revised: 03/08/2020] [Accepted: 03/12/2020] [Indexed: 01/19/2023]
Abstract
The compound eyes of flies exhibit striking variation in size, which has contributed to the adaptation of these animals to different habitats and their evolution of specialist behaviors. These differences in size are caused by differences in the number and/or size of ommatidia, which are specified during the development of the retinal field in the eye imaginal disc. While the genes and developmental mechanisms that regulate the formation of compound eyes are understood in great detail in the fruit fly Drosophila melanogaster, we know very little about the genetic changes and mechanistic alterations that lead to natural variation in ommatidia number and/or size, and thus overall eye size, within and between fly species. Understanding the genetic and developmental bases for this natural variation in eye size not only has great potential to help us understand adaptations in fly vision but also determine how eye size and organ size more generally are regulated. Here we explore the genetic and developmental mechanisms that could underlie natural differences in compound eye size within and among fly species based on our knowledge of eye development in D. melanogaster and the few cases where the causative genes and mechanisms have already been identified. We suggest that the fly eye provides an evolutionary and developmental framework to better understand the regulation and diversification of this crucial sensory organ globally at a systems level as well as the gene regulatory networks and mechanisms acting at the tissue, cellular and molecular levels. This article is categorized under: Establishment of Spatial and Temporal Patterns > Regulation of Size, Proportion, and Timing Invertebrate Organogenesis > Flies Comparative Development and Evolution > Regulation of Organ Diversity.
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Affiliation(s)
| | - Alistair P McGregor
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
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4
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Abstract
Molecules of the hedgehog (hh) family are involved in the specification and patterning of eyes in vertebrates and invertebrates. These organs, though, are of very different sizes, raising the question of how Hh molecules operate at such different scales. In this paper we discuss the strategies used by Hh to control the development of the two eye types in Drosophila: the large compound eye and the small ocellus. We first describe the distinct ways in which these two eyes develop and the evidence for the key role played by Hh in both; then we consider the potential for variation in the range of action of a "typical" morphogen and measure this range ("characteristic length") for Hh in different organs, including the compound eye and the ocellus. Finally, we describe how different feedback mechanisms are used to extend the Hh range of action to pattern the large and even the small eye. In the ocellus, the basic Hh signaling pathway adds to its dynamics the attenuation of its receptor as cell differentiate. This sole regulatory change can result in the decoding of the Hh gradient by receiving cells as a wave of constant speed. Therefore, in the fly ocellus, the Hh morphogen adds to its spatial patterning role a novel one: patterning along a time axis.
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5
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Sánchez-Aragón M, Cantisán-Gómez J, Luque CM, Brás-Pereira C, Lopes CS, Lemos MC, Casares F. A Toggle-Switch and a Feed-Forward Loop Engage in the Control of the Drosophila Retinal Determination Gene Network. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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6
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Kumar JP. The fly eye: Through the looking glass. Dev Dyn 2017; 247:111-123. [PMID: 28856763 DOI: 10.1002/dvdy.24585] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 08/14/2017] [Accepted: 08/14/2017] [Indexed: 12/20/2022] Open
Abstract
The developing eye-antennal disc of Drosophila melanogaster has been studied for more than a century, and it has been used as a model system to study diverse processes, such as tissue specification, organ growth, programmed cell death, compartment boundaries, pattern formation, cell fate specification, and planar cell polarity. The findings that have come out of these studies have informed our understanding of basic developmental processes as well as human disease. For example, the isolation of a white-eyed fly ultimately led to a greater appreciation of the role that sex chromosomes play in development, sex determination, and sex linked genetic disorders. Similarly, the discovery of the Sevenless receptor tyrosine kinase pathway not only revealed how the fate of the R7 photoreceptor is selected but it also helped our understanding of how disruptions in similar biochemical pathways result in tumorigenesis and cancer onset. In this article, I will discuss some underappreciated areas of fly eye development that are fertile for investigation and are ripe for producing exciting new breakthroughs. The topics covered here include organ shape, growth control, inductive signaling, and right-left symmetry. Developmental Dynamics 247:111-123, 2018. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Justin P Kumar
- Department of Biology, Indiana University, Bloomington, Indiana
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7
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Upadhyay A, Moss-Taylor L, Kim MJ, Ghosh AC, O'Connor MB. TGF-β Family Signaling in Drosophila. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a022152. [PMID: 28130362 DOI: 10.1101/cshperspect.a022152] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The transforming growth factor β (TGF-β) family signaling pathway is conserved and ubiquitous in animals. In Drosophila, fewer representatives of each signaling component are present compared with vertebrates, simplifying mechanistic study of the pathway. Although there are fewer family members, the TGF-β family pathway still regulates multiple and diverse functions in Drosophila. In this review, we focus our attention on several of the classic and best-studied functions for TGF-β family signaling in regulating Drosophila developmental processes such as embryonic and imaginal disc patterning, but we also describe several recently discovered roles in regulating hormonal, physiological, neuronal, innate immunity, and tissue homeostatic processes.
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Affiliation(s)
- Ambuj Upadhyay
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Lindsay Moss-Taylor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Myung-Jun Kim
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Arpan C Ghosh
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
| | - Michael B O'Connor
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, Minnesota 55455
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8
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Neto M, Naval-Sánchez M, Potier D, Pereira PS, Geerts D, Aerts S, Casares F. Nuclear receptors connect progenitor transcription factors to cell cycle control. Sci Rep 2017; 7:4845. [PMID: 28687780 PMCID: PMC5501803 DOI: 10.1038/s41598-017-04936-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 05/23/2017] [Indexed: 01/31/2023] Open
Abstract
The specification and growth of organs is controlled simultaneously by networks of transcription factors. While the connection between these transcription factors with fate determinants is increasingly clear, how they establish the link with the cell cycle is far less understood. Here we investigate this link in the developing Drosophila eye, where two transcription factors, the MEIS1 homologue hth and the Zn-finger tsh, synergize to stimulate the proliferation of naïve eye progenitors. Experiments combining transcriptomics, open-chromatin profiling, motif analysis and functional assays indicate that these progenitor transcription factors exert a global regulation of the proliferation program. Rather than directly regulating cell cycle genes, they control proliferation through an intermediary layer of nuclear receptors of the ecdysone/estrogen-signaling pathway. This regulatory subnetwork between hth, tsh and nuclear receptors might be conserved from Drosophila to mammals, as we find a significant co-overexpression of their human homologues in specific cancer types.
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Affiliation(s)
- Marta Neto
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | | | - Delphine Potier
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium
| | - Paulo S Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Dirk Geerts
- Department of Medical Biology L2-109, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Stein Aerts
- School of Medicine, University of Leuven, box 602 3000, Leuven, Belgium.
| | - Fernando Casares
- CABD, Andalusian Centre for Developmental Biology, CSIC-UPO-JA, 41013, Seville, Spain.
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9
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Marco Antonio DS, Hartfelder K. Toward an Understanding of Divergent Compound Eye Development in Drones and Workers of the Honeybee (Apis melliferaL.): A Correlative Analysis of Morphology and Gene Expression. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 328:139-156. [DOI: 10.1002/jez.b.22696] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 08/17/2016] [Accepted: 08/21/2016] [Indexed: 12/27/2022]
Affiliation(s)
- David S. Marco Antonio
- Departamento de Genética; Faculdade de Medicina de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto SP Brazil
| | - Klaus Hartfelder
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos; Faculdade de Medicina de Ribeirão Preto; Universidade de São Paulo; Ribeirão Preto SP Brazil
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10
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Fried P, Sánchez-Aragón M, Aguilar-Hidalgo D, Lehtinen B, Casares F, Iber D. A Model of the Spatio-temporal Dynamics of Drosophila Eye Disc Development. PLoS Comput Biol 2016; 12:e1005052. [PMID: 27626238 PMCID: PMC5023109 DOI: 10.1371/journal.pcbi.1005052] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 07/05/2016] [Indexed: 02/03/2023] Open
Abstract
Patterning and growth are linked during early development and have to be tightly controlled to result in a functional tissue or organ. During the development of the Drosophila eye, this linkage is particularly clear: the growth of the eye primordium mainly results from proliferating cells ahead of the morphogenetic furrow (MF), a moving signaling wave that sweeps across the tissue from the posterior to the anterior side, that induces proliferating cells anterior to it to differentiate and become cell cycle quiescent in its wake. Therefore, final eye disc size depends on the proliferation rate of undifferentiated cells and on the speed with which the MF sweeps across the eye disc. We developed a spatio-temporal model of the growing eye disc based on the regulatory interactions controlled by the signals Decapentaplegic (Dpp), Hedgehog (Hh) and the transcription factor Homothorax (Hth) and explored how the signaling patterns affect the movement of the MF and impact on eye disc growth. We used published and new quantitative data to parameterize the model. In particular, two crucial parameter values, the degradation rate of Hth and the diffusion coefficient of Hh, were measured. The model is able to reproduce the linear movement of the MF and the termination of growth of the primordium. We further show that the model can explain several mutant phenotypes, but fails to reproduce the previously observed scaling of the Dpp gradient in the anterior compartment.
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Affiliation(s)
- Patrick Fried
- Department of Biosystems, Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
| | | | | | - Birgitta Lehtinen
- Department of Biosystems, Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
| | - Fernando Casares
- CABD, CSIC and Universidad Pablo de Olavide, Campus UPO, Seville, Spain
| | - Dagmar Iber
- Department of Biosystems, Science and Engineering (D-BSSE), ETH Zurich, Basel, Switzerland
- Swiss Institute of Bioinformatics (SIB), Basel, Switzerland
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11
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Neto M, Aguilar-Hidalgo D, Casares F. Increased avidity for Dpp/BMP2 maintains the proliferation of progenitors-like cells in the Drosophila eye. Dev Biol 2016; 418:98-107. [PMID: 27502436 DOI: 10.1016/j.ydbio.2016.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 07/26/2016] [Accepted: 08/04/2016] [Indexed: 10/21/2022]
Abstract
During organ development, the progenitor state is transient, and depends on specific combinations of transcription factors and extracellular signals. Not surprisingly, abnormal maintenance of progenitor transcription factors may lead to tissue overgrowth, and the concurrence of signals from the local environment is often critical to trigger this overgrowth. Therefore, identifying specific combinations of transcription factors/signals promoting -or opposing- proliferation in progenitors is essential to understand normal development and disease. We have investigated this issue using the Drosophila eye as model. Transcription factors hth and tsh are transiently expressed in eye progenitors causing the expansion of the progenitor pool. However, if their co-expression is maintained experimentally, cell proliferation continues and differentiation is halted. Here we show that Hth+Tsh-induced tissue overgrowth requires the BMP2 Dpp and the abnormal hyperactivation of its pathway. Rather than using autocrine Dpp expression, Hth+Tsh cells increase their avidity for Dpp, produced locally, by upregulating extracellular matrix components. During normal development, Dpp represses hth and tsh ensuring that the progenitor state is transient. However, cells in which Hth+Tsh expression is forcibly maintained use Dpp to enhance their proliferation.
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Affiliation(s)
- Marta Neto
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Campus Universidad Pablo de Olavide, 41013 Seville, Spain; IBMC/Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Rua Alfredo Allen, 208, 4200-135 Porto, Portugal
| | - Daniel Aguilar-Hidalgo
- Department of Biological Physics, Max Planck Institute for the Physics of Complex Systems, 01187 Dresden, Germany
| | - Fernando Casares
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Campus Universidad Pablo de Olavide, 41013 Seville, Spain.
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12
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Barrios N, González-Pérez E, Hernández R, Campuzano S. The Homeodomain Iroquois Proteins Control Cell Cycle Progression and Regulate the Size of Developmental Fields. PLoS Genet 2015; 11:e1005463. [PMID: 26305360 PMCID: PMC4549242 DOI: 10.1371/journal.pgen.1005463] [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: 03/10/2015] [Accepted: 07/23/2015] [Indexed: 01/09/2023] Open
Abstract
During development, proper differentiation and final organ size rely on the control of territorial specification and cell proliferation. Although many regulators of these processes have been identified, how both are coordinated remains largely unknown. The homeodomain Iroquois/Irx proteins play a key, evolutionarily conserved, role in territorial specification. Here we show that in the imaginal discs, reduced function of Iroquois genes promotes cell proliferation by accelerating the G1 to S transition. Conversely, their increased expression causes cell-cycle arrest, down-regulating the activity of the Cyclin E/Cdk2 complex. We demonstrate that physical interaction of the Iroquois protein Caupolican with Cyclin E-containing protein complexes, through its IRO box and Cyclin-binding domains, underlies its activity in cell-cycle control. Thus, Drosophila Iroquois proteins are able to regulate cell-autonomously the growth of the territories they specify. Moreover, our results provide a molecular mechanism for a role of Iroquois/Irx genes as tumour suppressors. The correct development of body organs, with their characteristic size and shape, requires the coordination of cell division and cell differentiation. Here we show that the Iroquois proteins (Irx in vertebrates) slow down cell division in the Drosophila imaginal discs, in addition to their well-known role in cell fate and territorial specification. In humans, inactivating mutations at the Irx genes are associated to several types of cancer, thus allowing their classification as tumour suppressor genes. We have observed that Drosophila Iroquois genes similarly behave as tumour suppressor genes. Iroquois proteins belong to a family of homeodomain-containing transcriptional regulators. However, our results indicate that they control cell division by a transcription independent mechanism based on their physical interaction with Cyclin E containing complexes, a key player in cell-cycle progression. We have identified two evolutionary conserved domains of Iroquois proteins, different from the homeodomain, involved in that interaction. This new function of Iroquois proteins places them in a key position to coordinate growth and differentiation during normal development. Our results further suggest a molecular mechanism for their role in tumour suppression. Future studies of Irx genes should help to determine if a similar mechanism could operate to help cancer progression when Irx activity is compromised.
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Affiliation(s)
- Natalia Barrios
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Esther González-Pérez
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Rosario Hernández
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Sonsoles Campuzano
- Department of Development and Differentiation, Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
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13
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Lopes CS, Casares F. Eye selector logic for a coordinated cell cycle exit. PLoS Genet 2015; 11:e1004981. [PMID: 25695251 PMCID: PMC4335009 DOI: 10.1371/journal.pgen.1004981] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022] Open
Abstract
Organ-selector transcription factors control simultaneously cell differentiation and proliferation, ensuring the development of functional organs and their homeostasis. How this is achieved at the molecular level is still unclear. Here we have investigated how the transcriptional pulse of string/cdc25 (stg), the universal mitotic trigger, is regulated during Drosophila retina development as an example of coordinated deployment of differentiation and proliferation programs. We identify the eye specific stg enhancer, stg-FMW, and show that Pax6 selector genes, in cooperation with Eya and So, two members of the retinal determination network, activate stg-FMW, establishing a positive feed-forward loop. This loop is negatively modulated by the Meis1 protein, Hth. This regulatory logic is reminiscent of that controlling the expression of differentiation transcription factors. Our work shows that subjecting transcription factors and key cell cycle regulators to the same regulatory logic ensures the coupling between differentiation and proliferation programs during organ development. Organs develop from groups of undifferentiated cells that proliferate and differentiate into specific cell types. During development, the coupling between proliferation and differentiation programs ensures that enough cells of the different cell types are generated. This is critical for proper organ formation and function. Here, we use the developing Drosophila eye to examine how the coupling between these two programs is achieved. During eye development, progenitors are amplified before they exit the cell cycle and enter the differentiation program. This amplification step depends on an expression burst of the mitotic trigger string/cdc25, which, by forcing cells into mitosis, synchronizes cells in G1 just before differentiation onset. Thus string regulation acts as a hub where differentiation and proliferation programs are integrated. We identify a DNA element that controls the burst of string expression prior to differentiation, and show that it is regulated by the same gene network that triggers eye development. The transcription factor Pax6/Eyeless is a key regulator in this network. Eyeless acts cooperatively with Sine oculis and Eyes absent to regulate string, through a positive feed-forward loop. This loop is negatively modulated by the progenitor-specific transcription factor Homothorax/Meis1. This work shows that transcription factors that instruct cells to acquire an eye fate also control their proliferation regime, thus guaranteeing the coupling between proliferation and differentiation.
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Affiliation(s)
- Carla S. Lopes
- CABD (Andalusian Centre for Developmental Biology), C.S.I.C.-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- * E-mail: (FC); (CSL)
| | - Fernando Casares
- CABD (Andalusian Centre for Developmental Biology), C.S.I.C.-Universidad Pablo de Olavide-Junta de Andalucía, Seville, Spain
- * E-mail: (FC); (CSL)
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14
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Davie K, Jacobs J, Atkins M, Potier D, Christiaens V, Halder G, Aerts S. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet 2015; 11:e1004994. [PMID: 25679813 PMCID: PMC4334524 DOI: 10.1371/journal.pgen.1004994] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2014] [Accepted: 01/08/2015] [Indexed: 01/24/2023] Open
Abstract
Genomic enhancers regulate spatio-temporal gene expression by recruiting specific combinations of transcription factors (TFs). When TFs are bound to active regulatory regions, they displace canonical nucleosomes, making these regions biochemically detectable as nucleosome-depleted regions or accessible/open chromatin. Here we ask whether open chromatin profiling can be used to identify the entire repertoire of active promoters and enhancers underlying tissue-specific gene expression during normal development and oncogenesis in vivo. To this end, we first compare two different approaches to detect open chromatin in vivo using the Drosophila eye primordium as a model system: FAIRE-seq, based on physical separation of open versus closed chromatin; and ATAC-seq, based on preferential integration of a transposon into open chromatin. We find that both methods reproducibly capture the tissue-specific chromatin activity of regulatory regions, including promoters, enhancers, and insulators. Using both techniques, we screened for regulatory regions that become ectopically active during Ras-dependent oncogenesis, and identified 3778 regions that become (over-)activated during tumor development. Next, we applied motif discovery to search for candidate transcription factors that could bind these regions and identified AP-1 and Stat92E as key regulators. We validated the importance of Stat92E in the development of the tumors by introducing a loss of function Stat92E mutant, which was sufficient to rescue the tumor phenotype. Additionally we tested if the predicted Stat92E responsive regulatory regions are genuine, using ectopic induction of JAK/STAT signaling in developing eye discs, and observed that similar chromatin changes indeed occurred. Finally, we determine that these are functionally significant regulatory changes, as nearby target genes are up- or down-regulated. In conclusion, we show that FAIRE-seq and ATAC-seq based open chromatin profiling, combined with motif discovery, is a straightforward approach to identify functional genomic regulatory regions, master regulators, and gene regulatory networks controlling complex in vivo processes.
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Affiliation(s)
- Kristofer Davie
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Jelle Jacobs
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Mardelle Atkins
- Laboratory of Growth Control and Cancer Research, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for the Biology of Disease, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Delphine Potier
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Valerie Christiaens
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
| | - Georg Halder
- Laboratory of Growth Control and Cancer Research, Center for Human Genetics, KU Leuven, Leuven, Belgium
- VIB Center for the Biology of Disease, Laboratory for Molecular Cancer Biology, Leuven, Belgium
| | - Stein Aerts
- Laboratory of Computational Biology, Center for Human Genetics, KU Leuven, Leuven, Belgium
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15
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Mapping Gene Regulatory Networks in Drosophila Eye Development by Large-Scale Transcriptome Perturbations and Motif Inference. Cell Rep 2014; 9:2290-303. [DOI: 10.1016/j.celrep.2014.11.038] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 10/24/2014] [Accepted: 11/22/2014] [Indexed: 11/20/2022] Open
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16
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Ariza-Cosano A, Bensimon-Brito A, Gómez-Skarmeta JL, Bessa J. sox21a directs lateral line patterning by modulating FGF signaling. Dev Neurobiol 2014; 75:80-92. [PMID: 25044975 DOI: 10.1002/dneu.22211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 07/09/2014] [Accepted: 07/09/2014] [Indexed: 01/19/2023]
Abstract
The development of organs composed by repeated functional units is, in many cases, accomplished by the transition of cells from a progenitor to a differentiation domain, triggering a reiterated developmental program. Yet, how these discrete fields are formed during development is still a largely unresolved question. The posterior lateral line (pLL), a sensory organ present in fish and amphibians, develops from a primordium that migrates along the flanks of the animal periodically depositing neuromasts, the pLL functional units. In zebrafish (Danio rerio), the developmental program of the pLL is triggered by the transit of progenitor cells from a Wnt to a Fgf signaling domain. It has been proposed that these two fields are defined by the antagonistic activity of these two signaling pathways, but how they are formed and maintained is still an open question in the development of the pLL. In this work, we show that sox21a, an HMG -box transcription factor, is expressed within the Fgf domain. We demonstrate that, while the Fgf signaling pathway do not control sox21a, knockdown of sox21a causes impairment of Fgf signaling, expansion of the Wnt signaling domain and disruption of neuromast development. These results suggest that sox21a is a key player in the pLL primordium patterning, fine-tuning the border of the Fgf and Wnt signaling domains.
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Affiliation(s)
- Ana Ariza-Cosano
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-Universidad Pablo de Olavide-Junta de Andalucía, Ctra. Utrera Km 1, Seville, 41013, Spain
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Piñeiro C, Lopes CS, Casares F. A conserved transcriptional network regulates lamina development in the Drosophila visual system. Development 2014; 141:2838-47. [PMID: 24924198 DOI: 10.1242/dev.108670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The visual system of insects is a multilayered structure composed externally by the compound eye and internally by the three ganglia of the optic lobe: lamina, medulla and the lobula complex. The differentiation of lamina neurons depends heavily on Hedgehog (Hh) signaling, which is delivered by the incoming photoreceptor axons, and occurs in a wave-like fashion. Despite the primary role of lamina neurons in visual perception, it is still unclear how these neurons are specified from neuroepithelial (NE) progenitors. Here we show that a homothorax (hth)-eyes absent (eya)-sine oculis (so)-dachshund (dac) gene regulatory cassette is involved in this specification. Lamina neurons differentiate from NE progenitors that express hth, eya and so. One of the first events in the differentiation of lamina neurons is the upregulation of dac expression in response to Hh signaling. We show that this dac upregulation, which marks the transition from NE progenitors into lamina precursors, also requires Eya/So, the expression of which is locked in by mutual feedback. dac expression is crucial for lamina differentiation because it ensures repression of hth, a negative regulator of single-minded, and thus dac allows further lamina neuron differentiation. Therefore, the specification of lamina neurons is controlled by coupling the cell-autonomous hth-eya-so-dac regulatory cassette to Hh signaling.
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Affiliation(s)
- Cristina Piñeiro
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| | - Carla S Lopes
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
| | - Fernando Casares
- CABD (Andalusian Centre for Developmental Biology), CSIC-UPO-JA, Seville 41013, Spain
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18
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Arif S, Hilbrant M, Hopfen C, Almudi I, Nunes MDS, Posnien N, Kuncheria L, Tanaka K, Mitteroecker P, Schlötterer C, McGregor AP. Genetic and developmental analysis of differences in eye and face morphology between Drosophila simulans and Drosophila mauritiana. Evol Dev 2013; 15:257-67. [PMID: 23809700 PMCID: PMC3799016 DOI: 10.1111/ede.12027] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Eye and head morphology vary considerably among insects and even between closely related species of Drosophila. Species of the D. melanogaster subgroup, and other Drosophila species, exhibit a negative correlation between eye size and face width (FW); for example, D. mauritiana generally has bigger eyes composed of larger ommatidia and conversely a narrower face than its sibling species. To better understand the evolution of eye and head morphology, we investigated the genetic and developmental basis of differences in eye size and FW between male D. mauritiana and D. simulans. QTL mapping of eye size and FW showed that the major loci responsible for the interspecific variation in these traits are localized to different genomic regions. Introgression of the largest effect QTL underlying the difference in eye size resulted in flies with larger eyes but no significant difference in FW. Moreover, introgression of a QTL region on the third chromosome that contributes to the FW difference between these species affected FW, but not eye size. We also observed that this difference in FW is detectable earlier in the development of the eye-antennal disc than the difference in the size of the retinal field. Our results suggest that different loci that act at different developmental stages underlie changes in eye size and FW. Therefore, while there is a negative correlation between these traits in Drosophila, we show genetically that they also have the potential to evolve independently and this may help to explain the evolution of these traits in other insects.
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Affiliation(s)
- Saad Arif
- Max Planck Institute for Biology of Ageing, Robert‐Koch‐Straße 21, D‐50931 Cologne, Germany
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Marinho J, Martins T, Neto M, Casares F, Pereira PS. The nucleolar protein Viriato/Nol12 is required for the growth and differentiation progression activities of the Dpp pathway during Drosophila eye development. Dev Biol 2013; 377:154-65. [PMID: 23416177 DOI: 10.1016/j.ydbio.2013.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2012] [Revised: 01/30/2013] [Accepted: 02/01/2013] [Indexed: 11/19/2022]
Abstract
Drosophila Decapentaplegic (Dpp), a member of the BMP2/4 class of the TGF-βs, is required for organ growth, patterning and differentiation. However, much remains to be understood about the mechanisms acting downstream of these multiple roles. Here we investigate this issue during the development of the Drosophila eye. We have previously identified viriato (vito) as a dMyc-target gene encoding a nucleolar protein that is required for proper tissue growth in the developing eye. By carrying out a targeted in vivo double-RNAi screen to identify genes and pathways functioning with Vito during eye development, we found a strong genetic interaction between vito and members of the Dpp signaling pathway including the TGF-β receptors tkv (type I), put (type II), and the co-Smad medea (med). Analyzing the expression of the Dpp receptor Tkv and the activation pattern of the pathway's transducer, p-Mad, we found that vito is required for a correct signal transduction in Dpp-receiving cells. Overall, we validate the use of double RNAi to find specific genetic interactions and, in particular, we uncover a link between the Dpp pathway and Vito, a nucleolar component. vito would act genetically downstream of Dpp, playing an important role in maintaining a sufficient level of Dpp activity for the promotion of eye disc growth and regulation of photoreceptor differentiation in eye development.
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Affiliation(s)
- Joana Marinho
- Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, Porto 4150-180, Portugal
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Streit A, Tambalo M, Chen J, Grocott T, Anwar M, Sosinsky A, Stern CD. Experimental approaches for gene regulatory network construction: the chick as a model system. Genesis 2012; 51:296-310. [PMID: 23174848 DOI: 10.1002/dvg.22359] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 11/09/2012] [Accepted: 11/11/2012] [Indexed: 01/23/2023]
Abstract
Setting up the body plan during embryonic development requires the coordinated action of many signals and transcriptional regulators in a precise temporal sequence and spatial pattern. The last decades have seen an explosion of information describing the molecular control of many developmental processes. The next challenge is to integrate this information into logic "wiring diagrams" that visualize gene actions and outputs, have predictive power and point to key control nodes. Here, we provide an experimental workflow on how to construct gene regulatory networks using the chick as model system.
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Affiliation(s)
- Andrea Streit
- Department of Craniofacial Development and Stem Cell Biology, King's College London, London, United Kingdom.
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21
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Naval-Sánchez M, Potier D, Haagen L, Sánchez M, Munck S, Van de Sande B, Casares F, Christiaens V, Aerts S. Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions. Genome Res 2012; 23:74-88. [PMID: 23070853 PMCID: PMC3530685 DOI: 10.1101/gr.140426.112] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The identification of transcription factor binding sites, enhancers, and transcriptional target genes often relies on the integration of gene expression profiling and computational cis-regulatory sequence analysis. Methods for the prediction of cis-regulatory elements can take advantage of comparative genomics to increase signal-to-noise levels. However, gene expression data are usually derived from only one species. Here we investigate tissue-specific cross-species gene expression profiling by high-throughput sequencing, combined with cross-species motif discovery. First, we compared different methods for expression level quantification and cross-species integration using Tag-seq data. Using the optimal pipeline, we derived a set of genes with conserved expression during retinal determination across Drosophila melanogaster, Drosophila yakuba, and Drosophila virilis. These genes are enriched for binding sites of eye-related transcription factors including the zinc-finger Glass, a master regulator of photoreceptor differentiation. Validation of predicted Glass targets using RNA-seq in homozygous glass mutants confirms that the majority of our predictions are expressed downstream from Glass. Finally, we tested nine candidate enhancers by in vivo reporter assays and found eight of them to drive GFP in the eye disc, of which seven colocalize with the Glass protein, namely, scrt, chp, dpr10, CG6329, retn, Lim3, and dmrt99B. In conclusion, we show for the first time the combined use of cross-species expression profiling with cross-species motif discovery as a method to define a core developmental program, and we augment the candidate Glass targetome from a single known target gene, lozenge, to at least 62 conserved transcriptional targets.
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Affiliation(s)
- Marina Naval-Sánchez
- Laboratory of Computational Biology, Department of Human Genetics, University of Leuven, 3000 Leuven, Belgium
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Tsachaki M, Sprecher SG. Genetic and developmental mechanisms underlying the formation of theDrosophilacompound eye. Dev Dyn 2011; 241:40-56. [DOI: 10.1002/dvdy.22738] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2011] [Indexed: 01/15/2023] Open
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Brockmann A, Domínguez-Cejudo MA, Amore G, Casares F. Regulation of ocellar specification and size by twin of eyeless and homothorax. Dev Dyn 2011; 240:75-85. [PMID: 21104743 DOI: 10.1002/dvdy.22494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The retinal determination gene network (RDGN) constitutes a paradigm of a gene network controlling organ specification and growth. In this study, we probed the RDGN in the Drosophila ocelli, a set of simple eyes located on the fly's dorsal head, by studying the expression, regulation, and function of toy, hth, eya, and so, members of the Pax6, Meis, Eya, and Six gene families. Our results highlight the role of the pax6 gene toy, together with the hh signaling pathway, in the initiation of eya and so expression; the engagement of eya and so in a feedback loop necessary for their full expression; and the interplay between hh signaling and hth as a mechanism of organ size control, as general regulatory steps in the specification of visual organs.
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Affiliation(s)
- Anette Brockmann
- Centro Andaluz de Biología del Desarrollo (CABD), CSIC-UPO, Seville, Spain
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