1
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Bayer LV, Milano SN, Bratu DP. The mRNA dynamics underpinning translational control mechanisms of Drosophila melanogaster oogenesis. Biochem Soc Trans 2024:BST20231293. [PMID: 39263986 DOI: 10.1042/bst20231293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 08/20/2024] [Accepted: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Advances in the study of mRNAs have yielded major new insights into post-transcriptional control of gene expression. Focus on the spatial regulation of mRNAs in highly polarized cells has demonstrated that mRNAs translocate through cells as mRNA:protein granules (mRNPs). These complex self-assemblies containing nuclear and cytoplasmic proteins are fundamental to the coordinated translation throughout cellular development. Initial studies on translational control necessitated fixed tissue, but the last 30 years have sparked innovative live-cell studies in several cell types to deliver a far more nuanced picture of how mRNA-protein dynamics exert translational control. In this review, we weave together the events that underpin mRNA processes and showcase the pivotal studies that revealed how a multitude of protein factors engage with a transcript. We highlight a mRNA's ability to act as a 'super scaffold' to facilitate molecular condensate formation and further moderate translational control. We focus on the Drosophila melanogaster germline due to the extensive post-transcriptional regulation occurring during early oogenesis. The complexity of the spatio-temporal expression of maternal transcripts in egg chambers allows for the exploration of a wide range of mechanisms that are crucial to the life cycle of mRNAs.
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Affiliation(s)
- Livia V Bayer
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
| | - Samantha N Milano
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Program in Molecular, Cellular and Developmental Biology, The Graduate Center, City University of New York, New York, NY 10016, USA
| | - Diana P Bratu
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065, USA
- Program in Molecular, Cellular and Developmental Biology, The Graduate Center, City University of New York, New York, NY 10016, USA
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2
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Chekulaeva M. Mechanistic insights into the basis of widespread RNA localization. Nat Cell Biol 2024; 26:1037-1046. [PMID: 38956277 DOI: 10.1038/s41556-024-01444-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/20/2024] [Indexed: 07/04/2024]
Abstract
The importance of subcellular mRNA localization is well established, but the underlying mechanisms mostly remain an enigma. Early studies suggested that specific mRNA sequences recruit RNA-binding proteins (RBPs) to regulate mRNA localization. However, despite the observation of thousands of localized mRNAs, only a handful of these sequences and RBPs have been identified. This suggests the existence of alternative, and possibly predominant, mechanisms for mRNA localization. Here I re-examine currently described mRNA localization mechanisms and explore alternative models that could account for its widespread occurrence.
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Affiliation(s)
- Marina Chekulaeva
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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3
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Otis JP, Mowry KL. Hitting the mark: Localization of mRNA and biomolecular condensates in health and disease. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1807. [PMID: 37393916 PMCID: PMC10758526 DOI: 10.1002/wrna.1807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/29/2023] [Accepted: 06/06/2023] [Indexed: 07/04/2023]
Abstract
Subcellular mRNA localization is critical to a multitude of biological processes such as development of cellular polarity, embryogenesis, tissue differentiation, protein complex formation, cell migration, and rapid responses to environmental stimuli and synaptic depolarization. Our understanding of the mechanisms of mRNA localization must now be revised to include formation and trafficking of biomolecular condensates, as several biomolecular condensates that transport and localize mRNA have recently been discovered. Disruptions in mRNA localization can have catastrophic effects on developmental processes and biomolecular condensate biology and have been shown to contribute to diverse diseases. A fundamental understanding of mRNA localization is essential to understanding how aberrations in this biology contribute the etiology of numerous cancers though support of cancer cell migration and biomolecular condensate dysregulation, as well as many neurodegenerative diseases, through misregulation of mRNA localization and biomolecular condensate biology. This article is categorized under: RNA Export and Localization > RNA Localization RNA in Disease and Development > RNA in Disease RNA in Disease and Development > RNA in Development.
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Affiliation(s)
- Jessica P. Otis
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
| | - Kimberly L. Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI, United States, 02912
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4
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Abstract
By the time a Drosophila egg is laid, both major body axes have already been defined and it contains all the nutrients needed to develop into a free-living larva in 24 h. By contrast, it takes almost a week to make an egg from a female germline stem cell, during the complex process of oogenesis. This review will discuss key symmetry-breaking steps in Drosophila oogenesis that lead to the polarisation of both body axes: the asymmetric divisions of the germline stem cells; the selection of the oocyte from the 16-cell germline cyst; the positioning of the oocyte at the posterior of the cyst; Gurken signalling from the oocyte to polarise the anterior-posterior axis of the somatic follicle cell epithelium around the developing germline cyst; the signalling back from the posterior follicle cells to polarise the anterior-posterior axis of the oocyte; and the migration of the oocyte nucleus that specifies the dorsal-ventral axis. Since each event creates the preconditions for the next, I will focus on the mechanisms that drive these symmetry-breaking steps, how they are linked and the outstanding questions that remain to be answered.
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5
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Tingey M, Schnell SJ, Yu W, Saredy J, Junod S, Patel D, Alkurdi AA, Yang W. Technologies Enabling Single-Molecule Super-Resolution Imaging of mRNA. Cells 2022; 11:3079. [PMID: 36231040 PMCID: PMC9564294 DOI: 10.3390/cells11193079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/22/2022] [Accepted: 09/28/2022] [Indexed: 11/16/2022] Open
Abstract
The transient nature of RNA has rendered it one of the more difficult biological targets for imaging. This difficulty stems both from the physical properties of RNA as well as the temporal constraints associated therewith. These concerns are further complicated by the difficulty in imaging endogenous RNA within a cell that has been transfected with a target sequence. These concerns, combined with traditional concerns associated with super-resolution light microscopy has made the imaging of this critical target difficult. Recent advances have provided researchers the tools to image endogenous RNA in live cells at both the cellular and single-molecule level. Here, we review techniques used for labeling and imaging RNA with special emphases on various labeling methods and a virtual 3D super-resolution imaging technique.
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Affiliation(s)
| | | | | | | | | | | | | | - Weidong Yang
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
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6
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Milas A, Telley IA. Polarity Events in the Drosophila melanogaster Oocyte. Front Cell Dev Biol 2022; 10:895876. [PMID: 35602591 PMCID: PMC9117655 DOI: 10.3389/fcell.2022.895876] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 04/19/2022] [Indexed: 11/13/2022] Open
Abstract
Cell polarity is a pre-requirement for many fundamental processes in animal cells, such as asymmetric cell division, axon specification, morphogenesis and epithelial tissue formation. For all these different processes, polarization is established by the same set of proteins, called partitioning defective (Par) proteins. During development in Drosophila melanogaster, decision making on the cellular and organism level is achieved with temporally controlled cell polarization events. The initial polarization of Par proteins occurs as early as in the germline cyst, when one of the 16 cells becomes the oocyte. Another marked event occurs when the anterior–posterior axis of the future organism is defined by Par redistribution in the oocyte, requiring external signaling from somatic cells. Here, we review the current literature on cell polarity events that constitute the oogenesis from the stem cell to the mature egg.
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Affiliation(s)
- Ana Milas
- *Correspondence: Ana Milas, ; Ivo A. Telley,
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7
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Lu W, Lakonishok M, Serpinskaya AS, Gelfand VI. A novel mechanism of bulk cytoplasmic transport by cortical dynein in Drosophila ovary. eLife 2022; 11:e75538. [PMID: 35170428 PMCID: PMC8896832 DOI: 10.7554/elife.75538] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 02/16/2022] [Indexed: 11/22/2022] Open
Abstract
Cytoplasmic dynein, a major minus-end directed microtubule motor, plays essential roles in eukaryotic cells. Drosophila oocyte growth is mainly dependent on the contribution of cytoplasmic contents from the interconnected sister cells, nurse cells. We have previously shown that cytoplasmic dynein is required for Drosophila oocyte growth and assumed that it simply transports cargoes along microtubule tracks from nurse cells to the oocyte. Here, we report that instead of transporting individual cargoes along stationary microtubules into the oocyte, cortical dynein actively moves microtubules within nurse cells and from nurse cells to the oocyte via the cytoplasmic bridges, the ring canals. This robust microtubule movement is sufficient to drag even inert cytoplasmic particles through the ring canals to the oocyte. Furthermore, replacing dynein with a minus-end directed plant kinesin linked to the actin cortex is sufficient for transporting organelles and cytoplasm to the oocyte and driving its growth. These experiments show that cortical dynein performs bulk cytoplasmic transport by gliding microtubules along the cell cortex and through the ring canals to the oocyte. We propose that the dynein-driven microtubule flow could serve as a novel mode of fast cytoplasmic transport.
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Affiliation(s)
- Wen Lu
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Margot Lakonishok
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Anna S Serpinskaya
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
| | - Vladimir I Gelfand
- Department of Cell and Developmental Biology, Feinberg School of Medicine, Northwestern UniversityChicagoUnited States
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8
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Sankaranarayanan M, Emenecker RJ, Wilby EL, Jahnel M, Trussina IREA, Wayland M, Alberti S, Holehouse AS, Weil TT. Adaptable P body physical states differentially regulate bicoid mRNA storage during early Drosophila development. Dev Cell 2021; 56:2886-2901.e6. [PMID: 34655524 PMCID: PMC8555633 DOI: 10.1016/j.devcel.2021.09.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 01/01/2023]
Abstract
Ribonucleoprotein condensates can exhibit diverse physical states in vitro and in vivo. Despite considerable progress, the relevance of condensate physical states for in vivo biological function remains limited. Here, we investigated the physical properties of processing bodies (P bodies) and their impact on mRNA storage in mature Drosophila oocytes. We show that the conserved DEAD-box RNA helicase Me31B forms viscous P body condensates, which adopt an arrested physical state. We demonstrate that structurally distinct proteins and protein-protein interactions, together with RNA, regulate the physical properties of P bodies. Using live imaging and in situ hybridization, we show that the arrested state and integrity of P bodies support the storage of bicoid (bcd) mRNA and that egg activation modulates P body properties, leading to the release of bcd for translation in the early embryo. Together, this work provides an example of how physical states of condensates regulate cellular function in development.
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Affiliation(s)
- M Sankaranarayanan
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Ryan J Emenecker
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Elise L Wilby
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Marcus Jahnel
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Irmela R E A Trussina
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Matt Wayland
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Simon Alberti
- Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, 660 S. Euclid Ave., St. Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, 1 Brookings Drive, St. Louis, MO 63130, USA
| | - Timothy T Weil
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
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9
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Goldman CH, Neiswender H, Baker F, Veeranan-Karmegam R, Misra S, Gonsalvez GB. Optimal RNA binding by Egalitarian, a Dynein cargo adaptor, is critical for maintaining oocyte fate in Drosophila. RNA Biol 2021; 18:2376-2389. [PMID: 33904382 DOI: 10.1080/15476286.2021.1914422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
The Dynein motor is responsible for the localization of numerous mRNAs within Drosophila oocytes and embryos. The RNA binding protein, Egalitarian (Egl), is thought to link these various RNA cargoes with Dynein. Although numerous studies have shown that Egl is able to specifically associate with these RNAs, the nature of these interactions has remained elusive. Egl contains a central RNA binding domain that shares limited homology with an exonuclease, yet Egl binds to RNA without degrading it. Mutations have been identified within Egl that disrupt its association with its protein interaction partners, BicaudalD (BicD) and Dynein light chain (Dlc), but no mutants have been described that are specifically defective for RNA binding. In this report, we identified a series of positively charged residues within Egl that are required for RNA binding. Using corresponding RNA binding mutants, we demonstrate that specific RNA cargoes are more reliant on maximal Egl RNA biding activity for their correct localization in comparison to others. We also demonstrate that specification and maintenance of oocyte fate requires maximal Egl RNA binding activity. Even a subtle reduction in Egl's RNA binding activity completely disrupts this process. Our results show that efficient RNA localization at the earliest stages of oogenesis is required for specification of the oocyte and restriction of meiosis to a single cell.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA.,Department of Genetics, Davidson Life Sciences Complex, University of Georgia, Athens, GA, USA
| | - Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | - Frederick Baker
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
| | | | - Saurav Misra
- Dept. Of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS,USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, Augusta, GA, USA
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10
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Lasko P. Patterning the Drosophila embryo: A paradigm for RNA-based developmental genetic regulation. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1610. [PMID: 32543002 PMCID: PMC7583483 DOI: 10.1002/wrna.1610] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/17/2020] [Indexed: 12/16/2022]
Abstract
Embryonic anterior–posterior patterning is established in Drosophila melanogaster by maternally expressed genes. The mRNAs of several of these genes accumulate at either the anterior or posterior pole of the oocyte via a number of mechanisms. Many of these mRNAs are also under elaborate translational regulation. Asymmetric RNA localization coupled with spatially restricted translation ensures that their proteins are restricted to the position necessary for the developmental process that they drive. Bicoid (Bcd), the anterior determinant, and Oskar (Osk), the determinant for primordial germ cells and posterior patterning, have been studied particularly closely. In early embryos an anterior–posterior gradient of Bcd is established, activating transcription of different sets of zygotic genes depending on local Bcd concentration. At the posterior pole, Osk seeds formation of polar granules, ribonucleoprotein complexes that accumulate further mRNAs and proteins involved in posterior patterning and germ cell specification. After fertilization, polar granules associate with posterior nuclei and mature into nuclear germ granules. Osk accumulates in these granules, and either by itself or as part of the granules, stimulates germ cell division. This article is categorized under:RNA Export and Localization > RNA Localization Translation > Translation Regulation RNA in Disease and Development > RNA in Development
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Affiliation(s)
- Paul Lasko
- Department of Biology, McGill University, Montréal, Québec, Canada.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
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11
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Engel KL, Arora A, Goering R, Lo HYG, Taliaferro JM. Mechanisms and consequences of subcellular RNA localization across diverse cell types. Traffic 2020; 21:404-418. [PMID: 32291836 PMCID: PMC7304542 DOI: 10.1111/tra.12730] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/26/2020] [Accepted: 03/30/2020] [Indexed: 02/07/2023]
Abstract
Essentially all cells contain a variety of spatially restricted regions that are important for carrying out specialized functions. Often, these regions contain specialized transcriptomes that facilitate these functions by providing transcripts for localized translation. These transcripts play a functional role in maintaining cell physiology by enabling a quick response to changes in the cellular environment. Here, we review how RNA molecules are trafficked within cells, with a focus on the subcellular locations to which they are trafficked, mechanisms that regulate their transport and clinical disorders associated with misregulation of the process.
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Affiliation(s)
- Krysta L Engel
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ankita Arora
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Raeann Goering
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Hei-Yong G Lo
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - J Matthew Taliaferro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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12
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Fan P, Han B, Hu H, Wei Q, Zhang X, Meng L, Nie J, Tang X, Tian X, Zhang L, Wang L, Li J. Proteome of thymus and spleen reveals that 10-hydroxydec-2-enoic acid could enhance immunity in mice. Expert Opin Ther Targets 2020; 24:267-279. [PMID: 32077781 DOI: 10.1080/14728222.2020.1733529] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objectives: 10-hydroxydec-2-enoic acid (10-HDA), a unique component of royal jelly existing only in nature, has the potential to promote human health. Knowledge of 10-HDA in regulating immuno-activity, however, is lacking. The aim of our work is to gain a novel understanding of 10-HDA in promoting immunity.Methods: Immuno-suppressed mice were generated by cyclophosphamide injection, After 10-HDA supplementation to the mice to rescue their immunity, the proteomes of the thymus and spleen were analyzed.Results: The weight of the body, thymus, and spleen in cyclophosphamide-induced mice recovered by 10-HDA indicate its potential role in immuno-organ protection. In the thymus, the enhanced activity of pathways associated with DNA/RNA/protein activities may be critical for T-lymphocyte proliferation/differentiation, and cytotoxicity. In the spleen, the induced pathways involved in DNA/RNA/protein activities, and cell proliferative stimulation suggest their vital role in B-lymphocyte affinity maturation, antigen presentation, and macrophage activity. The up-regulated proteins highly connected in networks modulated by 10-HDA indicate that the mice may evolve tactics to respond to immuno-organ impairment by activating critical physiological processes.Conclusion: Our data constitute a proof-of-concept that 10-HDA is a potential agent to improve immunity in the thymus and spleen and offer a new venue for applying natural products to the therapy for hypoimmunity.
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Affiliation(s)
- Pei Fan
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China.,College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Bin Han
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Han Hu
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Qiaohong Wei
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Xufeng Zhang
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Lifeng Meng
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
| | - Jing Nie
- Department of Technology, Hunan SJA Laboratory Animal Co., Ltd, Changsha, PR China
| | - Xiaofeng Tang
- Department of Technology, Hunan SJA Laboratory Animal Co., Ltd, Changsha, PR China
| | - Xinyue Tian
- College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Lu Zhang
- College of Biological Engineering, Henan University of Technology, Zhengzhou, PR China
| | - Liping Wang
- Department of Research & Development, Henan Jianda Bio Sci. & Tech. Co., Ltd, Zhengzhou, PR China
| | - Jianke Li
- Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, PR China
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13
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Harrison JU, Parton RM, Davis I, Baker RE. Testing Models of mRNA Localization Reveals Robustness Regulated by Reducing Transport between Cells. Biophys J 2019; 117:2154-2165. [PMID: 31708163 PMCID: PMC6895595 DOI: 10.1016/j.bpj.2019.10.025] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 09/18/2019] [Accepted: 10/15/2019] [Indexed: 11/26/2022] Open
Abstract
Robust control of gene expression in both space and time is of central importance in the regulation of cellular processes and for multicellular development. However, the mechanisms by which robustness is achieved are generally not identified or well understood. For example, messenger RNA (mRNA) localization by molecular motor-driven transport is crucial for cell polarization in numerous contexts, but the regulatory mechanisms that enable this process to take place in the face of noise or significant perturbations are not fully understood. Here, we use a combined experimental-theoretical approach to characterize the robustness of gurken/transforming growth factor-α mRNA localization in Drosophila egg chambers, where the oocyte and 15 surrounding nurse cells are connected in a stereotypic network via intracellular bridges known as ring canals. We construct a mathematical model that encodes simplified descriptions of the range of steps involved in mRNA localization, including production and transport between and within cells until the final destination in the oocyte. Using Bayesian inference, we calibrate this model using quantitative single molecule fluorescence in situ hybridization data. By analyzing both the steady state and dynamic behaviors of the model, we provide estimates for the rates of different steps of the localization process as well as the extent of directional bias in transport through the ring canals. The model predicts that mRNA synthesis and transport must be tightly balanced to maintain robustness, a prediction that we tested experimentally using an overexpression mutant. Surprisingly, the overexpression mutant fails to display the anticipated degree of overaccumulation of mRNA in the oocyte predicted by the model. Through careful model-based analysis of quantitative data from the overexpression mutant, we show evidence of saturation of the transport of mRNA through ring canals. We conclude that this saturation engenders robustness of the localization process in the face of significant variation in the levels of mRNA synthesis.
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Affiliation(s)
- Jonathan U Harrison
- Zeeman Institute, Mathematical Institute, University of Warwick, Coventry, United Kingdom; Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom.
| | - Richard M Parton
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ilan Davis
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Ruth E Baker
- Wolfson Centre for Mathematical Biology, Mathematical Institute, University of Oxford, Oxford, United Kingdom
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14
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Illukkumbura R, Bland T, Goehring NW. Patterning and polarization of cells by intracellular flows. Curr Opin Cell Biol 2019; 62:123-134. [PMID: 31760155 PMCID: PMC6968950 DOI: 10.1016/j.ceb.2019.10.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 11/19/2022]
Abstract
Beginning with Turing’s seminal work [1], decades of research have demonstrated the fundamental ability of biochemical networks to generate and sustain the formation of patterns. However, it is increasingly appreciated that biochemical networks both shape and are shaped by physical and mechanical processes [2, 3, 4]. One such process is fluid flow. In many respects, the cytoplasm, membrane and actin cortex all function as fluids, and as they flow, they drive bulk transport of molecules throughout the cell. By coupling biochemical activity to long range molecular transport, flows can shape the distributions of molecules in space. Here we review the various types of flows that exist in cells, with the aim of highlighting recent advances in our understanding of how flows are generated and how they contribute to intracellular patterning processes, such as the establishment of cell polarity.
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Affiliation(s)
| | - Tom Bland
- The Francis Crick Institute, London, UK; Institute for the Physics of Living Systems, University College London, London, UK
| | - Nathan W Goehring
- The Francis Crick Institute, London, UK; Institute for the Physics of Living Systems, University College London, London, UK; MRC Laboratory for Molecular Cell Biology, University College London, London, UK.
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15
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Merkle JA, Wittes J, Schüpbach T. Signaling between somatic follicle cells and the germline patterns the egg and embryo of Drosophila. Curr Top Dev Biol 2019; 140:55-86. [PMID: 32591083 DOI: 10.1016/bs.ctdb.2019.10.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In Drosophila, specification of the embryonic body axes requires signaling between the germline and the somatic follicle cells. These signaling events are necessary to properly localize embryonic patterning determinants in the egg or eggshell during oogenesis. There are three maternal patterning systems that specify the anterior-posterior axis, and one that establishes the dorsal-ventral axis. We will first review oogenesis, focusing on the establishment of the oocyte and nurse cells and patterning of the follicle cells into different subpopulations. We then describe how two coordinated signaling events between the oocyte and follicle cells establish polarity of the oocyte and localize the anterior determinant bicoid, the posterior determinant oskar, and Gurken/epidermal growth factor (EGF), which breaks symmetry to initiate dorsal-ventral axis establishment. Next, we review how dorsal-ventral asymmetry of the follicle cells is transmitted to the embryo. This process also involves Gurken-EGF receptor (EGFR) signaling between the oocyte and follicle cells, leading to ventrally-restricted expression of the sulfotransferase Pipe. These events promote the ventral processing of Spaetzle, a ligand for Toll, which ultimately sets up the embryonic dorsal-ventral axis. We then describe the activation of the terminal patterning system by specialized polar follicle cells. Finally, we present open questions regarding soma-germline signaling during Drosophila oogenesis required for cell identity and embryonic axis formation.
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Affiliation(s)
- Julie A Merkle
- Department of Biology, University of Evansville, Evansville, IN, United States
| | - Julia Wittes
- Department of Biological Sciences, Columbia University, New York, NY, United States
| | - Trudi Schüpbach
- Department of Molecular Biology, Princeton University, Princeton, NJ, United States.
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16
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Peglion F, Goehring NW. Switching states: dynamic remodelling of polarity complexes as a toolkit for cell polarization. Curr Opin Cell Biol 2019; 60:121-130. [PMID: 31295650 PMCID: PMC6906085 DOI: 10.1016/j.ceb.2019.05.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/07/2019] [Accepted: 05/11/2019] [Indexed: 02/04/2023]
Abstract
Polarity is defined by the segregation of cellular components along a defined axis. To polarize robustly, cells must be able to break symmetry and subsequently amplify these nascent asymmetries. Finally, asymmetric localization of signaling molecules must be translated into functional regulation of downstream effector pathways. Central to these behaviors are a diverse set of cell polarity networks. Within these networks, molecules exhibit varied behaviors, dynamically switching among different complexes and states, active versus inactive, bound versus unbound, immobile versus diffusive. This ability to switch dynamically between states is intimately connected to the ability of molecules to generate asymmetric patterns within cells. Focusing primarily on polarity pathways governed by the conserved PAR proteins, we discuss strategies enabled by these dynamic behaviors that are used by cells to polarize. We highlight not only how switching between states is linked to the ability of polarity proteins to localize asymmetrically, but also how cells take advantage of 'state switching' to regulate polarity in time and space.
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Affiliation(s)
- Florent Peglion
- Cell Polarity, Migration and Cancer Unit, Institut Pasteur, UMR3691 CNRS, Equipe Labellisée Ligue Contre le Cancer, F-75015, Paris, France
| | - Nathan W Goehring
- The Francis Crick Institute, London, UK; MRC Laboratory for Molecular Cell Biology, UCL, London, UK.
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17
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van den Ameele J, Brand AH. Neural stem cell temporal patterning and brain tumour growth rely on oxidative phosphorylation. eLife 2019; 8:47887. [PMID: 31513013 PMCID: PMC6763261 DOI: 10.7554/elife.47887] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/11/2019] [Indexed: 02/07/2023] Open
Abstract
Translating advances in cancer research to clinical applications requires better insight into the metabolism of normal cells and tumour cells in vivo. Much effort has focused on understanding how glycolysis and oxidative phosphorylation (OxPhos) support proliferation, while their impact on other aspects of development and tumourigenesis remain largely unexplored. We found that inhibition of OxPhos in neural stem cells (NSCs) or tumours in the Drosophila brain not only decreases proliferation, but also affects many different aspects of stem cell behaviour. In NSCs, OxPhos dysfunction leads to a protracted G1/S-phase and results in delayed temporal patterning and reduced neuronal diversity. As a consequence, NSCs fail to undergo terminal differentiation, leading to prolonged neurogenesis into adulthood. Similarly, in brain tumours inhibition of OxPhos slows proliferation and prevents differentiation, resulting in reduced tumour heterogeneity. Thus, in vivo, highly proliferative stem cells and tumour cells require OxPhos for efficient growth and generation of diversity.
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Affiliation(s)
- Jelle van den Ameele
- The Gurdon Institute, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Andrea H Brand
- The Gurdon Institute, Cambridge, United Kingdom.,Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom
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18
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Goldman CH, Neiswender H, Veeranan-Karmegam R, Gonsalvez GB. The Egalitarian binding partners Dynein light chain and Bicaudal-D act sequentially to link mRNA to the Dynein motor. Development 2019; 146:dev.176529. [PMID: 31391195 DOI: 10.1242/dev.176529] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 07/15/2019] [Indexed: 01/24/2023]
Abstract
A conserved mechanism of polarity establishment is the localization of mRNA to specific cellular regions. Although it is clear that many mRNAs are transported along microtubules, much less is known about the mechanism by which these mRNAs are linked to microtubule motors. The RNA binding protein Egalitarian (Egl) is necessary for localization of several mRNAs in Drosophila oocytes and embryos. Egl also interacts with Dynein light chain (Dlc) and Bicaudal-D (BicD). The role of Dlc and BicD in mRNA localization has remained elusive. Both proteins are required for oocyte specification, as is Egl. Null alleles in these genes result in an oogenesis block. In this report, we used an shRNA-depletion strategy to overcome the oogenesis block. Our findings reveal that the primary function of Dlc is to promote Egl dimerization. Loss of dimerization compromises the ability of Egl to bind RNA. Consequently, Egl is not bound to cargo, and is not able to efficiently associate with BicD and the Dynein motor. Our results therefore identify the key molecular steps required for assembling a localization-competent mRNP.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Hannah Neiswender
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Rajalakshmi Veeranan-Karmegam
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd, Augusta, GA 30912, USA
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19
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Teixeira FK, Lehmann R. Translational Control during Developmental Transitions. Cold Spring Harb Perspect Biol 2019; 11:cshperspect.a032987. [PMID: 30082467 DOI: 10.1101/cshperspect.a032987] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The many steps of gene expression, from the transcription of a gene to the production of its protein product, are well understood. Yet, transcriptional regulation has been the focal point for the study of gene expression during development. However, quantitative studies reveal that messenger RNA (mRNA) levels are not necessarily good predictors of the respective proteins' levels in a cell. This discrepancy is, at least in part, the result of developmentally regulated, translational mechanisms that control the spatiotemporal regulation of gene expression. In this review, we focus on translational regulatory mechanisms mediating global transitions in gene expression: the shift from the maternal to the embryonic developmental program in the early embryo and the switch from the self-renewal of stem cells to differentiation in the adult.
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Affiliation(s)
| | - Ruth Lehmann
- Howard Hughes Medical Institute (HHMI) and Kimmel Center for Biology and Medicine of the Skirball Institute, Department of Cell Biology, New York University School of Medicine, New York, New York 10016
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20
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Asymmetric Inheritance of Cell Fate Determinants: Focus on RNA. Noncoding RNA 2019; 5:ncrna5020038. [PMID: 31075989 PMCID: PMC6630313 DOI: 10.3390/ncrna5020038] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 04/30/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022] Open
Abstract
During the last decade, and mainly primed by major developments in high-throughput sequencing technologies, the catalogue of RNA molecules harbouring regulatory functions has increased at a steady pace. Current evidence indicates that hundreds of mammalian RNAs have regulatory roles at several levels, including transcription, translation/post-translation, chromatin structure, and nuclear architecture, thus suggesting that RNA molecules are indeed mighty controllers in the flow of biological information. Therefore, it is logical to suggest that there must exist a series of molecular systems that safeguard the faithful inheritance of RNA content throughout cell division and that those mechanisms must be tightly controlled to ensure the successful segregation of key molecules to the progeny. Interestingly, whilst a handful of integral components of mammalian cells seem to follow a general pattern of asymmetric inheritance throughout division, the fate of RNA molecules largely remains a mystery. Herein, we will discuss current concepts of asymmetric inheritance in a wide range of systems, including prions, proteins, and finally RNA molecules, to assess overall the biological impact of RNA inheritance in cellular plasticity and evolutionary fitness.
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21
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Jouette J, Guichet A, Claret SB. Dynein-mediated transport and membrane trafficking control PAR3 polarised distribution. eLife 2019; 8:40212. [PMID: 30672465 PMCID: PMC6358217 DOI: 10.7554/elife.40212] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 01/03/2019] [Indexed: 12/14/2022] Open
Abstract
The scaffold protein PAR3 and the kinase PAR1 are essential proteins that control cell polarity. Their precise opposite localisations define plasma membrane domains with specific functions. PAR3 and PAR1 are mutually inhibited by direct or indirect phosphorylations, but their fates once phosphorylated are poorly known. Through precise spatiotemporal quantification of PAR3 localisation in the Drosophila oocyte, we identify several mechanisms responsible for its anterior cortex accumulation and its posterior exclusion. We show that PAR3 posterior plasma membrane exclusion depends on PAR1 and an endocytic mechanism relying on RAB5 and PI(4,5)P2. In a second phase, microtubules and the dynein motor, in connection with vesicular trafficking involving RAB11 and IKK-related kinase, IKKε, are required for PAR3 transport towards the anterior cortex. Altogether, our results point to a connection between membrane trafficking and dynein-mediated transport to sustain PAR3 asymmetry.
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Affiliation(s)
- Julie Jouette
- Institut Jacques Monod, CNRS, UMR 7592, Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - Antoine Guichet
- Institut Jacques Monod, CNRS, UMR 7592, Paris Diderot University, Sorbonne Paris Cité, Paris, France
| | - Sandra B Claret
- Institut Jacques Monod, CNRS, UMR 7592, Paris Diderot University, Sorbonne Paris Cité, Paris, France
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22
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Ciocanel MV, Sandstede B, Jeschonek SP, Mowry KL. Modeling microtubule-based transport and anchoring of mRNA. SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS 2018; 17:2855-2881. [PMID: 34135697 PMCID: PMC8205424 DOI: 10.1137/18m1186083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Localization of messenger RNA (mRNA) at the vegetal cortex plays an important role in the early development of Xenopus laevis oocytes. While it is known that molecular motors are responsible for the transport of mRNA cargo along microtubules to the cortex, the mechanisms of localization remain unclear. We model cargo transport along microtubules using partial differential equations with spatially-dependent rates. A theoretical analysis of reduced versions of our model predicts effective velocity and diffusion rates for the cargo and shows that randomness of microtubule networks enhances effective transport. A more complex model using parameters estimated from fluorescence microscopy data reproduces the spatial and timescales of mRNA localization observed in Xenopus oocytes, corroborates experimental hypotheses that anchoring may be necessary to achieve complete localization, and shows that anchoring of mRNA complexes actively transported to the cortex is most effective in achieving robust accumulation at the cortex.
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Affiliation(s)
| | - Björn Sandstede
- Division of Applied Mathematics, Brown University, Providence, RI
| | - Samantha P Jeschonek
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI
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23
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Kim EJY, Korotkevich E, Hiiragi T. Coordination of Cell Polarity, Mechanics and Fate in Tissue Self-organization. Trends Cell Biol 2018; 28:541-550. [DOI: 10.1016/j.tcb.2018.02.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 02/20/2018] [Accepted: 02/20/2018] [Indexed: 02/06/2023]
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24
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Veerapathiran S, Wohland T. Fluorescence techniques in developmental biology. J Biosci 2018; 43:541-553. [PMID: 30002271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advanced fluorescence techniques, commonly known as the F-techniques, measure the kinetics and the interactions of biomolecules with high sensitivity and spatiotemporal resolution. Applications of the F-techniques, which were initially limited to cells, were further extended to study in vivo protein organization and dynamics in whole organisms. The integration of F-techniques with multi-photon microscopy and light-sheet microscopy widened their applications in the field of developmental biology. It became possible to penetrate the thick tissues of living organisms and obtain good signal-to-noise ratio with reduced photo-induced toxicity. In this review, we discuss the principle and the applications of the three most commonly used F-techniques in developmental biology: Fluorescence Recovery After Photo-bleaching (FRAP), Fo¨ rster Resonance Energy Transfer (FRET), and Fluorescence Correlation and Cross-Correlation Spectroscopy (FCS and FCCS).
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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25
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26
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Stochastic Seeding Coupled with mRNA Self-Recruitment Generates Heterogeneous Drosophila Germ Granules. Curr Biol 2018; 28:1872-1881.e3. [PMID: 29861136 DOI: 10.1016/j.cub.2018.04.037] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/22/2022]
Abstract
The formation of ribonucleoprotein assemblies called germ granules is a conserved feature of germline development. In Drosophila, germ granules form at the posterior of the oocyte in a specialized cytoplasm called the germ plasm, which specifies germline fate during embryogenesis. mRNAs, including nanos (nos) and polar granule component (pgc), that function in germline development are localized to the germ plasm through their incorporation into germ granules, which deliver them to the primordial germ cells. Germ granules are nucleated by Oskar (Osk) protein and contain varying combinations and quantities of their constituent mRNAs, which are organized as spatially distinct, multi-copy homotypic clusters. The process that gives rise to such heterogeneous yet organized granules remains unknown. Here, we show that individual nos and pgc transcripts can populate the same nascent granule, and these first transcripts then act as seeds, recruiting additional like transcripts to form homotypic clusters. Within a granule, homotypic clusters grow independently of each other but depend on the simultaneous acquisition of additional Osk. Although granules can contain multiple clusters of a particular mRNA, granule mRNA content is dominated by cluster size. These results suggest that the accumulation of mRNAs in the germ plasm is controlled by the mRNAs themselves through their ability to form homotypic clusters; thus, RNA self-association drives germ granule mRNA localization. We propose that a stochastic seeding and self-recruitment mechanism enables granules to simultaneously incorporate many different mRNAs while ensuring that each becomes enriched to a functional threshold.
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27
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Lefebvre FA, Lécuyer É. Flying the RNA Nest: Drosophila Reveals Novel Insights into the Transcriptome Dynamics of Early Development. J Dev Biol 2018; 6:jdb6010005. [PMID: 29615554 PMCID: PMC5875563 DOI: 10.3390/jdb6010005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/01/2018] [Accepted: 03/05/2018] [Indexed: 01/02/2023] Open
Abstract
Early development is punctuated by a series of pervasive and fast paced transitions. These events reshape a differentiated oocyte into a totipotent embryo and allow it to gradually mount a genetic program of its own, thereby framing a new organism. Specifically, developmental transitions that ensure the maternal to embryonic control of developmental events entail a deep remodeling of transcriptional and transcriptomic landscapes. Drosophila provides an elegant and genetically tractable system to investigate these conserved changes at a dazzling developmental pace. Here, we review recent studies applying emerging technologies such as ribosome profiling, in situ Hi-C chromatin probing and live embryo RNA imaging to investigate the transcriptional dynamics at play during Drosophila embryogenesis. In light of this new literature, we revisit the main models of zygotic genome activation (ZGA). We also review the contributions played by zygotic transcription in shaping embryogenesis and explore emerging concepts of processes such as transcriptional bursting and transcriptional memory.
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Affiliation(s)
- Fabio Alexis Lefebvre
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montréal, QC H2W 1R7, Canada.
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1J4, Canada.
- Division of Experimental Medicine, McGill University, Montréal, QC H3A 0G4, Canada.
- IRCM, RNA Biology Laboratory, 110 Avenue des Pins, Ouest, Montréal, QC H2W 1R7, Canada.
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28
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Abstract
Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.
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Affiliation(s)
- Tatjana Trcek
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA.
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
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29
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Goldman CH, Gonsalvez GB. The Role of Microtubule Motors in mRNA Localization and Patterning Within the Drosophila Oocyte. Results Probl Cell Differ 2017; 63:149-168. [PMID: 28779317 DOI: 10.1007/978-3-319-60855-6_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Messenger RNA (mRNA) localization is a powerful and prevalent mechanism of post-transcriptional gene regulation, enabling the cell to produce protein at the exact location at which it is needed. The phenomenon of mRNA localization has been observed in many types of cells in organisms ranging from yeast to man. Thus, the process appears to be widespread and highly conserved. Several model systems have been used to understand the mechanism by which mRNAs are localized. One such model, and the focus of this chapter, is the egg chamber of the female Drosophila melanogaster. The polarity of the developing Drosophila oocyte and resulting embryo relies on the specific localization of three critical mRNAs: gurken, bicoid, and oskar. If these mRNAs are not localized during oogenesis, the resulting progeny will not survive. The study of these mRNAs has served as a model for understanding the general mechanisms by which mRNAs are sorted. In this chapter, we will discuss how the localization of these mRNAs enables polarity establishment. We will also discuss the role of motor proteins in the localization pathway. Finally, we will consider potential mechanisms by which mRNAs can be anchored at their site of localization. It is likely that the lessons learned using the Drosophila oocyte model system will be applicable to mRNAs that are localized in other organisms as well.
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Affiliation(s)
- Chandler H Goldman
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd., CB2917, Augusta, GA, 30912, USA
| | - Graydon B Gonsalvez
- Cellular Biology and Anatomy, Medical College of Georgia, Augusta University, 1459 Laney Walker Blvd., CB2917, Augusta, GA, 30912, USA.
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30
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Nieuwburg R, Nashchekin D, Jakobs M, Carter AP, Khuc Trong P, Goldstein RE, St Johnston D. Localised dynactin protects growing microtubules to deliver oskar mRNA to the posterior cortex of the Drosophila oocyte. eLife 2017; 6:e27237. [PMID: 29035202 PMCID: PMC5643094 DOI: 10.7554/elife.27237] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 09/19/2017] [Indexed: 11/13/2022] Open
Abstract
The localisation of oskar mRNA to the posterior of the Drosophila oocyte defines where the abdomen and germ cells form in the embryo. Kinesin 1 transports oskar mRNA to the oocyte posterior along a polarised microtubule cytoskeleton that grows from non-centrosomal microtubule organising centres (ncMTOCs) along the anterior/lateral cortex. Here, we show that the formation of this polarised microtubule network also requires the posterior regulation of microtubule growth. A missense mutation in the dynactin Arp1 subunit causes most oskar mRNA to localise in the posterior cytoplasm rather than cortically. oskar mRNA transport and anchoring are normal in this mutant, but the microtubules fail to reach the posterior pole. Thus, dynactin acts as an anti-catastrophe factor that extends microtubule growth posteriorly. Kinesin 1 transports dynactin to the oocyte posterior, creating a positive feedback loop that increases the length and persistence of the posterior microtubules that deliver oskar mRNA to the cortex.
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Affiliation(s)
- Ross Nieuwburg
- The Gurdon Institute and the Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Dmitry Nashchekin
- The Gurdon Institute and the Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
| | - Maximilian Jakobs
- The Department of Physiology, Development and NeuroscienceUniversity of CambridgeCambridgeUnited Kingdom
| | - Andrew P Carter
- Division of Structural StudiesMedical Research Council, Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Philipp Khuc Trong
- Department of Applied Mathematics and Theoretical PhysicsUniversity of Cambridge, Centre for Mathematical SciencesCambridgeUnited Kingdom
| | - Raymond E Goldstein
- Department of Applied Mathematics and Theoretical PhysicsUniversity of Cambridge, Centre for Mathematical SciencesCambridgeUnited Kingdom
| | - Daniel St Johnston
- The Gurdon Institute and the Department of GeneticsUniversity of CambridgeCambridgeUnited Kingdom
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31
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Trcek T, Lionnet T, Shroff H, Lehmann R. mRNA quantification using single-molecule FISH in Drosophila embryos. Nat Protoc 2016; 12:1326-1348. [PMID: 28594816 DOI: 10.1038/nprot.2017.030] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Spatial information is critical to the interrogation of developmental and tissue-level regulation of gene expression. However, this information is usually lost when global mRNA levels from tissues are measured using reverse transcriptase PCR, microarray analysis or high-throughput sequencing. By contrast, single-molecule fluorescence in situ hybridization (smFISH) preserves the spatial information of the cellular mRNA content with subcellular resolution within tissues. Here we describe an smFISH protocol that allows for the quantification of single mRNAs in Drosophila embryos, using commercially available smFISH probes (e.g., short fluorescently labeled DNA oligonucleotides) in combination with wide-field epifluorescence, confocal or instant structured illumination microscopy (iSIM, a super-resolution imaging approach) and a spot-detection algorithm. Fixed Drosophila embryos are hybridized in solution with a mixture of smFISH probes, mounted onto coverslips and imaged in 3D. Individual fluorescently labeled mRNAs are then localized within tissues and counted using spot-detection software to generate quantitative, spatially resolved gene expression data sets. With minimum guidance, a graduate student can successfully implement this protocol. The smFISH procedure described here can be completed in 4-5 d.
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Affiliation(s)
- Tatjana Trcek
- Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Timothée Lionnet
- Transcription Imaging Consortium, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Ruth Lehmann
- Howard Hughes Medical Institute, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, New York, USA
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