1
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Herriage HC, Calvi BR. Premature endocycling of Drosophila follicle cells causes pleiotropic defects in oogenesis. Genetics 2024; 226:iyae009. [PMID: 38302115 PMCID: PMC10990429 DOI: 10.1093/genetics/iyae009] [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: 10/18/2023] [Revised: 10/18/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
Endocycling cells grow and repeatedly duplicate their genome without dividing. Cells switch from mitotic cycles to endocycles in response to developmental signals during the growth of specific tissues in a wide range of organisms. The purpose of switching to endocycles, however, remains unclear in many tissues. Additionally, cells can switch to endocycles in response to conditional signals, which can have beneficial or pathological effects on tissues. However, the impact of these unscheduled endocycles on development is underexplored. Here, we use Drosophila ovarian somatic follicle cells as a model to examine the impact of unscheduled endocycles on tissue growth and function. Follicle cells normally switch to endocycles at mid-oogenesis. Inducing follicle cells to prematurely switch to endocycles resulted in the lethality of the resulting embryos. Analysis of ovaries with premature follicle cell endocycles revealed aberrant follicular epithelial structure and pleiotropic defects in oocyte growth, developmental gene amplification, and the migration of a special set of follicle cells known as border cells. Overall, these findings reveal how unscheduled endocycles can disrupt tissue growth and function to cause aberrant development.
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Affiliation(s)
- Hunter C Herriage
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
- Melvin and Bren Simon Cancer Center, Indianapolis, IN 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Bloomington, IN 47405, USA
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2
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Berg C, Sieber M, Sun J. Finishing the egg. Genetics 2024; 226:iyad183. [PMID: 38000906 PMCID: PMC10763546 DOI: 10.1093/genetics/iyad183] [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: 07/05/2023] [Accepted: 09/27/2023] [Indexed: 11/26/2023] Open
Abstract
Gamete development is a fundamental process that is highly conserved from early eukaryotes to mammals. As germ cells develop, they must coordinate a dynamic series of cellular processes that support growth, cell specification, patterning, the loading of maternal factors (RNAs, proteins, and nutrients), differentiation of structures to enable fertilization and ensure embryonic survival, and other processes that make a functional oocyte. To achieve these goals, germ cells integrate a complex milieu of environmental and developmental signals to produce fertilizable eggs. Over the past 50 years, Drosophila oogenesis has risen to the forefront as a system to interrogate the sophisticated mechanisms that drive oocyte development. Studies in Drosophila have defined mechanisms in germ cells that control meiosis, protect genome integrity, facilitate mRNA trafficking, and support the maternal loading of nutrients. Work in this system has provided key insights into the mechanisms that establish egg chamber polarity and patterning as well as the mechanisms that drive ovulation and egg activation. Using the power of Drosophila genetics, the field has begun to define the molecular mechanisms that coordinate environmental stresses and nutrient availability with oocyte development. Importantly, the majority of these reproductive mechanisms are highly conserved throughout evolution, and many play critical roles in the development of somatic tissues as well. In this chapter, we summarize the recent progress in several key areas that impact egg chamber development and ovulation. First, we discuss the mechanisms that drive nutrient storage and trafficking during oocyte maturation and vitellogenesis. Second, we examine the processes that regulate follicle cell patterning and how that patterning impacts the construction of the egg shell and the establishment of embryonic polarity. Finally, we examine regulatory factors that control ovulation, egg activation, and successful fertilization.
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Affiliation(s)
- Celeste Berg
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5065USA
| | - Matthew Sieber
- Department of Physiology, UT Southwestern Medical Center, Dallas, TX 75390USA
| | - Jianjun Sun
- Department of Physiology and Neurobiology, University of Connecticut, Storrs, CT 06269USA
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3
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Herriage HC, Calvi BR. Premature endocycling of Drosophila follicle cells causes pleiotropic defects in oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.10.10.561736. [PMID: 37873193 PMCID: PMC10592765 DOI: 10.1101/2023.10.10.561736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Endocycling cells grow and repeatedly duplicate their genome without dividing. Cells switch from mitotic cycles to endocycles in response to developmental signals during the growth of specific tissues in a wide range of organisms. The purpose of switching to endocycles, however, remains unclear in many tissues. Additionally, cells can switch to endocycles in response to conditional signals, which can have beneficial or pathological effects on tissues. However, the impact of these unscheduled endocycles on development is underexplored. Here, we use Drosophila ovarian somatic follicle cells as a model to examine the impact of unscheduled endocycles on tissue growth and function. Follicle cells normally switch to endocycles at mid-oogenesis. Inducing follicle cells to prematurely switch to endocycles resulted in lethality of the resulting embryos. Analysis of ovaries with premature follicle cell endocycles revealed aberrant follicular epithelial structure and pleiotropic defects in oocyte growth, developmental gene amplification, and the migration of a special set of follicle cells known as border cells. Overall, these findings reveal how unscheduled endocycles can disrupt tissue growth and function to cause aberrant development.
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Affiliation(s)
| | - Brian R. Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405
- Melvin and Bren Simon Cancer Center, Indianapolis, IN
- Indiana University School of Medicine, Bloomington, IN
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4
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Sarkar K, Kotb NM, Lemus A, Martin ET, McCarthy A, Camacho J, Iqbal A, Valm AM, Sammons MA, Rangan P. A feedback loop between heterochromatin and the nucleopore complex controls germ-cell-to-oocyte transition during Drosophila oogenesis. Dev Cell 2023; 58:2580-2596.e6. [PMID: 37673064 DOI: 10.1016/j.devcel.2023.08.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 04/12/2023] [Accepted: 08/09/2023] [Indexed: 09/08/2023]
Abstract
Germ cells differentiate into oocytes that launch the next generation upon fertilization. How the highly specialized oocyte acquires this distinct cell fate is poorly understood. During Drosophila oogenesis, H3K9me3 histone methyltransferase SETDB1 translocates from the cytoplasm to the nucleus of germ cells concurrently with oocyte specification. Here, we discovered that nuclear SETDB1 is required for silencing a cohort of differentiation-promoting genes by mediating their heterochromatinization. Intriguingly, SETDB1 is also required for upregulating 18 of the ∼30 nucleoporins (Nups) that compose the nucleopore complex (NPC), promoting NPC formation. NPCs anchor SETDB1-dependent heterochromatin at the nuclear periphery to maintain H3K9me3 and gene silencing in the egg chambers. Aberrant gene expression due to the loss of SETDB1 or Nups results in the loss of oocyte identity, cell death, and sterility. Thus, a feedback loop between heterochromatin and NPCs promotes transcriptional reprogramming at the onset of oocyte specification, which is critical for establishing oocyte identity.
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Affiliation(s)
- Kahini Sarkar
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Noor M Kotb
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA; Department of Biomedical Sciences, School of Public Health, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex Lemus
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Elliot T Martin
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alicia McCarthy
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Justin Camacho
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Ayman Iqbal
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Alex M Valm
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Morgan A Sammons
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA
| | - Prashanth Rangan
- Department of Biological Sciences and RNA Institute, University at Albany SUNY, Albany, NY 12222, USA.
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5
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Hashimoto Y, Sadano K, Miyata N, Ito H, Tanaka H. Novel role of DONSON in CMG helicase assembly during vertebrate DNA replication initiation. EMBO J 2023; 42:e114131. [PMID: 37458194 PMCID: PMC10476173 DOI: 10.15252/embj.2023114131] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/27/2023] [Accepted: 06/29/2023] [Indexed: 09/05/2023] Open
Abstract
CMG (Cdc45-MCM-GINS) helicase assembly at the replication origin is the culmination of eukaryotic DNA replication initiation. This process can be reconstructed in vitro using defined factors in Saccharomyces cerevisiae; however, in vertebrates, origin-dependent CMG formation has not yet been achieved partly due to the lack of a complete set of known initiator proteins. Since a microcephaly gene product, DONSON, was reported to remodel the CMG helicase under replication stress, we analyzed its role in DNA replication using a Xenopus cell-free system. We found that DONSON was essential for the replisome assembly. In vertebrates, DONSON physically interacted with GINS and Polε via its conserved N-terminal PGY and NPF motifs, and the DONSON-GINS interaction contributed to the replisome assembly. DONSON's chromatin association during replication initiation required the pre-replicative complex, TopBP1, and kinase activities of S-CDK and DDK. Both S-CDK and DDK required DONSON to trigger replication initiation. Moreover, human DONSON could substitute for the Xenopus protein in a cell-free system. These findings indicate that vertebrate DONSON is a novel initiator protein essential for CMG helicase assembly.
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Affiliation(s)
- Yoshitami Hashimoto
- School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Kota Sadano
- School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Nene Miyata
- School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Haruka Ito
- School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
| | - Hirofumi Tanaka
- School of Life SciencesTokyo University of Pharmacy and Life SciencesTokyoJapan
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6
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Mukherjee A, Schuppe M, Renault AD. The Lipid Phosphate Phosphatase Wunen Promotes Eggshell Formation and Is Essential for Fertility in Drosophila. BIOLOGY 2023; 12:1003. [PMID: 37508432 PMCID: PMC10376809 DOI: 10.3390/biology12071003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/22/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
The eggshell that surrounds insect eggs acts as a barrier, protecting against biotic factors and desiccation. The eggshell is a multi-layered structure which is synthesised by the somatic follicle cells that surround the developing oocyte. Although the temporal order of expression of the protein eggshell components goes someway to explaining how the different layers are built up, but how the precise three-dimensional structure is achieved and how lipid components responsible for desiccation resistance are incorporated are poorly understood. In this paper, we demonstrate that wunen, which encodes a lipid phosphate phosphatase, is necessary for fertility in Drosophila females. Compared to sibling controls, females null for wunen lay fewer eggs which subsequently collapse such that no larvae emerge. We show that this is due to a requirement for wunen in the ovarian follicle cells which is needed to produce an ordered and functional eggshell. Knockdown of a septate junction component also results in collapsed eggs, supporting the idea that similar to its role in embryonic tracheal development, Wunen in follicle cells also promotes septate junction function.
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Affiliation(s)
- Amrita Mukherjee
- MRC Toxicology Unit, Gleeson Building, Tennis Court Road, Cambridge CB2 1QR, UK
| | - Michaela Schuppe
- Institute for Organic Chemistry, Eberhard Karls University Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Andrew D Renault
- School of Life Sciences, University of Nottingham, Medical School, QMC, Nottingham NG7 2UH, UK
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7
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Wright GM, Menzel J, Tatman PD, Black JC. Transition from Transient DNA Rereplication to Inherited Gene Amplification Following Prolonged Environmental Stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539886. [PMID: 37214911 PMCID: PMC10197558 DOI: 10.1101/2023.05.08.539886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Cells require the ability to adapt to changing environmental conditions, however, it is unclear how these changes elicit stable permanent changes in genomes. We demonstrate that, in response to environmental metal exposure, the metallothionein (MT) locus undergoes DNA rereplication generating transient site-specific gene amplifications (TSSGs). Chronic metal exposure allows transition from MT TSSG to inherited MT gene amplification through homologous recombination within and outside of the MT locus. DNA rereplication of the MT locus is suppressed by H3K27me3 and EZH2. Long-term ablation of EZH2 activity eventually leads to integration and inheritance of MT gene amplifications without the selective pressure of metal exposure. The rereplication and inheritance of MT gene amplification is an evolutionarily conserved response to environmental metal from yeast to human. Our results describe a new paradigm for adaptation to environmental stress where targeted, transient DNA rereplication precedes stable inherited gene amplification.
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8
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Meng X, Dang HQ, Kapler GM. Developmentally Programmed Switches in DNA Replication: Gene Amplification and Genome-Wide Endoreplication in Tetrahymena. Microorganisms 2023; 11:microorganisms11020491. [PMID: 36838456 PMCID: PMC9967165 DOI: 10.3390/microorganisms11020491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/29/2022] [Accepted: 02/09/2023] [Indexed: 02/18/2023] Open
Abstract
Locus-specific gene amplification and genome-wide endoreplication generate the elevated copy number of ribosomal DNA (rDNA, 9000 C) and non-rDNA (90 C) chromosomes in the developing macronucleus of Tetrahymena thermophila. Subsequently, all macronuclear chromosomes replicate once per cell cycle during vegetative growth. Here, we describe an unanticipated, programmed switch in the regulation of replication initiation in the rDNA minichromosome. Early in development, the 21 kb rDNA minichromosome is preferentially amplified from 2 C to ~800 C from well-defined origins, concurrent with genome-wide endoreplication (2 C to 8-16 C) in starved mating Tetrahymena (endoreplication (ER) Phase 1). Upon refeeding, rDNA and non-rDNA chromosomes achieve their final copy number through resumption of just the endoreplication program (ER Phase 2). Unconventional rDNA replication intermediates are generated primarily during ER phase 2, consistent with delocalized replication initiation and possible formation of persistent RNA-DNA hybrids. Origin usage and replication fork elongation are affected in non-rDNA chromosomes as well. Despite the developmentally programmed 10-fold reduction in the ubiquitous eukaryotic initiator, the Origin Recognition Complex (ORC), active initiation sites are more closely spaced in ER phases 1 and 2 compared to vegetative growing cells. We propose that initiation site selection is relaxed in endoreplicating macronuclear chromosomes and may be less dependent on ORC.
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Affiliation(s)
- Xiangzhou Meng
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hung Quang Dang
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Alstem Bioscience, Richmond, CA 94806, USA
| | - Geoffrey M. Kapler
- Department of Cell Biology and Genetics, Texas A&M University Health Science Center, Bryan, TX 77807, USA
- Correspondence: ; Tel.: +1-979-574-3901
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9
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Abstract
In this chapter, we highlight examples of the diverse array of developmental, cellular, and biochemical insights that can be gained by using Drosophila melanogaster oogenesis as a model tissue. We begin with an overview of ovary development and adult oogenesis. Then we summarize how the adult Drosophila ovary continues to advance our understanding of stem cells, cell cycle, cell migration, cytoplasmic streaming, nurse cell dumping, and cell death. We also review emerging areas of study, including the roles of lipid droplets, ribosomes, and nuclear actin in egg development. Finally, we conclude by discussing the growing conservation of processes and signaling pathways that regulate oogenesis and female reproduction from flies to humans.
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10
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Soriano A, Petit C, Ryan S, Jemc JC. Tracking Follicle Cell Development. Methods Mol Biol 2023; 2626:151-177. [PMID: 36715904 DOI: 10.1007/978-1-0716-2970-3_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Somatic follicle cells are critical support cells for Drosophila oogenesis, as they provide signals and molecules needed to produce a mature egg. Throughout this process, the follicle cells differentiate into multiple subpopulations and transition between three different cell cycle programs to support nurse cell and oocyte development. The follicle cells are mitotic in early egg chamber development, as they cover the germline cyst. In mid-oogenesis, follicle cells switch from mitosis to endocycling, increasing their ploidy from 2C to 16C. Finally, in late oogenesis, cells transition from endocycling to gene amplification, increasing the copy number of a small subset of genes, including the genes encoding proteins required for egg maturation. In order to explore the genetic regulation of these cell cycle switches and follicle cell development and specification, clonal analysis and the GAL4/UAS system are used frequently to reduce or increase expression of genes of interest. These genetic approaches combined with immunohistochemistry and in situ hybridization are powerful tools for characterizing the mechanisms regulating follicle cell development and the mitosis/endocycle and endocycle/gene amplification transitions. This chapter describes the genetic tools available to manipulate gene expression in follicle cells, as well as the methods and reagents that can be utilized to explore gene expression throughout follicle cell development.
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Affiliation(s)
- Adrianna Soriano
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Houston Baptist University, Houston, TX, USA
| | | | - Savannah Ryan
- Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Jennifer C Jemc
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.
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11
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Molano-Fernández M, Hickson ID, Herranz H. Cyclin E overexpression in the Drosophila accessory gland induces tissue dysplasia. Front Cell Dev Biol 2023; 10:992253. [PMID: 36704199 PMCID: PMC9871066 DOI: 10.3389/fcell.2022.992253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 12/23/2022] [Indexed: 01/12/2023] Open
Abstract
The regulation of the cell division cycle is governed by a complex network of factors that together ensure that growing or proliferating cells maintain a stable genome. Defects in this system can lead to genomic instability that can affect tissue homeostasis and thus compromise human health. Variations in ploidy and cell heterogeneity are observed frequently in human cancers. Here, we examine the consequences of upregulating the cell cycle regulator Cyclin E in the Drosophila melanogaster male accessory gland. The accessory gland is the functional analog of the human prostate. This organ is composed of a postmitotic epithelium that is emerging as a powerful in vivo system for modelling different aspects of tumor initiation and progression. We show that Cyclin E upregulation in this model is sufficient to drive tissue dysplasia. Cyclin E overexpression drives endoreplication and affects DNA integrity, which results in heterogeneous nuclear and cellular composition and variable degrees of DNA damage. We present evidence showing that, despite the presence of genotoxic stress, those cells are resistant to apoptosis and thus defective cells are not eliminated from the tissue. We also show that Cyclin E-expressing cells in the accessory gland display mitochondrial DNA aggregates that colocalize with Cyclin E protein. Together, the findings presented here show that Cyclin E upregulation in postmitotic cells of the accessory gland organ causes cellular defects such as genomic instability and mitochondrial defects, eventually leading to tissue dysplasia. This study highlights novel mechanisms by which Cyclin E might contribute to disease initiation and progression.
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Affiliation(s)
- Maria Molano-Fernández
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ian D. Hickson
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark,Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Copenhagen, Denmark
| | - Héctor Herranz
- Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark,*Correspondence: Héctor Herranz,
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12
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Fischer U, Meese E. Gene Amplification in Tumor Cells: Developed De Novo or Adopted from Stem Cells. Cells 2022; 12:cells12010148. [PMID: 36611942 PMCID: PMC9818554 DOI: 10.3390/cells12010148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 12/31/2022] Open
Abstract
Gene amplifications have been known for several decades as physiological processes in amphibian and flies, e.g., during eggshell development in Drosophila and as part of pathological processes in humans, specifically in tumors and drug-resistant cells. The long-held belief that a physiological gene amplification does not occur in humans was, however, fundamental questioned by findings that showed gene amplification in human stem cells. We hypothesis that the physiological and the pathological, i.e., tumor associated processes of gene amplification share at their beginning the same underlying mechanism. Re-replication was reported both in the context of tumor related genome instability and during restricted time windows in Drosophila development causing the known developmental gene amplification in Drosophila. There is also growing evidence that gene amplification and re-replication were present in human stem cells. It appears likely that stem cells utilize a re-replication mechanism that has been developed early in evolution as a powerful tool to increase gene copy numbers very efficiently. Here, we show that, several decades ago, there was already evidence of gene amplification in non-tumor mammalian cells, but that was not recognized at the time and interpreted accordingly. We give an overview on gene amplifications during normal mammalian development, the possible mechanism that enable gene amplification and hypothesize how tumors adopted this capability for gene amplification.
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13
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Noncanonical function of Capicua as a growth termination signal in Drosophila oogenesis. Proc Natl Acad Sci U S A 2022; 119:e2123467119. [PMID: 35881788 PMCID: PMC9351367 DOI: 10.1073/pnas.2123467119] [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] [Indexed: 01/28/2023] Open
Abstract
Capicua (Cic) proteins are conserved HMG-box transcriptional repressors that control receptor tyrosine kinase (RTK) signaling responses and are implicated in human neurological syndromes and cancer. While Cic is known to exist as short (Cic-S) and long (Cic-L) isoforms with identical HMG-box and associated core regions but distinct N termini, most previous studies have focused on Cic-S, leaving the function of Cic-L unexplored. Here we show that Cic-L acts in two capacities during Drosophila oogenesis: 1) as a canonical sensor of RTK signaling in somatic follicle cells, and 2) as a regulator of postmitotic growth in germline nurse cells. In these latter cells, Cic-L behaves as a temporal signal that terminates endoreplicative growth before they dump their contents into the oocyte. We show that Cic-L is necessary and sufficient for nurse cell endoreplication arrest and induces both stabilization of CycE and down-regulation of Myc. Surprisingly, this function depends mainly on the Cic-L-specific N-terminal module, which is capable of acting independently of the Cic HMG-box-containing core. Mirroring these observations, basal metazoans possess truncated Cic-like proteins composed only of Cic-L N-terminal sequences, suggesting that this module plays unique, ancient roles unrelated to the canonical function of Cic.
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14
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Chakravarti A, Thirimanne HN, Brown S, Calvi BR. Drosophila p53 isoforms have overlapping and distinct functions in germline genome integrity and oocyte quality control. eLife 2022; 11:61389. [PMID: 35023826 PMCID: PMC8758136 DOI: 10.7554/elife.61389] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
p53 gene family members in humans and other organisms encode a large number of protein isoforms whose functions are largely undefined. Using Drosophila as a model, we find that a p53B isoform is expressed predominantly in the germline where it colocalizes with p53A into subnuclear bodies. It is only p53A, however, that mediates the apoptotic response to ionizing radiation in the germline and soma. In contrast, p53A and p53B are both required for the normal repair of meiotic DNA breaks, an activity that is more crucial when meiotic recombination is defective. We find that in oocytes with persistent DNA breaks p53A is also required to activate a meiotic pachytene checkpoint. Our findings indicate that Drosophila p53 isoforms have DNA lesion and cell type-specific functions, with parallels to the functions of mammalian p53 family members in the genotoxic stress response and oocyte quality control.
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Affiliation(s)
| | | | - Savanna Brown
- Department of Biology, Indiana University, Bloomington, United States
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, United States
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15
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Yun HS, Lee J, Kim JY, Sim YJ, Lee CW, Park JK, Kim JS, Ahn J, Song JY, Baek JH, Hwang SG. A novel function of HRP-3 in regulating cell cycle progression via the HDAC-E2F1-Cyclin E pathway in lung cancer. Cancer Sci 2021; 113:145-155. [PMID: 34714604 PMCID: PMC8748221 DOI: 10.1111/cas.15183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 10/06/2021] [Accepted: 10/12/2021] [Indexed: 11/29/2022] Open
Abstract
To improve the poor survival rate of lung cancer patients, we investigated the role of HDGF‐related protein 3 (HRP‐3) as a potential biomarker for lung cancer. The expression of endogenous HRP‐3 in human lung cancer tissues and xenograft tumor models is indicative of its clinical relevance in lung cancer. Additionally, we demonstrated that HRP‐3 directly binds to the E2F1 promoter on chromatin. Interestingly, HRP‐3 depletion in A549 cells impedes the binding of HRP‐3 to the E2F1 promoter; this in turn hampers the interaction between Histone H3/H4 and HDAC1/2 on the E2F1 promoter, while concomitantly inducing Histone H3/H4 acetylation around the E2F1 promoter. The enhanced Histone H3/H4 acetylation on the E2F1 promoter through HRP‐3 depletion increases the transcription level of E2F1. Furthermore, the increased E2F1 transcription levels lead to the enhanced transcription of Cyclin E, known as the E2F1‐responsive gene, thus inducing S‐phase accumulation. Therefore, our study provides evidence for the utility of HRP‐3 as a biomarker for the prognosis and treatment of lung cancer. Furthermore, we delineated the capacity of HRP‐3 to regulate the E2F1 transcription level via histone deacetylation.
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Affiliation(s)
- Hong Shik Yun
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Janet Lee
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Ju-Young Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea.,Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Ye-Ji Sim
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Chang-Woo Lee
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jong Kuk Park
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jae-Sung Kim
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jiyeon Ahn
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jie-Young Song
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
| | - Jeong-Hwa Baek
- Radiation Biology Research Team, Research Center, Dongnam Institute of Radiological and Medical Sciences, Busan, Korea
| | - Sang-Gu Hwang
- Division of Radiation Biomedical Research, Korea Institute of Radiological and Medical Sciences, Seoul, Korea
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16
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Kim M, Delos Santos K, Moon NS. Proper CycE-Cdk2 activity in endocycling tissues requires regulation of the cyclin-dependent kinase inhibitor Dacapo by dE2F1b in Drosophila. Genetics 2021; 217:1-15. [PMID: 33683365 DOI: 10.1093/genetics/iyaa029] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 12/06/2020] [Indexed: 01/05/2023] Open
Abstract
Polyploidy is an integral part of development and is associated with cellular stress, aging, and pathological conditions. The endocycle, comprised of successive rounds of G and S phases without mitosis, is widely employed to produce polyploid cells in plants and animals. In Drosophila, maintenance of the endocycle is dependent on E2F-governed oscillations of Cyclin E (CycE)-Cdk2 activity, which is known to be largely regulated at the level of transcription. In this study, we report an additional level of E2F-dependent control of CycE-Cdk2 activity during the endocycle. Genetic experiments revealed that an alternative isoform of Drosophila de2f1, dE2F1b, regulates the expression of the p27CIP/KIP-like Cdk inhibitor Dacapo (Dap). We provide evidence showing that dE2F1b-dependent Dap expression in endocycling tissues is necessary for setting proper CycE-Cdk2 activity. Furthermore, we demonstrate that dE2F1b is required for proliferating cell nuclear antigen expression that establishes a negative feedback loop in S phase. Overall, our study reveals previously unappreciated E2F-dependent regulatory networks that are critical for the periodic transition between G and S phases during the endocycle.
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Affiliation(s)
- Minhee Kim
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec H3A 1B1 Canada
| | - Keemo Delos Santos
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec H3A 1B1 Canada
| | - Nam-Sung Moon
- Department of Biology, Developmental Biology Research Initiative, McGill University, Montreal, Quebec H3A 1B1 Canada
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17
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Blatt P, Wong-Deyrup SW, McCarthy A, Breznak S, Hurton MD, Upadhyay M, Bennink B, Camacho J, Lee MT, Rangan P. RNA degradation is required for the germ-cell to maternal transition in Drosophila. Curr Biol 2021; 31:2984-2994.e7. [PMID: 33989522 PMCID: PMC8319052 DOI: 10.1016/j.cub.2021.04.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 03/26/2021] [Accepted: 04/20/2021] [Indexed: 10/21/2022]
Abstract
In sexually reproducing animals, the oocyte contributes a large supply of RNAs that are essential to launch development upon fertilization. The mechanisms that regulate the composition of the maternal RNA contribution during oogenesis are unclear. Here, we show that a subset of RNAs expressed during the early stages of oogenesis is subjected to regulated degradation during oocyte specification. Failure to remove these RNAs results in oocyte dysfunction and death. We identify the RNA-degrading Super Killer complex and No-Go Decay factor Pelota as key regulators of oogenesis via targeted degradation of specific RNAs expressed in undifferentiated germ cells. These regulators target RNAs enriched for cytidine sequences that are bound by the polypyrimidine tract binding protein Half pint. Thus, RNA degradation helps orchestrate a germ cell-to-maternal transition that gives rise to the maternal contribution to the zygote.
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Affiliation(s)
- Patrick Blatt
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222
| | - Siu Wah Wong-Deyrup
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222
| | - Alicia McCarthy
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222; 10x Genomics, Inc., 6230 Stoneridge Mall Road, Pleasanton, CA, 94588
| | - Shane Breznak
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222
| | - Matthew D Hurton
- University of Pittsburgh, Department of Biological Sciences; 4249 Fifth Avenue, Pittsburgh, PA 15260
| | - Maitreyi Upadhyay
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222; Department of Stem Cell and Regenerative Biology, Sherman Fairchild 100, Harvard University, 7 Divinity Avenue, Cambridge, MA 02138
| | - Benjamin Bennink
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222
| | - Justin Camacho
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222
| | - Miler T Lee
- University of Pittsburgh, Department of Biological Sciences; 4249 Fifth Avenue, Pittsburgh, PA 15260.
| | - Prashanth Rangan
- University at Albany, Department of Biological Sciences, RNA Institute; 1400 Washington Avenue, LSRB 2033D, Albany, NY 12222.
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18
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Molecular Targets and Associated Signaling Pathways of Jingshu Granules in Ovarian Cysts Based on Systemic Pharmacological Analysis. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6660087. [PMID: 33623786 PMCID: PMC7875638 DOI: 10.1155/2021/6660087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/09/2021] [Indexed: 11/18/2022]
Abstract
Background More than a third of women could develop ovarian cysts during their lifetime. Jingshu granules are used for the treatment of gynecological disease of primary dysmenorrhea. However, the molecular mechanisms of Jingshu granules in ovarian cysts are still unreported. We aimed to find the active ingredients, molecular targets, and potential signaling pathways of Jingshu granules in ovarian cysts by using the systemic pharmacological analysis. Methods Firstly, the effect of Jingshu granules on female hormones and reproductive organs of young female rats was evaluated. Secondly, candidate pharmaceutical ingredients of Jingshu granules were retrieved from the traditional Chinese medicine systems pharmacology (TCMSP) database and analysis platform. Potential protein targets for the active ingredients in Jingshu granules were then identified according to the oral bioavailability and drug-likeness indices. Thirdly, ovarian cyst-related gene targets were screened based on different databases. Finally, enrichment analysis was used to analyze the potential biological function of intersection targets between Jingshu granules and ovarian cysts. Results In young female rats, Jingshu granules reduced the secretion of estradiol, progesterone, and prolactin and could affect the development of the uterus. This suggested that Jingshu granules played roles in hormone secretion and reproduction. From the TCMSP, a total of 1021 pharmaceutical ingredients of Jingshu granules were retrieved. After further screening, a total of 166 active ingredients and 159 protein targets of Jingshu granules were identified. In addition, 4488 gene targets of ovarian cysts were screened out. After taking the intersection, a total of 110 intersection targets were identified between potential protein targets of Jingshu granules and gene targets of ovarian cysts. In the functional analysis of 110 intersection targets, 8 signaling pathways including progesterone-mediated oocyte maturation (MAPK8 and CDK1 involved), GnRH signaling pathway (JUN involved), T cell receptor signaling pathway and Toll-like receptor signaling pathway (MAPK1 involved), NOD-like receptor signaling pathway (TNF, IL6, and IL1B involved), p53 signaling pathway (CDK2 and CDK4 involved), VEGF signaling pathway (MAPK14 involved), and PPAR signaling pathway (PPARG involved) were obtained. Conclusion Our study revealed that Jingshu granules could function in patients with ovarian cysts through a number of molecular targets and signaling pathways. Our study may provide a new field into the mechanisms of Jingshu granules in ovarian cysts, from the molecular to the signaling pathway level.
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19
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Menzel J, Tatman P, Black JC. Isolation and analysis of rereplicated DNA by Rerep-Seq. Nucleic Acids Res 2020; 48:e58. [PMID: 32239215 PMCID: PMC7261181 DOI: 10.1093/nar/gkaa197] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/05/2020] [Accepted: 03/16/2020] [Indexed: 01/31/2023] Open
Abstract
Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities and adaptive potential. The origins of gene amplifications have remained elusive; however, DNA rereplication has been implicated as a source of gene amplifications. The inability to determine which sequences are rereplicated and under what conditions have made it difficult to determine the validity of the proposed models. Here we present Rerep-Seq, a technique that selectively enriches for rereplicated DNA in preparation for analysis by DNA sequencing that can be applied to any species. We validated Rerep-Seq by simulating DNA rereplication in yeast and human cells. Using Rerep-Seq, we demonstrate that rereplication induced in Saccharomyces cerevisiae by deregulated origin licensing is non-random and defined by broad domains that span multiple replication origins and topological boundaries.
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Affiliation(s)
- Johannes Menzel
- University of Colorado Anschutz Medical Campus, Department of Pharmacology, 12800 E 19th Ave, Aurora, CO 80045, USA.,University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, 12800 E 19th Ave, Aurora, CO 80045, USA
| | - Philip Tatman
- University of Colorado Anschutz Medical Campus, Department of Pharmacology, 12800 E 19th Ave, Aurora, CO 80045, USA.,University of Colorado Anschutz Medical Campus, Medical Scientist Training Program, 12800 E 19th Ave, Aurora, CO 80045, USA
| | - Joshua C Black
- University of Colorado Anschutz Medical Campus, Department of Pharmacology, 12800 E 19th Ave, Aurora, CO 80045, USA.,University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, 12800 E 19th Ave, Aurora, CO 80045, USA.,University of Colorado Anschutz Medical Campus, Medical Scientist Training Program, 12800 E 19th Ave, Aurora, CO 80045, USA
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20
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Santa-Cruz Mateos C, Valencia-Expósito A, Palacios IM, Martín-Bermudo MD. Integrins regulate epithelial cell shape by controlling the architecture and mechanical properties of basal actomyosin networks. PLoS Genet 2020; 16:e1008717. [PMID: 32479493 PMCID: PMC7263567 DOI: 10.1371/journal.pgen.1008717] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 03/16/2020] [Indexed: 01/01/2023] Open
Abstract
Forces generated by the actomyosin cytoskeleton are key contributors to many morphogenetic processes. The actomyosin cytoskeleton organises in different types of networks depending on intracellular signals and on cell-cell and cell-extracellular matrix (ECM) interactions. However, actomyosin networks are not static and transitions between them have been proposed to drive morphogenesis. Still, little is known about the mechanisms that regulate the dynamics of actomyosin networks during morphogenesis. This work uses the Drosophila follicular epithelium, real-time imaging, laser ablation and quantitative analysis to study the role of integrins on the regulation of basal actomyosin networks organisation and dynamics and the potential contribution of this role to cell shape. We find that elimination of integrins from follicle cells impairs F-actin recruitment to basal medial actomyosin stress fibers. The available F-actin redistributes to the so-called whip-like structures, present at tricellular junctions, and into a new type of actin-rich protrusions that emanate from the basal cortex and project towards the medial region. These F-actin protrusions are dynamic and changes in total protrusion area correlate with periodic cycles of basal myosin accumulation and constriction pulses of the cell membrane. Finally, we find that follicle cells lacking integrin function show increased membrane tension and reduced basal surface. Furthermore, the actin-rich protrusions are responsible for these phenotypes as their elimination in integrin mutant follicle cells rescues both tension and basal surface defects. We thus propose that the role of integrins as regulators of stress fibers plays a key role on controlling epithelial cell shape, as integrin disruption promotes reorganisation into other types of actomyosin networks, in a manner that interferes with proper expansion of epithelial basal surfaces. Morphogenesis involves global changes in tissue architecture driven by cell shape changes. Mechanical forces generated by actomyosin networks and force transmission through adhesive complexes power these changes. The actomyosin cytoskeleton organises in different types of networks, which localise to precise regions and perform distinct roles. However, they are rarely independent and, often, reorganisation of a given structure can promote the formation of another, conversions proposed to underlie many morphogenetic processes. Nonetheless, the mechanisms controlling actomyosin network dynamics during morphogenesis remain poorly characterised. Here, using the Drosophila follicular epithelium, we show that cell-ECM interactions mediated by integrins are required for the correct distribution of actin in the different actin networks. Elimination of integrins results in redistribution of actin from stress fibers into a new type of protrusions that dynamically emanate from the cortex and extend into the stress fibers. Changes in area protrusions correlate with bursts of myosin accumulated in stress fibers and constriction pulses of the cell membrane. We also found that integrin mutant cells show increased membrane tension and reduced basal cell surface. As these defects are rescued by eliminating the F-actin protrusions, we believe these structures prevent proper basal surface growth. Thus, we propose that integrin function as regulators of stress fibers assembly and maintenance controls epithelial cell shape, as its disruption promotes reorganisation into other actomyosin networks, conversions that interfere with proper epithelial basal surface expansion.
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Affiliation(s)
- Carmen Santa-Cruz Mateos
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Carretera de Utrera,Sevilla, Spain
| | - Andrea Valencia-Expósito
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Carretera de Utrera,Sevilla, Spain
| | - Isabel M. Palacios
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - María D. Martín-Bermudo
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide/CSIC/JA, Carretera de Utrera,Sevilla, Spain
- * E-mail:
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21
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Armstrong RL, Das S, Hill CA, Duronio RJ, Nordman JT. Rif1 Functions in a Tissue-Specific Manner To Control Replication Timing Through Its PP1-Binding Motif. Genetics 2020; 215:75-87. [PMID: 32144132 PMCID: PMC7198277 DOI: 10.1534/genetics.120.303155] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early- and late-replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.
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Affiliation(s)
- Robin L Armstrong
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Souradip Das
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232
| | - Christina A Hill
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Robert J Duronio
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, North Carolina 27599
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina 27599
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37232
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22
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McDaniel SL, Hollatz AJ, Branstad AM, Gaskill MM, Fox CA, Harrison MM. Tissue-Specific DNA Replication Defects in Drosophila melanogaster Caused by a Meier-Gorlin Syndrome Mutation in Orc4. Genetics 2020; 214:355-367. [PMID: 31818869 PMCID: PMC7017028 DOI: 10.1534/genetics.119.302938] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/05/2019] [Indexed: 02/07/2023] Open
Abstract
Meier-Gorlin syndrome is a rare recessive disorder characterized by a number of distinct tissue-specific developmental defects. Genes encoding members of the origin recognition complex (ORC) and additional proteins essential for DNA replication (CDC6, CDT1, GMNN, CDC45, MCM5, and DONSON) are mutated in individuals diagnosed with MGS. The essential role of ORC is to license origins during the G1 phase of the cell cycle, but ORC has also been implicated in several nonreplicative functions. Because of its essential role in DNA replication, ORC is required for every cell division during development. Thus, it is unclear how the Meier-Gorlin syndrome mutations in genes encoding ORC lead to the tissue-specific defects associated with the disease. To begin to address these issues, we used Cas9-mediated genome engineering to generate a Drosophila melanogaster model of individuals carrying a specific Meier-Gorlin syndrome mutation in ORC4 along with control strains. Together these strains provide the first metazoan model for an MGS mutation in which the mutation was engineered at the endogenous locus along with precisely defined control strains. Flies homozygous for the engineered MGS allele reach adulthood, but with several tissue-specific defects. Genetic analysis revealed that this Orc4 allele was a hypomorph. Mutant females were sterile, and phenotypic analyses suggested that defects in DNA replication was an underlying cause. By leveraging the well-studied Drosophila system, we provide evidence that a disease-causing mutation in Orc4 disrupts DNA replication, and we propose that in individuals with MGS defects arise preferentially in tissues with a high-replication demand.
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Affiliation(s)
- Stephen L McDaniel
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Allison J Hollatz
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Anna M Branstad
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Marissa M Gaskill
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Catherine A Fox
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
| | - Melissa M Harrison
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53706
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23
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Leiblich A, Hellberg JEEU, Sekar A, Gandy C, Mendes CC, Redhai S, Mason J, Wainwright M, Marie P, Goberdhan DCI, Hamdy FC, Wilson C. Mating induces switch from hormone-dependent to hormone-independent steroid receptor-mediated growth in Drosophila secondary cells. PLoS Biol 2019; 17:e3000145. [PMID: 31589603 PMCID: PMC6797231 DOI: 10.1371/journal.pbio.3000145] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 10/17/2019] [Accepted: 09/16/2019] [Indexed: 01/19/2023] Open
Abstract
Male reproductive glands like the mammalian prostate and the paired Drosophila melanogaster accessory glands secrete seminal fluid components that enhance fecundity. In humans, the prostate, stimulated by environmentally regulated endocrine and local androgens, grows throughout adult life. We previously showed that in fly accessory glands, secondary cells (SCs) and their nuclei also grow in adults, a process enhanced by mating and controlled by bone morphogenetic protein (BMP) signalling. Here, we demonstrate that BMP-mediated SC growth is dependent on the receptor for the developmental steroid ecdysone, whose concentration is reported to reflect sociosexual experience in adults. BMP signalling appears to regulate ecdysone receptor (EcR) levels via one or more mechanisms involving the EcR's N terminus or the RNA sequence that encodes it. Nuclear growth in virgin males is dependent on ecdysone, some of which is synthesised in SCs. However, mating induces additional BMP-mediated nuclear growth via a cell type-specific form of hormone-independent EcR signalling, which drives genome endoreplication in a subset of adult SCs. Switching to hormone-independent endoreplication after mating allows growth and secretion to be hyperactivated independently of ecdysone levels in SCs, permitting more rapid replenishment of the accessory gland luminal contents. Our data suggest mechanistic parallels between this physiological, behaviour-induced signalling switch and altered pathological signalling associated with prostate cancer progression.
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Affiliation(s)
- Aaron Leiblich
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | | | - Aashika Sekar
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Carina Gandy
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Claudia C. Mendes
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Siamak Redhai
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - John Mason
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Mark Wainwright
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Pauline Marie
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Deborah C. I. Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Freddie C. Hamdy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Clive Wilson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
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24
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Knapp EM, Li W, Sun J. Downregulation of homeodomain protein Cut is essential for Drosophila follicle maturation and ovulation. Development 2019; 146:dev179002. [PMID: 31444217 PMCID: PMC6765176 DOI: 10.1242/dev.179002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/19/2019] [Indexed: 01/19/2023]
Abstract
Proper development and maturation of a follicle is essential for successful ovulation and reproduction; however, the molecular mechanisms for follicle maturation, particularly for somatic follicle cell differentiation, are poorly understood. During Drosophila oogenesis, the somatic follicle cells encasing oocytes undergo two distinct well-established transitions: the mitotic to endocycle switch at stage 6/7 and the endocycle to gene amplification switch at stage10A/10B. Here, we identify a novel third follicle cell transition that occurs in the final stages of oogenesis (stage 13/14). This late follicle cell transition is characterized by upregulation of the transcription factor Hindsight (Hnt), and downregulation of the homeodomain transcription factor Cut and the zinc-finger transcription factor Tramtrack-69 (Ttk69). We demonstrate that inducing expression of Cut in stage 14 follicle cells is sufficient to inhibit follicle rupture and ovulation through its negative regulation of Hnt and promotion of Ttk69 expression. Our work illustrates the importance of the stage13/14 transition for follicle maturation and demonstrates the complex regulation required for somatic follicle cells to differentiate into a state primed for follicle rupture and ovulation.
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Affiliation(s)
- Elizabeth M Knapp
- Department of Physiology & Neurobiology, University of Connecticut, Storrs, CT 06269, USA
| | - Wei Li
- Department of Physiology & Neurobiology, University of Connecticut, Storrs, CT 06269, USA
| | - Jianjun Sun
- Department of Physiology & Neurobiology, University of Connecticut, Storrs, CT 06269, USA
- Institute for Systems Genomics, University of Connecticut, Storrs, CT 06269, USA
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25
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The Initial Stage of Tumorigenesis in Drosophila Epithelial Tissues. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019. [PMID: 31520350 DOI: 10.1007/978-3-030-23629-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Cancer development originates in a single mutant cell transformed from a normal cell, including further evolution of pro-tumor cells through additional mutations into malignant cancer tissues. Data from recent studies, however, suggest that most pro-tumor cells do not develop into tumors but remain dormant within or are prophylactically eliminated from tissues unless bestowed with additional driver mutations. Drosophila melanogaster has provided very efficient model systems, such as imaginal discs and ovarian follicular epithelia, to study the initial stage of tumorigenesis. This review will focus on the behaviors of emerging pro-tumor cells surrounded by normal cells and situations where they initiate tumor development.
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26
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Abstract
In all kingdoms of life, DNA is used to encode hereditary information. Propagation of the genetic material between generations requires timely and accurate duplication of DNA by semiconservative replication prior to cell division to ensure each daughter cell receives the full complement of chromosomes. DNA synthesis of daughter strands starts at discrete sites, termed replication origins, and proceeds in a bidirectional manner until all genomic DNA is replicated. Despite the fundamental nature of these events, organisms have evolved surprisingly divergent strategies that control replication onset. Here, we discuss commonalities and differences in replication origin organization and recognition in the three domains of life.
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Affiliation(s)
- Babatunde Ekundayo
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Franziska Bleichert
- Quantitative Biology, Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- * E-mail:
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27
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Rotelli MD, Policastro RA, Bolling AM, Killion AW, Weinberg AJ, Dixon MJ, Zentner GE, Walczak CE, Lilly MA, Calvi BR. A Cyclin A-Myb-MuvB-Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PLoS Genet 2019; 15:e1008253. [PMID: 31291240 PMCID: PMC6645565 DOI: 10.1371/journal.pgen.1008253] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 07/22/2019] [Accepted: 06/18/2019] [Indexed: 12/30/2022] Open
Abstract
Endoreplication is a cell cycle variant that entails cell growth and periodic genome duplication without cell division, and results in large, polyploid cells. Cells switch from mitotic cycles to endoreplication cycles during development, and also in response to conditional stimuli during wound healing, regeneration, aging, and cancer. In this study, we use integrated approaches in Drosophila to determine how mitotic cycles are remodeled into endoreplication cycles, and how similar this remodeling is between induced and developmental endoreplicating cells (iECs and devECs). Our evidence suggests that Cyclin A / CDK directly activates the Myb-MuvB (MMB) complex to induce transcription of a battery of genes required for mitosis, and that repression of CDK activity dampens this MMB mitotic transcriptome to promote endoreplication in both iECs and devECs. iECs and devECs differed, however, in that devECs had reduced expression of E2F1-dependent genes that function in S phase, whereas repression of the MMB transcriptome in iECs was sufficient to induce endoreplication without a reduction in S phase gene expression. Among the MMB regulated genes, knockdown of AurB protein and other subunits of the chromosomal passenger complex (CPC) induced endoreplication, as did knockdown of CPC-regulated cytokinetic, but not kinetochore, proteins. Together, our results indicate that the status of a CycA-Myb-MuvB-AurB network determines the decision to commit to mitosis or switch to endoreplication in both iECs and devECs, and suggest that regulation of different steps of this network may explain the known diversity of polyploid cycle types in development and disease.
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Affiliation(s)
- Michael D. Rotelli
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Robert A. Policastro
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Anna M. Bolling
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Andrew W. Killion
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Abraham J. Weinberg
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Michael J. Dixon
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Gabriel E. Zentner
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
| | - Claire E. Walczak
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Mary A. Lilly
- National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Brian R. Calvi
- Department of Biology. Indiana University, Bloomington, Indiana, United States of America
- Melvin and Bren Simon Cancer Center, Indianapolis, Indiana, United States of America
- Indiana University School of Medicine, Bloomington, Indiana, United States of America
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28
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Lo PK, Huang YC, Corcoran D, Jiao R, Deng WM. Inhibition of Notch signaling by the p105 and p180 subunits of Drosophila chromatin assembly factor 1 is required for follicle cell proliferation. J Cell Sci 2019; 132:jcs.224170. [PMID: 30630896 DOI: 10.1242/jcs.224170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 12/31/2018] [Indexed: 01/13/2023] Open
Abstract
Chromatin assembly factor 1 (CAF1), a histone chaperone that mediates the deposition of histone H3/H4 onto newly synthesized DNA, is involved in Notch signaling activation during Drosophila wing imaginal disc development. Here, we report another side of CAF1, wherein the subunits CAF1-p105 and CAF1-p180 (also known as CAF1-105 and CAF1-180, respectively) inhibit expression of Notch target genes and show this is required for proliferation of Drosophila ovarian follicle cells. Loss-of-function of either CAF1-p105 or CAF1-p180 caused premature activation of Notch signaling reporters and early expression of the Notch target Hindsight (Hnt, also known as Pebbled), leading to Cut downregulation and inhibition of follicle cell mitosis. Our studies further show Notch is functionally responsible for these phenotypes observed in both the CAF1-p105- and CAF1-p180-deficient follicle cells. Moreover, we reveal that CAF1-p105- and CAF1-p180-dependent Cut expression is essential for inhibiting Hnt expression in follicle cells during their mitotic stage. These findings together indicate a novel negative-feedback regulatory loop between Cut and Hnt underlying CAF1-p105 and CAF-p180 regulation, which is crucial for follicle cell differentiation. In conclusion, our studies suggest CAF1 plays a dual role to sustain cell proliferation by positively or negatively regulating Drosophila Notch signaling in a tissue-context-dependent manner.
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Affiliation(s)
- Pang-Kuo Lo
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yi-Chun Huang
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - David Corcoran
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Renjie Jiao
- Sino-French Hoffmann Institute, School of Basic Medical Sciences, Guangzhou Medical University, Dongfengxi Road 195, Guangzhou 510182, China.,The Second Affiliated Hospital of Guangzhou Medical University, Changgangdong Road 250, Guangzhou 510260, China
| | - Wu-Min Deng
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
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29
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Munden A, Rong Z, Sun A, Gangula R, Mallal S, Nordman JT. Rif1 inhibits replication fork progression and controls DNA copy number in Drosophila. eLife 2018; 7:39140. [PMID: 30277458 PMCID: PMC6185109 DOI: 10.7554/elife.39140] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/01/2018] [Indexed: 12/22/2022] Open
Abstract
Control of DNA copy number is essential to maintain genome stability and ensure proper cell and tissue function. In Drosophila polyploid cells, the SNF2-domain-containing SUUR protein inhibits replication fork progression within specific regions of the genome to promote DNA underreplication. While dissecting the function of SUUR's SNF2 domain, we identified an interaction between SUUR and Rif1. Rif1 has many roles in DNA metabolism and regulates the replication timing program. We demonstrate that repression of DNA replication is dependent on Rif1. Rif1 localizes to active replication forks in a partially SUUR-dependent manner and directly regulates replication fork progression. Importantly, SUUR associates with replication forks in the absence of Rif1, indicating that Rif1 acts downstream of SUUR to inhibit fork progression. Our findings uncover an unrecognized function of the Rif1 protein as a regulator of replication fork progression.
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Affiliation(s)
- Alexander Munden
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Zhan Rong
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Amanda Sun
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
| | - Rama Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, United States
| | - Simon Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, United States.,Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, United States
| | - Jared T Nordman
- Department of Biological Sciences, Vanderbilt University, Nashville, United States
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30
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Mendiratta S, Gatto A, Almouzni G. Histone supply: Multitiered regulation ensures chromatin dynamics throughout the cell cycle. J Cell Biol 2018; 218:39-54. [PMID: 30257851 PMCID: PMC6314538 DOI: 10.1083/jcb.201807179] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/05/2018] [Accepted: 09/12/2018] [Indexed: 12/14/2022] Open
Abstract
Mendiratta et al. review the interplay between the different regulatory layers that affect the transcription and dynamics of distinct histone H3 variants along the cell cycle. As the building blocks of chromatin, histones are central to establish and maintain particular chromatin states associated with given cell fates. Importantly, histones exist as distinct variants whose expression and incorporation into chromatin are tightly regulated during the cell cycle. During S phase, specialized replicative histone variants ensure the bulk of the chromatinization of the duplicating genome. Other non-replicative histone variants deposited throughout the cell cycle at specific loci use pathways uncoupled from DNA synthesis. Here, we review the particular dynamics of expression, cellular transit, assembly, and disassembly of replicative and non-replicative forms of the histone H3. Beyond the role of histone variants in chromatin dynamics, we review our current knowledge concerning their distinct regulation to control their expression at different levels including transcription, posttranscriptional processing, and protein stability. In light of this unique regulation, we highlight situations where perturbations in histone balance may lead to cellular dysfunction and pathologies.
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Affiliation(s)
- Shweta Mendiratta
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Alberto Gatto
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France.,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
| | - Genevieve Almouzni
- Institut Curie, Paris Sciences et Lettres Research University, Centre National de la Recherche Scientifique, UMR3664, Equipe Labellisée Ligue contre le Cancer, Paris, France .,Sorbonne Universités, Université Pierre et Marie Curie Paris 06, Centre National de la Recherche Scientifique, UMR3664, Paris, France
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31
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Guarner A, Morris R, Korenjak M, Boukhali M, Zappia MP, Van Rechem C, Whetstine JR, Ramaswamy S, Zou L, Frolov MV, Haas W, Dyson NJ. E2F/DP Prevents Cell-Cycle Progression in Endocycling Fat Body Cells by Suppressing dATM Expression. Dev Cell 2017; 43:689-703.e5. [PMID: 29233476 PMCID: PMC5901703 DOI: 10.1016/j.devcel.2017.11.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 08/28/2017] [Accepted: 11/07/2017] [Indexed: 10/18/2022]
Abstract
To understand the consequences of the complete elimination of E2F regulation, we profiled the proteome of Drosophila dDP mutants that lack functional E2F/DP complexes. The results uncovered changes in the larval fat body, a differentiated tissue that grows via endocycles. We report an unexpected mechanism of E2F/DP action that promotes quiescence in this tissue. In the fat body, dE2F/dDP limits cell-cycle progression by suppressing DNA damage responses. Loss of dDP upregulates dATM, allowing cells to sense and repair DNA damage and increasing replication of loci that are normally under-replicated in wild-type tissues. Genetic experiments show that ectopic dATM is sufficient to promote DNA synthesis in wild-type fat body cells. Strikingly, reducing dATM levels in dDP-deficient fat bodies restores cell-cycle control, improves tissue morphology, and extends animal development. These results show that, in some cellular contexts, dE2F/dDP-dependent suppression of DNA damage signaling is key for cell-cycle control and needed for normal development.
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Affiliation(s)
- Ana Guarner
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Robert Morris
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Michael Korenjak
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Myriam Boukhali
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Maria Paula Zappia
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Avenue, Chicago, IL 60607, USA
| | - Capucine Van Rechem
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Johnathan R Whetstine
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Sridhar Ramaswamy
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Lee Zou
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Maxim V Frolov
- Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, 900 S Ashland Avenue, Chicago, IL 60607, USA
| | - Wilhelm Haas
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA
| | - Nicholas J Dyson
- Massachusetts General Hospital Cancer Center and Harvard Medical School, Building 149 13(th) Street, Charlestown, MA 02129, USA.
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32
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DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression. Genetics 2017; 207:29-47. [PMID: 28874453 PMCID: PMC5586379 DOI: 10.1534/genetics.115.186627] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation.
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33
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Stormo BM, Fox DT. Polyteny: still a giant player in chromosome research. Chromosome Res 2017; 25:201-214. [PMID: 28779272 PMCID: PMC5768140 DOI: 10.1007/s10577-017-9562-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 07/19/2017] [Accepted: 07/21/2017] [Indexed: 12/17/2022]
Abstract
In this era of high-resolution mapping of chromosome territories, topological interactions, and chromatin states, it is increasingly appreciated that the positioning of chromosomes and their interactions within the nucleus is critical for cellular function. Due to their large size and distinctive structure, polytene chromosomes have contributed a wealth of knowledge regarding chromosome regulation. In this review, we discuss the diversity of polytene chromosomes in nature and in disease, examine the recurring structural features of polytene chromosomes in terms of what they reveal about chromosome biology, and discuss recent advances regarding how polytene chromosomes are assembled and disassembled. After over 130 years of study, these giant chromosomes are still powerful tools to understand chromosome biology.
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Affiliation(s)
- Benjamin M Stormo
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, NC, 27710, USA.
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34
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Rapid DNA Synthesis During Early Drosophila Embryogenesis Is Sensitive to Maternal Humpty Dumpty Protein Function. Genetics 2017; 207:935-947. [PMID: 28942426 DOI: 10.1534/genetics.117.300318] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 09/20/2017] [Indexed: 12/29/2022] Open
Abstract
Problems with DNA replication cause cancer and developmental malformations. It is not fully understood how DNA replication is coordinated with development and perturbed in disease. We had previously identified the Drosophila gene humpty dumpty (hd), and showed that null alleles cause incomplete DNA replication, tissue undergrowth, and lethality. Animals homozygous for the missense allele, hd272-9 , were viable, but adult females had impaired amplification of eggshell protein genes in the ovary, resulting in the maternal effects of thin eggshells and embryonic lethality. Here, we show that expression of an hd transgene in somatic cells of the ovary rescues amplification and eggshell synthesis but not embryo viability. The germline of these mothers remain mutant for the hd272-9 allele, resulting in reduced maternal Hd protein and embryonic arrest during mitosis of the first few S/M nuclear cleavage cycles with chromosome instability and chromosome bridges. Epistasis analysis of hd with the rereplication mutation plutonium indicates that the chromosome bridges of hd embryos are the result of a failed attempt to segregate incompletely replicated sister chromatids. This study reveals that maternally encoded Humpty dumpty protein is essential for DNA replication and genome integrity during the little-understood embryonic S/M cycles. Moreover, the two hd272-9 maternal-effect phenotypes suggest that ovarian gene amplification and embryonic cleavage are two time periods in development that are particularly sensitive to mild deficits in DNA replication function. This last observation has broader relevance for interpreting why mild mutations in the human ortholog of humpty dumpty and other DNA replication genes cause tissue-specific malformations of microcephalic dwarfisms.
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35
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Zhang C, Montooth KL, Calvi BR. Incompatibility between mitochondrial and nuclear genomes during oogenesis results in ovarian failure and embryonic lethality. Development 2017; 144:2490-2503. [PMID: 28576772 DOI: 10.1242/dev.151951] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/27/2017] [Indexed: 12/11/2022]
Abstract
Mitochondrial dysfunction can cause female infertility. An important unresolved issue is the extent to which incompatibility between mitochondrial and nuclear genomes contributes to female infertility. It has previously been shown that a mitochondrial haplotype from D. simulans (simw501 ) is incompatible with a nuclear genome from the D. melanogaster strain Oregon-R (OreR), resulting in impaired development, which was enhanced at higher temperature. This mito-nuclear incompatibility is between alleles of the nuclear-encoded mitochondrial tyrosyl-tRNA synthetase (Aatm) and the mitochondrial-encoded tyrosyl-tRNA that it aminoacylates. Here, we show that this mito-nuclear incompatibility causes a severe temperature-sensitive female infertility. The OreR nuclear genome contributed to death of ovarian germline stem cells and reduced egg production, which was further enhanced by the incompatibility with simw501 mitochondria. Mito-nuclear incompatibility also resulted in aberrant egg morphology and a maternal-effect on embryonic chromosome segregation and survival, which was completely dependent on the temperature and mito-nuclear genotype of the mother. Our findings show that maternal mito-nuclear incompatibility during Drosophila oogenesis has severe consequences for egg production and embryonic survival, with important broader relevance to human female infertility and mitochondrial replacement therapy.
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Affiliation(s)
- Chunyang Zhang
- Department of Biology, Indiana University Bloomington, IN 47401, USA
| | - Kristi L Montooth
- School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA
| | - Brian R Calvi
- Department of Biology, Indiana University Bloomington, IN 47401, USA
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36
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Teuscher M, Ströhlein N, Birkenbach M, Schultheis D, Schoppmeier M. TC003132 is essential for the follicle stem cell lineage in telotrophic Tribolium oogenesis. Front Zool 2017; 14:26. [PMID: 28533810 PMCID: PMC5438533 DOI: 10.1186/s12983-017-0212-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 05/11/2017] [Indexed: 12/31/2022] Open
Abstract
Background Stem cells are undifferentiated cells with a potential for self-renewal, which are essential to support normal development and homeostasis. To gain insight into the molecular mechanisms underlying adult stem cell biology and organ evolution, we use the telotrophic ovary of the beetle Tribolium. To this end, we participated in a large-scale RNAi screen in the red flour beetle Tribolium, which identified functions in embryonic and postembryonic development for more than half of the Tribolium genes. Results We identified TC003132 as candidate gene for the follicle stem cell linage in telotrophic Tribolium oogenesis. TC003132 belongs to the Casein Kinase 2 substrate family (CK2S), which in humans is associated with the proliferative activity of different cancers. Upon TC003132 RNAi, central pre-follicular cells are lost, which results in termination of oogenesis. Given that also Notch-signalling is required to promote the mitotic activity of central pre-follicular cells, we performed epistasis experiments with Notch and cut. In addition, we identified a putative follicle stem cell population by monitoring the mitotic pattern of wild type and TC003132 depleted follicle cells by EdU incorporations. In TC003132 RNAi these putative FSCs cease the expression of differentiation makers and are eventually lost. Conclusions TC003132 depleted pre-follicular cells neither react to mitosis or endocycle stimulating signals, suggesting that TC003132 provides competence for differentiation cues. This may resemble the situation in C. elegans were CK2 is required to maintain the balance between proliferation and differentiation in the germ line. Since the earliest effect of TC003132 RNAi is characterized by the loss of putative FSCs, we posit that TC003132 crucially contributes to the proliferation or maintenance of follicle stem cells in the telotrophic Tribolium ovary. Electronic supplementary material The online version of this article (doi:10.1186/s12983-017-0212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthias Teuscher
- Department Biology, Developmental Biology Unit, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Nadi Ströhlein
- Department Biology, Developmental Biology Unit, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Markus Birkenbach
- Department Biology, Developmental Biology Unit, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Germany
| | - Dorothea Schultheis
- Present address: Institute of Neuropathology, University Hospital Erlangen, Schwabachanlage 6, 91054 Erlangen, Germany
| | - Michael Schoppmeier
- Department Biology, Developmental Biology Unit, Friedrich-Alexander-University Erlangen-Nuremberg, Staudtstr. 5, 91058 Erlangen, Germany
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37
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Mensah LB, Goberdhan DCI, Wilson C. mTORC1 signalling mediates PI3K-dependent large lipid droplet accumulation in Drosophila ovarian nurse cells. Biol Open 2017; 6:563-570. [PMID: 28302666 PMCID: PMC5450313 DOI: 10.1242/bio.022210] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 03/15/2017] [Indexed: 01/15/2023] Open
Abstract
Insulin and insulin-like growth factor signalling (IIS), which is primarily mediated by the PI3-kinase (PI3K)/PTEN/Akt kinase signalling cassette, is a highly evolutionarily conserved pathway involved in co-ordinating growth, development, ageing and nutrient homeostasis with dietary intake. It controls transcriptional regulators, in addition to promoting signalling by mechanistic target of rapamycin (mTOR) complex 1 (mTORC1), which stimulates biosynthesis of proteins and other macromolecules, and drives organismal growth. Previous studies in nutrient-storing germline nurse cells of the Drosophila ovary showed that a cytoplasmic pool of activated phosphorylated Akt (pAkt) controlled by Pten, an antagonist of IIS, cell-autonomously regulates accumulation of large lipid droplets in these cells at late stages of oogenesis. Here, we show that the large lipid droplet phenotype induced by Pten mutation is strongly suppressed when mTor function is removed. Furthermore, nurse cells lacking either Tsc1 or Tsc2, which negatively regulate mTORC1 activity, also accumulate large lipid droplets via a mechanism involving Rheb, the downstream G-protein target of TSC2, which positively regulates mTORC1. We conclude that elevated IIS/mTORC1 signalling is both necessary and sufficient to induce large lipid droplet formation in late-stage nurse cells, suggesting roles for this pathway in aspects of lipid droplet biogenesis, in addition to control of lipid metabolism.
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Affiliation(s)
- Lawrence B Mensah
- Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA
| | - Deborah C I Goberdhan
- Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
| | - Clive Wilson
- Department of Physiology, Anatomy and Genetics, University of Oxford, Le Gros Clark Building, South Parks Road, Oxford OX1 3QX, UK
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Abstract
Ongoing work shows that misplaced epithelial cells have the capacity to reintegrate back into tissue layers. This movement appears to underlie tissue stability and may also control aspects of tissue structure. A recent study reveals that cell reintegration in at least one tissue, the Drosophila follicular epithelium, is based on adhesion molecules that line lateral cell surfaces. In this article we will review these observations, discuss their implications for epithelial tissue development and maintenance, and identify future directions for study.
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Affiliation(s)
- Tyler J Wilson
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Dan T Bergstralh
- Department of Biology, University of Rochester, Rochester, NY, USA
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39
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Duhart JC, Parsons TT, Raftery LA. The repertoire of epithelial morphogenesis on display: Progressive elaboration of Drosophila egg structure. Mech Dev 2017; 148:18-39. [PMID: 28433748 DOI: 10.1016/j.mod.2017.04.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 04/07/2017] [Accepted: 04/12/2017] [Indexed: 12/26/2022]
Abstract
Epithelial structures are foundational for tissue organization in all metazoans. Sheets of epithelial cells form lateral adhesive junctions and acquire apico-basal polarity perpendicular to the surface of the sheet. Genetic analyses in the insect model, Drosophila melanogaster, have greatly advanced our understanding of how epithelial organization is established, and how it is modulated during tissue morphogenesis. Major insights into collective cell migrations have come from analyses of morphogenetic movements within the adult follicular epithelium that cooperates with female germ cells to build a mature egg. Epithelial follicle cells progress through tightly choreographed phases of proliferation, patterning, reorganization and migrations, before they differentiate to form the elaborate structures of the eggshell. Distinct structural domains are organized by differential adhesion, within which lateral junctions are remodeled to further shape the organized epithelia. During collective cell migrations, adhesive interactions mediate supracellular organization of planar polarized macromolecules, and facilitate crawling over the basement membrane or traction against adjacent cell surfaces. Comparative studies with other insects are revealing the diversification of morphogenetic movements for elaboration of epithelial structures. This review surveys the repertoire of follicle cell morphogenesis, to highlight the coordination of epithelial plasticity with progressive differentiation of a secretory epithelium. Technological advances will keep this tissue at the leading edge for interrogating the precise spatiotemporal regulation of normal epithelial reorganization events, and provide a framework for understanding pathological tissue dysplasia.
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Affiliation(s)
- Juan Carlos Duhart
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4004, United States
| | - Travis T Parsons
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4004, United States
| | - Laurel A Raftery
- School of Life Sciences, University of Nevada, Las Vegas, 4505 S. Maryland Parkway, Las Vegas, NV 89154-4004, United States.
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40
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Sekelsky J. DNA Repair in Drosophila: Mutagens, Models, and Missing Genes. Genetics 2017; 205:471-490. [PMID: 28154196 PMCID: PMC5289830 DOI: 10.1534/genetics.116.186759] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/18/2016] [Indexed: 12/22/2022] Open
Abstract
The numerous processes that damage DNA are counterbalanced by a complex network of repair pathways that, collectively, can mend diverse types of damage. Insights into these pathways have come from studies in many different organisms, including Drosophila melanogaster Indeed, the first ideas about chromosome and gene repair grew out of Drosophila research on the properties of mutations produced by ionizing radiation and mustard gas. Numerous methods have been developed to take advantage of Drosophila genetic tools to elucidate repair processes in whole animals, organs, tissues, and cells. These studies have led to the discovery of key DNA repair pathways, including synthesis-dependent strand annealing, and DNA polymerase theta-mediated end joining. Drosophila appear to utilize other major repair pathways as well, such as base excision repair, nucleotide excision repair, mismatch repair, and interstrand crosslink repair. In a surprising number of cases, however, DNA repair genes whose products play important roles in these pathways in other organisms are missing from the Drosophila genome, raising interesting questions for continued investigations.
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Affiliation(s)
- Jeff Sekelsky
- Department of Biology and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, North Carolina 27599
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41
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Duronio RJ, Marzluff WF. Coordinating cell cycle-regulated histone gene expression through assembly and function of the Histone Locus Body. RNA Biol 2017; 14:726-738. [PMID: 28059623 DOI: 10.1080/15476286.2016.1265198] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Metazoan replication-dependent (RD) histone genes encode the only known cellular mRNAs that are not polyadenylated. These mRNAs end instead in a conserved stem-loop, which is formed by an endonucleolytic cleavage of the pre-mRNA. The genes for all 5 histone proteins are clustered in all metazoans and coordinately regulated with high levels of expression during S phase. Production of histone mRNAs occurs in a nuclear body called the Histone Locus Body (HLB), a subdomain of the nucleus defined by a concentration of factors necessary for histone gene transcription and pre-mRNA processing. These factors include the scaffolding protein NPAT, essential for histone gene transcription, and FLASH and U7 snRNP, both essential for histone pre-mRNA processing. Histone gene expression is activated by Cyclin E/Cdk2-mediated phosphorylation of NPAT at the G1-S transition. The concentration of factors within the HLB couples transcription with pre-mRNA processing, enhancing the efficiency of histone mRNA biosynthesis.
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Affiliation(s)
- Robert J Duronio
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,b Department of Genetics , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA
| | - William F Marzluff
- a Department of Biology , University of North Carolina , Chapel Hill , NC , USA.,c Integrative Program for Biological and Genome Sciences , University of North Carolina , Chapel Hill , NC , USA.,d Lineberger Comprehensive Cancer Center , University of North Carolina , Chapel Hill , NC , USA.,e Department of Biochemistry and Biophysics , University of North Carolina , Chapel Hill , NC , USA
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Multiple mechanisms contribute to double-strand break repair at rereplication forks in Drosophila follicle cells. Proc Natl Acad Sci U S A 2016; 113:13809-13814. [PMID: 27849606 DOI: 10.1073/pnas.1617110113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Rereplication generates double-strand breaks (DSBs) at sites of fork collisions and causes genomic damage, including repeat instability and chromosomal aberrations. However, the primary mechanism used to repair rereplication DSBs varies across different experimental systems. In Drosophila follicle cells, developmentally regulated rereplication is used to amplify six genomic regions, two of which contain genes encoding eggshell proteins. We have exploited this system to test the roles of several DSB repair pathways during rereplication, using fork progression as a readout for DSB repair efficiency. Here we show that a null mutation in the microhomology-mediated end-joining (MMEJ) component, polymerase θ/mutagen-sensitive 308 (mus308), exhibits a sporadic thin eggshell phenotype and reduced chorion gene expression. Unlike other thin eggshell mutants, mus308 displays normal origin firing but reduced fork progression at two regions of rereplication. We also find that MMEJ compensates for loss of nonhomologous end joining to repair rereplication DSBs in a site-specific manner. Conversely, we show that fork progression is enhanced in the absence of both Drosophila Rad51 homologs, spindle-A and spindle-B, revealing homologous recombination is active and actually impairs fork movement during follicle cell rereplication. These results demonstrate that several DSB repair pathways are used during rereplication in the follicle cells and their contribution to productive fork progression is influenced by genomic position and repair pathway competition. Furthermore, our findings illustrate that specific rereplication DSB repair pathways can have major effects on cellular physiology, dependent upon genomic context.
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The Histone Variant H3.3 Is Enriched at Drosophila Amplicon Origins but Does Not Mark Them for Activation. G3-GENES GENOMES GENETICS 2016; 6:1661-71. [PMID: 27172191 PMCID: PMC4889662 DOI: 10.1534/g3.116.028068] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Eukaryotic DNA replication begins from multiple origins. The origin recognition complex (ORC) binds origin DNA and scaffolds assembly of a prereplicative complex (pre-RC), which is subsequently activated to initiate DNA replication. In multicellular eukaryotes, origins do not share a strict DNA consensus sequence, and their activity changes in concert with chromatin status during development, but mechanisms are ill-defined. Previous genome-wide analyses in Drosophila and other organisms have revealed a correlation between ORC binding sites and the histone variant H3.3. This correlation suggests that H3.3 may designate origin sites, but this idea has remained untested. To address this question, we examined the enrichment and function of H3.3 at the origins responsible for developmental gene amplification in the somatic follicle cells of the Drosophila ovary. We found that H3.3 is abundant at these amplicon origins. H3.3 levels remained high when replication initiation was blocked, indicating that H3.3 is abundant at the origins before activation of the pre-RC. H3.3 was also enriched at the origins during early oogenesis, raising the possibility that H3.3 bookmarks sites for later amplification. However, flies null mutant for both of the H3.3 genes in Drosophila did not have overt defects in developmental gene amplification or genomic replication, suggesting that H3.3 is not essential for the assembly or activation of the pre-RC at origins. Instead, our results imply that the correlation between H3.3 and ORC sites reflects other chromatin attributes that are important for origin function.
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Aughey GN, Grice SJ, Liu JL. The Interplay between Myc and CTP Synthase in Drosophila. PLoS Genet 2016; 12:e1005867. [PMID: 26889675 PMCID: PMC4759343 DOI: 10.1371/journal.pgen.1005867] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 01/23/2016] [Indexed: 01/24/2023] Open
Abstract
CTP synthase (CTPsyn) is essential for the biosynthesis of pyrimidine nucleotides. It has been shown that CTPsyn is incorporated into a novel cytoplasmic structure which has been termed the cytoophidium. Here, we report that Myc regulates cytoophidium formation during Drosophila oogenesis. We have found that Myc protein levels correlate with cytoophidium abundance in follicle epithelia. Reducing Myc levels results in cytoophidium loss and small nuclear size in follicle cells, while overexpression of Myc increases the length of cytoophidia and the nuclear size of follicle cells. Ectopic expression of Myc induces cytoophidium formation in late stage follicle cells. Furthermore, knock-down of CTPsyn is sufficient to suppress the overgrowth phenotype induced by Myc overexpression, suggesting CTPsyn acts downstream of Myc and is required for Myc-mediated cell size control. Taken together, our data suggest a functional link between Myc, a renowned oncogene, and the essential nucleotide biosynthetic enzyme CTPsyn. The coordination of metabolism with cell growth is critical for regulation of organismal development. Therefore there is significant interplay between metabolic enzymes and key developmental regulators such as transcription factors. The enzyme CTP synthase (CTPsyn) is essential for metabolic homeostasis as well as growth and development, due to its role in synthesising precursors for many fundamental cellular macromolecules such as RNA and lipids. However, the mechanisms by which CTPsyn is regulated during development are little understood. Here we have shown that Myc, an oncogene and a key developmental regulator, is necessary and sufficient for the assembly of CTPsyn-containing macrostructures termed cytoophidia. We show that the presence of CTPsyn is required for Myc to mediate its effect on cell growth during Drosophila oogenesis. Roles for CTPsyn and Myc in tumourigenesis have been well established and both proteins have been considered promising therapeutic targets. By better understanding the relationship between these two proteins, we can gain important insights, not only into tumour pathology and aetiology, but also metazoan developmental processes.
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Affiliation(s)
- Gabriel N. Aughey
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Stuart J. Grice
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Ji-Long Liu
- MRC Functional Genomics Unit, Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Fischer U, Backes C, Raslan A, Keller A, Meier C, Meese E. Gene amplification during differentiation of mammalian neural stem cells in vitro and in vivo. Oncotarget 2016; 6:7023-39. [PMID: 25760141 PMCID: PMC4466667 DOI: 10.18632/oncotarget.3248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/28/2015] [Indexed: 11/25/2022] Open
Abstract
In development of amphibians and flies, gene amplification is one of mechanisms to increase gene expression. In mammalian cells, gene amplification seems to be restricted to tumorigenesis and acquiring of drug-resistance in cancer cells. Here, we report a complex gene amplification pattern in mouse neural progenitor cells during differentiation with approximately 10% of the genome involved. Half of the amplified mouse chromosome regions overlap with amplified regions previously reported in human neural progenitor cells, indicating conserved mechanisms during differentiation. Using fluorescence in situ hybridization, we verified the amplification in single cells of primary mouse mesencephalon E14 (embryonic stage) neurosphere cells during differentiation. In vivo we confirmed gene amplifications of the TRP53 gene in cryosections from mouse embryos at stage E11.5. Gene amplification is not only a cancer-related mechanism but is also conserved in evolution, occurring during differentiation of mammalian neural stem cells
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Affiliation(s)
- Ulrike Fischer
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
| | - Christina Backes
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany.,Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Abdulrahman Raslan
- Department of Anatomy and Cell Biology, Saarland University, 66421 Homburg/Saar, Germany
| | - Andreas Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Carola Meier
- Department of Anatomy and Cell Biology, Saarland University, 66421 Homburg/Saar, Germany
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Homburg/Saar, Germany
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Romani P, Gargiulo G, Cavaliere V. The ecdysone receptor signalling regulates microvilli formation in follicular epithelial cells. Cell Mol Life Sci 2016; 73:409-25. [PMID: 26223269 PMCID: PMC11108565 DOI: 10.1007/s00018-015-1999-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 07/03/2015] [Accepted: 07/22/2015] [Indexed: 11/27/2022]
Abstract
Epithelial morphogenesis contributes greatly to the development and homeostasis of the organs and body parts. Here, we analysed the consequences of impaired ecdysone receptor (EcR) signalling in the Drosophila follicular epithelium. Besides governing cell growth, the three EcR isoforms act redundantly in controlling follicle cell positioning. Flattening of the microvilli and an aberrant actin cytoskeleton arise from defective EcR signalling in follicle cells, and these defects impact on the organisation of the oocyte membrane. We found that this signalling governs a complex molecular network since its impairment affects key molecules as atypical protein kinase C and activated Moesin. Interestingly, the activity of the transcription factor Tramtrack69 isoform is required for microvilli and their actin core morphogenesis as well as for follicle cell positioning. In conclusion, our findings provide evidence of novel roles for EcR signalling and Tramtrack69 transcription factor in controlling stage-specific differentiation events that take place in the follicular epithelium.
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Affiliation(s)
- Patrizia Romani
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, Via Selmi, 3, 40126, Bologna, Italy.
| | - Giuseppe Gargiulo
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, Via Selmi, 3, 40126, Bologna, Italy
| | - Valeria Cavaliere
- Dipartimento di Farmacia e Biotecnologie, FaBiT, Università di Bologna, Via Selmi, 3, 40126, Bologna, Italy.
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Swanson CI, Meserve JH, McCarter PC, Thieme A, Mathew T, Elston TC, Duronio RJ. Expression of an S phase-stabilized version of the CDK inhibitor Dacapo can alter endoreplication. Development 2015; 142:4288-98. [PMID: 26493402 DOI: 10.1242/dev.115006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 10/12/2015] [Indexed: 01/01/2023]
Abstract
In developing organisms, divergence from the canonical cell division cycle is often necessary to ensure the proper growth, differentiation, and physiological function of a variety of tissues. An important example is endoreplication, in which endocycling cells alternate between G and S phase without intervening mitosis or cytokinesis, resulting in polyploidy. Although significantly different from the canonical cell cycle, endocycles use regulatory pathways that also function in diploid cells, particularly those involved in S phase entry and progression. A key S phase regulator is the Cyclin E-Cdk2 kinase, which must alternate between periods of high (S phase) and low (G phase) activity in order for endocycling cells to achieve repeated rounds of S phase and polyploidy. The mechanisms that drive these oscillations of Cyclin E-Cdk2 activity are not fully understood. Here, we show that the Drosophila Cyclin E-Cdk2 inhibitor Dacapo (Dap) is targeted for destruction during S phase via a PIP degron, contributing to oscillations of Dap protein accumulation during both mitotic cycles and endocycles. Expression of a PIP degron mutant Dap attenuates endocycle progression but does not obviously affect proliferating diploid cells. A mathematical model of the endocycle predicts that the rate of destruction of Dap during S phase modulates the endocycle by regulating the length of G phase. We propose from this model and our in vivo data that endo S phase-coupled destruction of Dap reduces the threshold of Cyclin E-Cdk2 activity necessary to trigger the subsequent G-S transition, thereby influencing endocycle oscillation frequency and the extent of polyploidy.
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Affiliation(s)
- Christina I Swanson
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joy H Meserve
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Patrick C McCarter
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Alexis Thieme
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Tony Mathew
- Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Timothy C Elston
- Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, NC 27599, USA Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC 27599, USA Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC 27599, USA Department of Biology, University of North Carolina, Chapel Hill, NC 27599, USA Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
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Regulation of CTP Synthase Filament Formation During DNA Endoreplication in Drosophila. Genetics 2015; 201:1511-23. [PMID: 26482795 DOI: 10.1534/genetics.115.180737] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Accepted: 10/13/2015] [Indexed: 12/20/2022] Open
Abstract
CTP synthase (CTPsyn) plays an essential role in DNA, RNA, and lipid synthesis. Recent studies in bacteria, yeast, and Drosophila all reveal a polymeric CTPsyn structure, which dynamically regulates its enzymatic activity. However, the molecular mechanism underlying the formation of CTPsyn polymers is not completely understood. In this study, we found that reversible ubiquitination regulates the dynamic assembly of the filamentous structures of Drosophila CTPsyn. We further determined that the proto-oncogene Cbl, an E3 ubiquitin ligase, controls CTPsyn filament formation in endocycles. While the E3 ligase activity of Cbl is required for CTPsyn filament formation, Cbl does not affect the protein levels of CTPsyn. It remains unclear whether the regulation of CTPsyn filaments by Cbl is through direct ubiquitination of CTPsyn. In the absence of Cbl or with knockdown of CTPsyn, the progression of the endocycle-associated S phase was impaired. Furthermore, overexpression of wild-type, but not enzymatically inactive CTPsyn, rescued the endocycle defect in Cbl mutant cells. Together, these results suggest that Cbl influences the nucleotide pool balance and controls CTPsyn filament formation in endocycles. This study links Cbl-mediated ubiquitination to the polymerization of a metabolic enzyme and reveals a role for Cbl in endocycles during Drosophila development.
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Tatomer DC, Rizzardi LF, Curry KP, Witkowski AM, Marzluff WF, Duronio RJ. Drosophila Symplekin localizes dynamically to the histone locus body and tricellular junctions. Nucleus 2015; 5:613-25. [PMID: 25493544 DOI: 10.4161/19491034.2014.990860] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The scaffolding protein Symplekin is part of multiple complexes involved in generating and modifying the 3' end of mRNAs, including cleavage-polyadenylation, histone pre-mRNA processing and cytoplasmic polyadenylation. To study these functions in vivo, we examined the localization of Symplekin during development and generated mutations of the Drosophila Symplekin gene. Mutations in Symplekin that reduce Symplekin protein levels alter the efficiency of both poly A(+) and histone mRNA 3' end formation resulting in lethality or sterility. Histone mRNA synthesis takes place at the histone locus body (HLB) and requires a complex composed of Symplekin and several polyadenylation factors that associates with the U7 snRNP. Symplekin is present in the HLB in the early embryo when Cyclin E/Cdk2 is active and histone genes are expressed and is absent from the HLB in cells that have exited the cell cycle. During oogenesis, Symplekin is preferentially localized to HLBs during S-phase in endoreduplicating follicle cells when histone mRNA is synthesized. After the completion of endoreplication, Symplekin accumulates in the cytoplasm, in addition to the nucleoplasm, and localizes to tricellular junctions of the follicle cell epithelium. This localization depends on the RNA binding protein ypsilon schachtel. CPSF-73 and a number of mRNAs are localized at this same site, suggesting that Symplekin participates in cytoplasmic polyadenylation at tricellular junctions.
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Key Words
- CTD, RNA polymerase II C-terminal domain
- Drosophila
- HCC, histone cleavage complex
- HDE, histone downstream element
- HLB, histone locus body
- Madm, MLF1-adaptor molecule
- PAP, poly (A) polymerase
- PAS, poly A signal
- RNA processing, Symplekin
- Rp49, ribosomal protein L32
- SL, stem loop
- SLBP, stem loop binding protein
- Sym, Symplekin
- cas, castor
- gene expression
- histone mRNA
- nuclear bodies
- sop, ribosomal protein S2
- yps, ypsilon schachtel
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Affiliation(s)
- Deirdre C Tatomer
- a Department of Biology ; University of North Carolina ; Chapel Hill , NC USA
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50
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Liu J, Zimmer K, Rusch DB, Paranjape N, Podicheti R, Tang H, Calvi BR. DNA sequence templates adjacent nucleosome and ORC sites at gene amplification origins in Drosophila. Nucleic Acids Res 2015; 43:8746-61. [PMID: 26227968 PMCID: PMC4605296 DOI: 10.1093/nar/gkv766] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/16/2015] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic origins of DNA replication are bound by the origin recognition complex (ORC), which scaffolds assembly of a pre-replicative complex (pre-RC) that is then activated to initiate replication. Both pre-RC assembly and activation are strongly influenced by developmental changes to the epigenome, but molecular mechanisms remain incompletely defined. We have been examining the activation of origins responsible for developmental gene amplification in Drosophila. At a specific time in oogenesis, somatic follicle cells transition from genomic replication to a locus-specific replication from six amplicon origins. Previous evidence indicated that these amplicon origins are activated by nucleosome acetylation, but how this affects origin chromatin is unknown. Here, we examine nucleosome position in follicle cells using micrococcal nuclease digestion with Ilumina sequencing. The results indicate that ORC binding sites and other essential origin sequences are nucleosome-depleted regions (NDRs). Nucleosome position at the amplicons was highly similar among developmental stages during which ORC is or is not bound, indicating that being an NDR is not sufficient to specify ORC binding. Importantly, the data suggest that nucleosomes and ORC have opposite preferences for DNA sequence and structure. We propose that nucleosome hyperacetylation promotes pre-RC assembly onto adjacent DNA sequences that are disfavored by nucleosomes but favored by ORC.
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Affiliation(s)
- Jun Liu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kurt Zimmer
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Douglas B Rusch
- Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Neha Paranjape
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Ram Podicheti
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47405, USA
| | - Haixu Tang
- School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA
| | - Brian R Calvi
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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