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Nisa A, Kumar R, Ramasamy S, Kolloli A, Olejnik J, Jalloh S, Gummuluru S, Subbian S, Bushkin Y. Modulations of Homeostatic ACE2, CD147, GRP78 Pathways Correlate with Vascular and Endothelial Performance Markers during Pulmonary SARS-CoV-2 Infection. Cells 2024; 13:432. [PMID: 38474396 PMCID: PMC10930588 DOI: 10.3390/cells13050432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
The pathologic consequences of Coronavirus Disease-2019 (COVID-19) include elevated inflammation and dysregulated vascular functions associated with thrombosis. In general, disruption of vascular homeostasis and ensuing prothrombotic events are driven by activated platelets, monocytes, and macrophages, which form aggregates (thrombi) attached to the endothelium lining of vessel walls. However, molecular pathways underpinning the pathological interactions between myeloid cells and endothelium during COVID-19 remain undefined. Here, we tested the hypothesis that modulations in the expression of cellular receptors angiotensin-converting enzyme 2 (ACE2), CD147, and glucose-regulated protein 78 (GRP78), which are involved in homeostasis and endothelial performance, are the hallmark responses induced by SARS-CoV-2 infection. Cultured macrophages and lungs of hamster model systems were used to test this hypothesis. The results indicate that while macrophages and endothelial cells are less likely to support SARS-CoV-2 proliferation, these cells may readily respond to inflammatory stimuli generated by the infected lung epithelium. SARS-CoV-2 induced modulations of tested cellular receptors correlated with corresponding changes in the mRNA expression of coagulation cascade regulators and endothelial integrity components in infected hamster lungs. Among these markers, tissue factor (TF) had the best correlation for prothrombotic events during SARS-CoV-2 infection. Furthermore, the single-molecule fluorescence in situ hybridization (smFISH) method alone was sufficient to determine the peak and resolution phases of SARS-CoV-2 infection and enabled screening for cellular markers co-expressed with the virus. These findings suggest possible molecular pathways for exploration of novel drugs capable of blocking the prothrombotic shift events that exacerbate COVID-19 pathophysiology and control the disease.
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Affiliation(s)
- Annuurun Nisa
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
| | - Ranjeet Kumar
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
| | - Santhamani Ramasamy
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
| | - Afsal Kolloli
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
| | - Judith Olejnik
- Department of Virology, Immunology & Microbiology, Boston University School of Medicine, Boston, MA 02130, USA; (J.O.); (S.J.); (S.G.)
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA 02218, USA
| | - Sallieu Jalloh
- Department of Virology, Immunology & Microbiology, Boston University School of Medicine, Boston, MA 02130, USA; (J.O.); (S.J.); (S.G.)
| | - Suryaram Gummuluru
- Department of Virology, Immunology & Microbiology, Boston University School of Medicine, Boston, MA 02130, USA; (J.O.); (S.J.); (S.G.)
| | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
| | - Yuri Bushkin
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA; (A.N.); (R.K.); (S.R.); (A.K.)
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Hwang JY, Monday HR, Yan J, Gompers A, Buxbaum AR, Sawicka KJ, Singer RH, Castillo PE, Zukin RS. CPEB3-dependent increase in GluA2 subunits impairs excitatory transmission onto inhibitory interneurons in a mouse model of fragile X. Cell Rep 2022; 39:110853. [PMID: 35675768 PMCID: PMC9671216 DOI: 10.1016/j.celrep.2022.110853] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/05/2021] [Accepted: 05/01/2022] [Indexed: 01/29/2023] Open
Abstract
Fragile X syndrome (FXS) is a leading cause of inherited intellectual disability and autism. Whereas dysregulated RNA translation in Fmr1 knockout (KO) mice, a model of FXS, is well studied, little is known about aberrant transcription. Using single-molecule mRNA detection, we show that mRNA encoding the AMPAR subunit GluA2 (but not GluA1) is elevated in dendrites and at transcription sites of hippocampal neurons of Fmr1 KO mice, indicating elevated GluA2 transcription. We identify CPEB3, a protein implicated in memory consolidation, as an upstream effector critical to GluA2 mRNA expression in FXS. Increased GluA2 mRNA is translated into an increase in GluA2 subunits, a switch in synaptic AMPAR phenotype from GluA2-lacking, Ca2+-permeable to GluA2-containing, Ca2+-impermeable, reduced inhibitory synaptic transmission, and loss of NMDAR-independent LTP at glutamatergic synapses onto CA1 inhibitory interneurons. These factors could contribute to an excitatory/inhibitory imbalance-a common theme in FXS and other autism spectrum disorders.
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Affiliation(s)
- Jee-Yeon Hwang
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Department of Pharmacology and Neuroscience, Creighton University School of Medicine, Omaha, NE 68178, USA,These authors contributed equally,Lead contact,Correspondence: (J.-Y.H.), (R.S.Z.)
| | - Hannah R. Monday
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Present address: Department of Molecular and Cellular Biology and Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA,These authors contributed equally
| | - Jingqi Yan
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA,These authors contributed equally
| | - Andrea Gompers
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Center for Immunology and Infectious Diseases, University of California, Davis, Davis, CA 95616, USA,These authors contributed equally
| | - Adina R. Buxbaum
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Department of Structural & Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA,Present address: Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kirsty J. Sawicka
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Present address: Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, UK
| | - Robert H. Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Department of Structural & Cell Biology, Albert Einstein College of Medicine, New York, NY 10461, USA,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA,These authors contributed equally
| | - Pablo E. Castillo
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,Department of Psychiatry and Behavioral Sciences, Albert Einstein College of Medicine, New York, NY 10461, USA,These authors contributed equally
| | - R. Suzanne Zukin
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, New York, NY 10461, USA,These authors contributed equally,Correspondence: (J.-Y.H.), (R.S.Z.)
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3
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Morita Y, Katakura Y, Takegawa K, Higuchi Y. Correlative Localization Analysis Between mRNA and Enhanced Green Fluorescence Protein-Fused Protein by a Single-Molecule Fluorescence in situ Hybridization Using an egfp Probe in Aspergillus oryzae. Front Fungal Biol 2021; 2:721398. [PMID: 37744096 PMCID: PMC10512357 DOI: 10.3389/ffunb.2021.721398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/09/2021] [Indexed: 09/26/2023]
Abstract
Although subcellular localization analysis of proteins fused with enhanced green fluorescence protein (EGFP) has been widely conducted in filamentous fungi, little is known about the localization of messenger RNAs (mRNAs) encoding the EGFP-fused proteins. In this study, we performed single-molecule fluorescence in situ hybridization (smFISH) using an egfp probe to simultaneously visualize EGFP-fused proteins and their mRNAs in the hyphal cells of the filamentous fungus Aspergillus oryzae. We investigated the subcellular localization of mRNAs encoding cytoplasmic EGFP, an actin marker protein Lifeact tagged with EGFP, and several EGFP-fused proteins AoSec22, AoSnc1, AoVam3, and AoUapC that localize to the endoplasmic reticulum (ER), the apical vesicle cluster Spitzenkörper, vacuolar membrane, and plasma membrane, respectively. Visualization of these mRNAs by smFISH demonstrated that each mRNA exhibited distinct localization patterns likely depending on the mRNA sequence. In particular, we revealed that mRNAs encoding Lifeact-EGFP, EGFP-AoSec22, EGFP-AoVam3, and AoUapC-EGFP, but not cytoplasmic EGFP and EGFP-AoSnc1, were preferentially localized at the apical cell, suggesting certain mechanisms to regulate the existence of these transcripts among hyphal regions. Our findings provide the distinct localization information of each mRNA in the hyphal cells of A. oryzae.
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Affiliation(s)
| | | | | | - Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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4
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Savulescu AF, Brackin R, Bouilhol E, Dartigues B, Warrell JH, Pimentel MR, Beaume N, Fortunato IC, Dallongeville S, Boulle M, Soueidan H, Agou F, Schmoranzer J, Olivo-Marin JC, Franco CA, Gomes ER, Nikolski M, Mhlanga MM. Interrogating RNA and protein spatial subcellular distribution in smFISH data with DypFISH. Cell Rep Methods 2021; 1:100068. [PMID: 35474672 PMCID: PMC9017151 DOI: 10.1016/j.crmeth.2021.100068] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/15/2021] [Accepted: 08/03/2021] [Indexed: 12/17/2022]
Abstract
Advances in single-cell RNA sequencing have allowed for the identification of cellular subtypes on the basis of quantification of the number of transcripts in each cell. However, cells might also differ in the spatial distribution of molecules, including RNAs. Here, we present DypFISH, an approach to quantitatively investigate the subcellular localization of RNA and protein. We introduce a range of analytical techniques to interrogate single-molecule RNA fluorescence in situ hybridization (smFISH) data in combination with protein immunolabeling. DypFISH is suited to study patterns of clustering of molecules, the association of mRNA-protein subcellular localization with microtubule organizing center orientation, and interdependence of mRNA-protein spatial distributions. We showcase how our analytical tools can achieve biological insights by utilizing cell micropatterning to constrain cellular architecture, which leads to reduction in subcellular mRNA distribution variation, allowing for the characterization of their localization patterns. Furthermore, we show that our method can be applied to physiological systems such as skeletal muscle fibers.
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Affiliation(s)
- Anca F. Savulescu
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7295 Cape Town, South Africa
| | - Robyn Brackin
- Advanced Medical Bioimaging, Charité – Universitätsmedizin, 10-117 Berlin, Germany
| | - Emmanuel Bouilhol
- Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, 33077 Bordeaux, France
| | - Benjamin Dartigues
- Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France
| | - Jonathan H. Warrell
- Molecular Biophysics & Biochemistry, Yale University, New Haven, CT 06520, USA
| | - Mafalda R. Pimentel
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Nicolas Beaume
- Division of Chemical, Systems & Synthetic Biology, Institute for Infectious Disease & Molecular Medicine, Faculty of Health Sciences, University of Cape Town, 7295 Cape Town, South Africa
| | - Isabela C. Fortunato
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | | | - Mikaël Boulle
- Chemogenomic and Biological Screening Core Facility, C2RT, Department of Structural Biology and Chemistry, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
- Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Hayssam Soueidan
- Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France
| | - Fabrice Agou
- Chemogenomic and Biological Screening Core Facility, C2RT, Department of Structural Biology and Chemistry, Institut Pasteur, 25 rue du Dr. Roux, 75724 Paris Cedex 15, France
- Department of Structural Biology and Chemistry, URA 2185, Pasteur Institute, Paris, France
| | - Jan Schmoranzer
- Advanced Medical Bioimaging, Charité – Universitätsmedizin, 10-117 Berlin, Germany
| | | | - Claudio A. Franco
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Edgar R. Gomes
- Instituto de Medicina Molecular, Faculdade de Medicina Universidade de Lisboa, 1649-028 Lisbon, Portugal
| | - Macha Nikolski
- Université de Bordeaux, Bordeaux Bioinformatics Center, 33000 Bordeaux, France
- Université de Bordeaux, CNRS, IBGC, UMR 5095, 33077 Bordeaux, France
| | - Musa M. Mhlanga
- Radboud Institute for Molecular Life Sciences (RIMLS), Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
- Epigenomics & Single Cell Biophysics Group, Department of Cell Biology, FNWI, Radboud University, 6525 GA Nijmegen, the Netherlands
- Department of Human Genetics, Radboud University Medical Center, 6525 GA Nijmegen, the Netherlands
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5
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Higuchi Y, Takegawa K. Single-Molecule FISH Reveals Subcellular Localization of α-Amylase and Actin mRNAs in the Filamentous Fungus Aspergillus oryzae. Front Microbiol 2020; 11:578862. [PMID: 33072046 PMCID: PMC7536267 DOI: 10.3389/fmicb.2020.578862] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 09/01/2020] [Indexed: 11/13/2022] Open
Abstract
The machinery for mRNA localization is one of crucial molecular structures allowing cellular spatiotemporal organization of protein synthesis. Although the molecular mechanisms underlying mRNA localization have been thoroughly investigated in unicellular organisms, little is known about multicellular and multinuclear filamentous fungi. Here, we conducted single-molecule fluorescence in situ hybridization (smFISH) to first visualize the mRNA molecules of α-amylase, which are encoded by amyB, and which are thought to be abundantly secreted from the hyphal tips of the industrially important fungus Aspergillus oryzae. Consistent with previous biochemical studies, fluorescein amidite (FAM) fluorescence derived from amyB expression was observed in A. oryzae hyphae cultured in a minimal medium containing maltose instead of glucose as the sole carbon source. Moreover, after more than 1 h incubation with fresh maltose-containing medium, the fluorescence of amyB mRNAs was observed throughout the cells, suggesting α-amylase secretion potentially from each cell, instead of the hyphal tip only. Furthermore, in cultures with complete medium containing maltose, amyB mRNAs were excluded from the tip regions, where no nuclei exist. In contrast, mRNAs of actin, encoded by actA, were localized mainly to the tip, where actin proteins also preferentially reside. Collectively, our smFISH analyses revealed distinct localization patterns of α-amylase and actin mRNAs in A. oryzae hyphal cells.
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Affiliation(s)
- Yujiro Higuchi
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Kaoru Takegawa
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
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6
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Markey FB, Parashar V, Batish M. Methods for spatial and temporal imaging of the different steps involved in RNA processing at single-molecule resolution. Wiley Interdiscip Rev RNA 2020; 12:e1608. [PMID: 32543077 DOI: 10.1002/wrna.1608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 05/06/2020] [Accepted: 05/07/2020] [Indexed: 12/26/2022]
Abstract
RNA plays a quintessential role as a messenger of information from genotype (DNA) to phenotype (proteins), as well as acts as a regulatory molecule (noncoding RNAs). All steps in the journey of RNA from synthesis (transcription), splicing, transport, localization, translation, to its eventual degradation, comprise important steps in gene expression, thereby controlling the fate of the cell. This lifecycle refers to the majority of RNAs (primarily mRNAs), but not other RNAs such as tRNAs. Imaging these processes in fixed cells and in live cells has been an important tool in developing an understanding of the regulatory steps in RNAs journey. Single-cell and single-molecule imaging techniques enable a much deeper understanding of cellular biology, which is not possible with bulk studies involving RNA isolated from a large pool of cells. Classic techniques, such as fluorescence in situ hybridization (FISH), as well as more recent aptamer-based approaches, have provided detailed insights into RNA localization, and have helped to predict the functions carried out by many RNA species. However, there are still certain processing steps that await high-resolution imaging, which is an exciting and upcoming area of research. In this review, we will discuss the methods that have revolutionized single-molecule resolution imaging in general, the steps of RNA processing in which these methods have been used, and new emerging technologies. This article is categorized under: RNA Export and Localization > RNA Localization RNA Methods > RNA Analyses in Cells RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
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Affiliation(s)
- Fatu Badiane Markey
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA
| | - Vijay Parashar
- Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
| | - Mona Batish
- Department of Microbiology, Biochemistry and Molecular Genetics, New Jersey Medical School, Rutgers University, Newark, New Jersey, USA.,Department of Medical and Molecular Sciences, University of Delaware, Newark, Delaware, USA
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7
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Hormoz S, Singer ZS, Linton JM, Antebi YE, Shraiman BI, Elowitz MB. Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements. Cell Syst 2019; 3:419-433.e8. [PMID: 27883889 DOI: 10.1016/j.cels.2016.10.015] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 06/01/2016] [Accepted: 10/18/2016] [Indexed: 12/28/2022]
Abstract
As they proliferate, living cells undergo transitions between specific molecularly and developmentally distinct states. Despite the functional centrality of these transitions in multicellular organisms, it has remained challenging to determine which transitions occur and at what rates without perturbations and cell engineering. Here, we introduce kin correlation analysis (KCA) and show that quantitative cell-state transition dynamics can be inferred, without direct observation, from the clustering of cell states on pedigrees (lineage trees). Combining KCA with pedigrees obtained from time-lapse imaging and endpoint single-molecule RNA-fluorescence in situ hybridization (RNA-FISH) measurements of gene expression, we determined the cell-state transition network of mouse embryonic stem (ES) cells. This analysis revealed that mouse ES cells exhibit stochastic and reversible transitions along a linear chain of states ranging from 2C-like to epiblast-like. Our approach is broadly applicable and may be applied to systems with irreversible transitions and non-stationary dynamics, such as in cancer and development.
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Affiliation(s)
- Sahand Hormoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA
| | - Zakary S Singer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - James M Linton
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yaron E Antebi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Boris I Shraiman
- Kavli Institute for Theoretical Physics, University of California, Santa Barbara, CA 93106, USA.
| | - Michael B Elowitz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute (HHMI) and Department of Applied Physics, California Institute of Technology, Pasadena, CA 91125, USA.
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8
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Gaspar I, Wippich F, Ephrussi A. Enzymatic production of single-molecule FISH and RNA capture probes. RNA 2017; 23:1582-1591. [PMID: 28698239 PMCID: PMC5602115 DOI: 10.1261/rna.061184.117] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 06/22/2017] [Indexed: 05/20/2023]
Abstract
Arrays of singly labeled short oligonucleotides that hybridize to a specific target revolutionized RNA biology, enabling quantitative, single-molecule microscopy analysis and high-efficiency RNA/RNP capture. Here, we describe a simple and efficient method that allows flexible functionalization of inexpensive DNA oligonucleotides by different fluorescent dyes or biotin using terminal deoxynucleotidyl transferase and custom-made functional group conjugated dideoxy-UTP. We show that (i) all steps of the oligonucleotide labeling-including conjugation, enzymatic synthesis, and product purification-can be performed in a standard biology laboratory, (ii) the process yields >90%, often >95% labeled product with minimal carryover of impurities, and (iii) the oligonucleotides can be labeled with different dyes or biotin, allowing single-molecule FISH, RNA affinity purification, and Northern blot analysis to be performed.
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Affiliation(s)
- Imre Gaspar
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Frank Wippich
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg 69117, Germany
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9
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Huelsz-Prince G, van Zon JS. Canalization of C. elegans Vulva Induction against Anatomical Variability. Cell Syst 2017; 4:219-230.e6. [PMID: 28215526 PMCID: PMC5330807 DOI: 10.1016/j.cels.2017.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Revised: 09/29/2016] [Accepted: 01/11/2017] [Indexed: 11/24/2022]
Abstract
It is a fundamental open question as to how embryos develop into complex adult organisms with astounding reproducibility, particularly because cells are inherently variable on the molecular level. During C. elegans vulva induction, the anchor cell induces cell fate in the vulva precursor cells in a distance-dependent manner. Surprisingly, we found that initial anchor cell position was highly variable and caused variability in cell fate induction. However, we observed that vulva induction was "canalized," i.e., the variability in anchor cell position and cell fate was progressively reduced, resulting in an invariant spatial pattern of cell fates at the end of induction. To understand the mechanism of canalization, we quantified induction dynamics as a function of anchor cell position during the canalization process. Our experiments, combined with mathematical modeling, showed that canalization required a specific combination of long-range induction, lateral inhibition, and cell migration that is also found in other developmental systems.
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Lee C, Sorensen EB, Lynch TR, Kimble J. C. elegans GLP-1/Notch activates transcription in a probability gradient across the germline stem cell pool. eLife 2016; 5:e18370. [PMID: 27705743 PMCID: PMC5094854 DOI: 10.7554/elife.18370] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/04/2016] [Indexed: 12/26/2022] Open
Abstract
C. elegans Notch signaling maintains a pool of germline stem cells within their single-celled mesenchymal niche. Here we investigate the Notch transcriptional response in germline stem cells using single-molecule fluorescence in situ hybridization coupled with automated, high-throughput quantitation. This approach allows us to distinguish Notch-dependent nascent transcripts in the nucleus from mature mRNAs in the cytoplasm. We find that Notch-dependent active transcription sites occur in a probabilistic fashion and, unexpectedly, do so in a steep gradient across the stem cell pool. Yet these graded nuclear sites create a nearly uniform field of mRNAs that extends beyond the region of transcriptional activation. Therefore, active transcription sites provide a precise view of where the Notch-dependent transcriptional complex is productively engaged. Our findings offer a new window into the Notch transcriptional response and demonstrate the importance of assaying nascent transcripts at active transcription sites as a readout for canonical signaling.
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Affiliation(s)
- ChangHwan Lee
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Erika B Sorensen
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Tina R Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
| | - Judith Kimble
- Howard Hughes Medical Institute, University of Wisconsin-Madison, Madison, United States
- Department of Biochemistry, University of Wisconsin-Madison, Madison, United States
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11
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Isel C, Munier S, Naffakh N. Experimental Approaches to Study Genome Packaging of Influenza A Viruses. Viruses 2016; 8:v8080218. [PMID: 27517951 PMCID: PMC4997580 DOI: 10.3390/v8080218] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 07/26/2016] [Accepted: 08/01/2016] [Indexed: 11/16/2022] Open
Abstract
The genome of influenza A viruses (IAV) consists of eight single-stranded negative sense viral RNAs (vRNAs) encapsidated into viral ribonucleoproteins (vRNPs). It is now well established that genome packaging (i.e., the incorporation of a set of eight distinct vRNPs into budding viral particles), follows a specific pathway guided by segment-specific cis-acting packaging signals on each vRNA. However, the precise nature and function of the packaging signals, and the mechanisms underlying the assembly of vRNPs into sub-bundles in the cytoplasm and their selective packaging at the viral budding site, remain largely unknown. Here, we review the diverse and complementary methods currently being used to elucidate these aspects of the viral cycle. They range from conventional and competitive reverse genetics, single molecule imaging of vRNPs by fluorescence in situ hybridization (FISH) and high-resolution electron microscopy and tomography of budding viral particles, to solely in vitro approaches to investigate vRNA-vRNA interactions at the molecular level.
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Affiliation(s)
- Catherine Isel
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS), Institut de Biologie Moléculaire et Cellulaire (IBMC), 15 rue René Descartes, 67084 Strasbourg, France.
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
| | - Sandie Munier
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 3569, 75016 Paris, France.
- Unité de Génétique Moléculaire des Virus à ARN, Sorbonne Paris Cité, Université Paris Diderot, 75013 Paris, France.
| | - Nadia Naffakh
- Département de Virologie, Unité de Génétique Moléculaire des Virus à ARN, Institut Pasteur, 75015 Paris, France.
- Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche 3569, 75016 Paris, France.
- Unité de Génétique Moléculaire des Virus à ARN, Sorbonne Paris Cité, Université Paris Diderot, 75013 Paris, France.
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