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Blake LA, De La Cruz A, Wu B. Imaging spatiotemporal translation regulation in vivo. Semin Cell Dev Biol 2024; 154:155-164. [PMID: 36963991 PMCID: PMC10514244 DOI: 10.1016/j.semcdb.2023.03.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/26/2023]
Abstract
Translation is regulated spatiotemporally to direct protein synthesis when and where it is needed. RNA localization and local translation have been observed in various subcellular compartments, allowing cells to rapidly and finely adjust their proteome post-transcriptionally. Local translation on membrane-bound organelles is important to efficiently synthesize proteins targeted to the organelles. Protein-RNA phase condensates restrict RNA spatially in membraneless organelles and play essential roles in translation regulation and RNA metabolism. In addition, the temporal translation kinetics not only determine the amount of protein produced, but also serve as an important checkpoint for the quality of ribosomes, mRNAs, and nascent proteins. Translation imaging provides a unique capability to study these fundamental processes in the native environment. Recent breakthroughs in imaging enabled real-time visualization of translation of single mRNAs, making it possible to determine the spatial distribution and key biochemical parameters of in vivo translation dynamics. Here we reviewed the recent advances in translation imaging methods and their applications to study spatiotemporal translation regulation in vivo.
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Affiliation(s)
- Lauren A Blake
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ana De La Cruz
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Bin Wu
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; The Center for Cell Dynamics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Kwan Z, Paulose Nadappuram B, Leung MM, Mohagaonkar S, Li A, Amaradasa KS, Chen J, Rothery S, Kibreab I, Fu J, Sanchez-Alonso JL, Mansfield CA, Subramanian H, Kondrashov A, Wright PT, Swiatlowska P, Nikolaev VO, Wojciak-Stothard B, Ivanov AP, Edel JB, Gorelik J. Microtubule-Mediated Regulation of β 2AR Translation and Function in Failing Hearts. Circ Res 2023; 133:944-958. [PMID: 37869877 PMCID: PMC10635332 DOI: 10.1161/circresaha.123.323174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 10/24/2023]
Abstract
BACKGROUND β1AR (beta-1 adrenergic receptor) and β2AR (beta-2 adrenergic receptor)-mediated cyclic adenosine monophosphate signaling has distinct effects on cardiac function and heart failure progression. However, the mechanism regulating spatial localization and functional compartmentation of cardiac β-ARs remains elusive. Emerging evidence suggests that microtubule-dependent trafficking of mRNP (messenger ribonucleoprotein) and localized protein translation modulates protein compartmentation in cardiomyocytes. We hypothesized that β-AR compartmentation in cardiomyocytes is accomplished by selective trafficking of its mRNAs and localized translation. METHODS The localization pattern of β-AR mRNA was investigated using single molecule fluorescence in situ hybridization and subcellular nanobiopsy in rat cardiomyocytes. The role of microtubule on β-AR mRNA localization was studied using vinblastine, and its effect on receptor localization and function was evaluated with immunofluorescent and high-throughput Förster resonance energy transfer microscopy. An mRNA protein co-detection assay identified plausible β-AR translation sites in cardiomyocytes. The mechanism by which β-AR mRNA is redistributed post-heart failure was elucidated by single molecule fluorescence in situ hybridization, nanobiopsy, and high-throughput Förster resonance energy transfer microscopy on 16 weeks post-myocardial infarction and detubulated cardiomyocytes. RESULTS β1AR and β2AR mRNAs show differential localization in cardiomyocytes, with β1AR found in the perinuclear region and β2AR showing diffuse distribution throughout the cell. Disruption of microtubules induces a shift of β2AR transcripts toward the perinuclear region. The close proximity between β2AR transcripts and translated proteins suggests that the translation process occurs in specialized, precisely defined cellular compartments. Redistribution of β2AR transcripts is microtubule-dependent, as microtubule depolymerization markedly reduces the number of functional receptors on the membrane. In failing hearts, both β1AR and β2AR mRNAs are redistributed toward the cell periphery, similar to what is seen in cardiomyocytes undergoing drug-induced detubulation. This suggests that t-tubule remodeling contributes to β-AR mRNA redistribution and impaired β2AR function in failing hearts. CONCLUSIONS Asymmetrical microtubule-dependent trafficking dictates differential β1AR and β2AR localization in healthy cardiomyocyte microtubules, underlying the distinctive compartmentation of the 2 β-ARs on the plasma membrane. The localization pattern is altered post-myocardial infarction, resulting from transverse tubule remodeling, leading to distorted β2AR-mediated cyclic adenosine monophosphate signaling.
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MESH Headings
- Rats
- Animals
- In Situ Hybridization, Fluorescence
- Heart Failure/metabolism
- Receptors, Adrenergic, beta-2/genetics
- Receptors, Adrenergic, beta-2/metabolism
- Myocardial Infarction/metabolism
- Myocytes, Cardiac/metabolism
- Cyclic AMP/metabolism
- Receptors, Adrenergic, beta-1/metabolism
- Microtubules/metabolism
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Adenosine Monophosphate/metabolism
- Adenosine Monophosphate/pharmacology
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Affiliation(s)
- Zoe Kwan
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
- Department of Chemistry (Z.K., B.P.N., A.P.I., J.B.E.), Imperial College London, United Kingdom
| | - Binoy Paulose Nadappuram
- Department of Chemistry (Z.K., B.P.N., A.P.I., J.B.E.), Imperial College London, United Kingdom
- Department of Pure and Applied Chemistry, University of Strathclyde, United Kingdom (B.P.N.)
| | - Manton M. Leung
- Sir William Dunn School of Pathology, University of Oxford, United Kingdom (M.M.L.)
| | - Sanika Mohagaonkar
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Ao Li
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Kumuthu S. Amaradasa
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Ji Chen
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Stephen Rothery
- FILM Facility, Imperial College London, United Kingdom (S.R.)
| | - Iyobel Kibreab
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Jiarong Fu
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Jose L. Sanchez-Alonso
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Catherine A. Mansfield
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | | | - Alexander Kondrashov
- Division of Cancer and Stem Cells, University of Nottingham Biodiscovery Institute, United Kingdom (A.K.)
| | - Peter T. Wright
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
- School of Life and Health Sciences, University of Roehampton, United Kingdom (P.T.W.)
| | - Pamela Swiatlowska
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Viacheslav O. Nikolaev
- Institute of Experimental Cardiovascular Research, University Medical Center, Hamburg-Eppendorf, Germany (H.S., V.O.N.)
| | - Beata Wojciak-Stothard
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
| | - Aleksandar P. Ivanov
- Department of Chemistry (Z.K., B.P.N., A.P.I., J.B.E.), Imperial College London, United Kingdom
| | - Joshua B. Edel
- Department of Chemistry (Z.K., B.P.N., A.P.I., J.B.E.), Imperial College London, United Kingdom
| | - Julia Gorelik
- National Heart and Lung Institute (Z.K., S.M., A.L., K.S.A., J.C., I.K., J.F., J.L.S.-A., C.A.M., P.S., B.W.-S., P.T.W., J.G.), Imperial College London, United Kingdom
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Birnbaum R, Biswas J, Singer RH, Sharp DJ. mRNA Localization and Local Translation of the Microtubule Severing Enzyme, Fidgetin-Like 2, in Polarization, Migration and Outgrowth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537087. [PMID: 37131812 PMCID: PMC10153175 DOI: 10.1101/2023.04.17.537087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Cell motility requires strict spatiotemporal control of protein expression. During cell migration, mRNA localization and local translation in subcellular areas like the leading edge and protrusions are particularly advantageous for regulating the reorganization of the cytoskeleton. Fidgetin-Like 2 (FL2), a microtubule severing enzyme (MSE) that restricts migration and outgrowth, localizes to the leading edge of protrusions where it severs dynamic microtubules. FL2 is primarily expressed during development but in adulthood, is spatially upregulated at the leading edge minutes after injury. Here, we show mRNA localization and local translation in protrusions of polarized cells are responsible for FL2 leading edge expression after injury. The data suggests that the RNA binding protein IMP1 is involved in the translational regulation and stabilization of FL2 mRNA, in competition with the miRNA let-7. These data exemplify the role of local translation in microtubule network reorganization during migration and elucidate an unexplored MSE protein localization mechanism.
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Affiliation(s)
- Rayna Birnbaum
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jeetayu Biswas
- Present address: Department of Medicine, Weill Cornell Medicine, New York Presbyterian Hospital, New York, NY 10021, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H. Singer
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - David J. Sharp
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
- Microcures, Inc., Research and Development, Bronx, NY, 10461, USA
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Sadashivaiah V, Tippani M, Page SC, Kwon SH, Bach SV, Bharadwaj RA, Hyde TM, Kleinman JE, Jaffe AE, Maynard KR. SUFI: an automated approach to spectral unmixing of fluorescent multiplex images captured in mouse and post-mortem human brain tissues. BMC Neurosci 2023; 24:6. [PMID: 36698068 PMCID: PMC9878864 DOI: 10.1186/s12868-022-00765-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 12/06/2022] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Multispectral fluorescence imaging coupled with linear unmixing is a form of image data collection and analysis that allows for measuring multiple molecular signals in a single biological sample. Multiple fluorescent dyes, each measuring a unique molecule, are simultaneously measured and subsequently "unmixed" to provide a read-out for each molecular signal. This strategy allows for measuring highly multiplexed signals in a single data capture session, such as multiple proteins or RNAs in tissue slices or cultured cells, but can often result in mixed signals and bleed-through problems across dyes. Existing spectral unmixing algorithms are not optimized for challenging biological specimens such as post-mortem human brain tissue, and often require manual intervention to extract spectral signatures. We therefore developed an intuitive, automated, and flexible package called SUFI: spectral unmixing of fluorescent images. RESULTS This package unmixes multispectral fluorescence images by automating the extraction of spectral signatures using vertex component analysis, and then performs one of three unmixing algorithms derived from remote sensing. We evaluate these remote sensing algorithms' performances on four unique biological datasets and compare the results to unmixing results obtained using ZEN Black software (Zeiss). We lastly integrate our unmixing pipeline into the computational tool dotdotdot, which is used to quantify individual RNA transcripts at single cell resolution in intact tissues and perform differential expression analysis, and thereby provide an end-to-end solution for multispectral fluorescence image analysis and quantification. CONCLUSIONS In summary, we provide a robust, automated pipeline to assist biologists with improved spectral unmixing of multispectral fluorescence images.
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Affiliation(s)
- Vijay Sadashivaiah
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.
| | - Madhavi Tippani
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Stephanie C Page
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Sang Ho Kwon
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Svitlana V Bach
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Rahul A Bharadwaj
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
| | - Thomas M Hyde
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Joel E Kleinman
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
| | - Andrew E Jaffe
- Department of Genetic Medicine, McKusick-Nathans Institute, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, 21205, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Kristen R Maynard
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD, 21205, USA.
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5
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Bradbury JJ, Lovegrove HE, Giralt-Pujol M, Herbert SP. Analysis of mRNA Subcellular Distribution in Collective Cell Migration. Methods Mol Biol 2023; 2608:389-407. [PMID: 36653719 DOI: 10.1007/978-1-0716-2887-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The movement of groups of cells by collective cell migration requires division of labor between group members. Therefore, distinct cell identities, unique cell behaviors, and specific cellular roles are acquired by cells undergoing collective movement. A key driving force behind the acquisition of discrete cell states is the precise control of where, when, and how genes are expressed, both at the subcellular and supracellular level. Unraveling the mechanisms underpinning the spatiotemporal control of gene expression in collective cell migration requires not only suitable experimental models but also high-resolution imaging of messenger RNA and protein localization during this process. In recent times, the highly stereotyped growth of new blood vessels by sprouting angiogenesis has become a paradigm for understanding collective cell migration, and consequently this has led to the development of numerous user-friendly in vitro models of angiogenesis. In parallel, single-molecule fluorescent in situ hybridization (smFISH) has come to the fore as a powerful technique that allows quantification of both RNA number and RNA spatial distribution in cells and tissues. Moreover, smFISH can be combined with immunofluorescence to understand the precise interrelationship between RNA and protein distribution. Here, we describe methods for use of smFISH and immunofluorescence microscopy in in vitro angiogenesis models to enable the investigation of RNA and protein expression and localization during endothelial collective cell migration.
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Affiliation(s)
- Joshua J Bradbury
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Holly E Lovegrove
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Marta Giralt-Pujol
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shane P Herbert
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.
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Moriarty RA, Mili S, Stroka KM. RNA localization in confined cells depends on cellular mechanical activity and contributes to confined migration. iScience 2022; 25:103845. [PMID: 35198898 PMCID: PMC8850802 DOI: 10.1016/j.isci.2022.103845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/30/2021] [Accepted: 01/27/2022] [Indexed: 11/30/2022] Open
Abstract
Cancer cells experience mechanical confining forces during metastasis and, consequently, can alter their migratory mechanisms. Localization of numerous mRNAs to cell protrusions contributes to cell polarization and migration and is controlled by proteins that can bind RNA and/or cytoskeletal elements, such as the adenomatous polyposis coli (APC). Here, we demonstrate that peripheral localization of APC-dependent RNAs in cells within confined microchannels is cell type dependent. This varying phenotype is determined by the levels of a detyrosinated tubulin network. We show that this network is regulated by mechanoactivity and that cells with mechanosensitive ion channels and increased myosin II activity direct peripheral localization of the RAB13 APC-dependent RNA. Through specific mislocalization of the RAB13 RNA, we show that peripheral RNA localization contributes to confined cell migration. Our results indicate that a cell’s mechanical activity determines its ability to peripherally target RNAs and utilize them for movement in confinement. Peripheral localization of APC-dependent RNAs in confinement depends on cell type RNA localization in confined cells is controlled by the mechanoactivity of cells RNA localization phenotype is influenced by the detyrosinated tubulin network Peripheral RNA accumulation functionally contributes to confined cell migration
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Affiliation(s)
- Rebecca A. Moriarty
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, MD 20742, USA
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
- Corresponding author
| | - Kimberly M. Stroka
- Fischell Department of Bioengineering, University of Maryland College Park, College Park, MD 20742, USA
- Maryland Biophysics Program, University of Maryland College Park, College Park, MD 20742, USA
- Center for Stem Cell Biology & Regenerative Medicine, University of Maryland Baltimore, Baltimore, MD 21202, USA
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland Baltimore, Baltimore, MD 21202, USA
- Corresponding author
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Xu W, Biswas J, Singer RH, Rosbash M. Targeted RNA editing: novel tools to study post-transcriptional regulation. Mol Cell 2022; 82:389-403. [PMID: 34739873 PMCID: PMC8792254 DOI: 10.1016/j.molcel.2021.10.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/22/2023]
Abstract
RNA binding proteins (RBPs) regulate nearly all post-transcriptional processes within cells. To fully understand RBP function, it is essential to identify their in vivo targets. Standard techniques for profiling RBP targets, such as crosslinking immunoprecipitation (CLIP) and its variants, are limited or suboptimal in some situations, e.g. when compatible antibodies are not available and when dealing with small cell populations such as neuronal subtypes and primary stem cells. This review summarizes and compares several genetic approaches recently designed to identify RBP targets in such circumstances. TRIBE (targets of RNA binding proteins identified by editing), RNA tagging, and STAMP (surveying targets by APOBEC-mediated profiling) are new genetic tools useful for the study of post-transcriptional regulation and RBP identification. We describe the underlying RNA base editing technology, recent applications, and therapeutic implications.
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Affiliation(s)
- Weijin Xu
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Michael Rosbash
- Howard Hughes Medical Institute, Department of Biology, Brandeis University, Waltham, MA 02451, USA.
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Cawte AD, Iino H, Unrau PJ, Rueda DS. Single-Molecule RNA Imaging Using Mango II Arrays. Methods Mol Biol 2022; 2404:267-280. [PMID: 34694614 DOI: 10.1007/978-1-0716-1851-6_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
In recent years, fluorogenic RNA aptamers, such as Spinach, Broccoli, Corn, Mango, Coral, and Pepper have gathered traction as an efficient alternative labeling strategy for background-free imaging of cellular RNAs. However, their application has been somewhat limited by relatively inefficient folding and fluorescent stability. With the recent advent of novel RNA-Mango variants which are improved in both fluorescence intensity and folding stability in tandem arrays, it is now possible to image RNAs with single-molecule sensitivity. Here we discuss the protocol for imaging Mango II tagged RNAs in both fixed and live cells.
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Affiliation(s)
- Adam D Cawte
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London, UK
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
- Developmental Epigenetics, Department of Biochemistry, University of Oxford, Oxford, UK
| | - Haruki Iino
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London, UK
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
| | - David S Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, London, UK.
- Section of Virology, Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK.
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9
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Yang S, Xiong Y, Du Y, Wang YJ, Zhang L, Shen F, Liu YJ, Liu X, Yang P. Ultrasensitive Trace Sample Proteomics Unraveled the Protein Remodeling during Mesenchymal-Amoeboid Transition. Anal Chem 2021; 94:768-776. [PMID: 34928127 DOI: 10.1021/acs.analchem.1c03212] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Deep mining the proteome of trace biological samples is critical for biomedical applications. However, it remains a challenge due to the loss of analytes caused by current sample preparation procedures. To address this, we recently developed a single-pot and miniaturized in-solution digestion (SMID) method for minute sample handling with three streamlined steps and completed within 3 h. The SMID approach outperformed the traditional workflow in substantially saving time, reducing sample loss, and exhibiting extensive applicability for 10-100 000 cell analysis. This user-friendly and high-sensitivity strategy enables ∼5300 proteins and 53 000 peptides to be confidently identified within 1 h of mass spectrometry (MS) time from a small amount of 1000 HeLa cells. In addition, we accurately and robustly detected proteomes in 10 mouse oocytes with excellent reproducibility. We further adopted SMID for the proteome analysis in cell migration under confinement, which induced cells to undergo a mesenchymal-amoeboid transition (MAT). During the MAT, a systematic quantitative proteome map of 1000 HeLa cells was constructed with seven expression profile clusters, which illustrated the application of SMID and provided a fundamental resource to investigate the mechanism of MAT.
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Affiliation(s)
- Shuang Yang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yueting Xiong
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yang Du
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Ya-Jun Wang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Lei Zhang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Fenglin Shen
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Yan-Jun Liu
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Xiaohui Liu
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
| | - Pengyuan Yang
- The Fifth People's Hospital of Shanghai, Zhongshan Hospital, and Shanghai Key Laboratory of Medical Epigenetics, International Co-Laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, China
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10
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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 REPORTS 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] [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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11
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Das S, Vera M, Gandin V, Singer RH, Tutucci E. Intracellular mRNA transport and localized translation. Nat Rev Mol Cell Biol 2021; 22:483-504. [PMID: 33837370 PMCID: PMC9346928 DOI: 10.1038/s41580-021-00356-8] [Citation(s) in RCA: 126] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/25/2021] [Indexed: 02/08/2023]
Abstract
Fine-tuning cellular physiology in response to intracellular and environmental cues requires precise temporal and spatial control of gene expression. High-resolution imaging technologies to detect mRNAs and their translation state have revealed that all living organisms localize mRNAs in subcellular compartments and create translation hotspots, enabling cells to tune gene expression locally. Therefore, mRNA localization is a conserved and integral part of gene expression regulation from prokaryotic to eukaryotic cells. In this Review, we discuss the mechanisms of mRNA transport and local mRNA translation across the kingdoms of life and at organellar, subcellular and multicellular resolution. We also discuss the properties of messenger ribonucleoprotein and higher order RNA granules and how they may influence mRNA transport and local protein synthesis. Finally, we summarize the technological developments that allow us to study mRNA localization and local translation through the simultaneous detection of mRNAs and proteins in single cells, mRNA and nascent protein single-molecule imaging, and bulk RNA and protein detection methods.
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Affiliation(s)
- Sulagna Das
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA
| | - Maria Vera
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | | | - Robert H. Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY, USA.,Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, New York, NY, USA.,Janelia Research Campus of the HHMI, Ashburn, VA, USA.,;
| | - Evelina Tutucci
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,;
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12
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Dermit M, Dodel M, Lee FCY, Azman MS, Schwenzer H, Jones JL, Blagden SP, Ule J, Mardakheh FK. Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells. Dev Cell 2020; 55:298-313.e10. [PMID: 33171110 PMCID: PMC7660134 DOI: 10.1016/j.devcel.2020.10.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/01/2020] [Accepted: 10/08/2020] [Indexed: 12/24/2022]
Abstract
Translation of ribosomal protein-coding mRNAs (RP-mRNAs) constitutes a key step in ribosome biogenesis, but the mechanisms that modulate RP-mRNA translation in coordination with other cellular processes are poorly defined. Here, we show that subcellular localization of RP-mRNAs acts as a key regulator of their translation during cell migration. As cells migrate into their surroundings, RP-mRNAs localize to the actin-rich cell protrusions. This localization is mediated by La-related protein 6 (LARP6), an RNA-binding protein that is enriched in protrusions. Protrusions act as hotspots of translation for RP-mRNAs, enhancing RP synthesis, ribosome biogenesis, and the overall protein synthesis in migratory cells. In human breast carcinomas, epithelial-to-mesenchymal transition (EMT) upregulates LARP6 expression to enhance protein synthesis and support invasive growth. Our findings reveal LARP6-mediated mRNA localization as a key regulator of ribosome biogenesis during cell migration and demonstrate a role for this process in cancer progression downstream of EMT.
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Affiliation(s)
- Maria Dermit
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Martin Dodel
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Flora C Y Lee
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Muhammad S Azman
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Hagen Schwenzer
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - J Louise Jones
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Sarah P Blagden
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Jernej Ule
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, Queen Square, London WC1N 3BG, UK
| | - Faraz K Mardakheh
- Centre for Cancer Cell and Molecular Biology, Barts Cancer Institute, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK.
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13
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Costa G, Bradbury JJ, Tarannum N, Herbert SP. RAB13 mRNA compartmentalisation spatially orients tissue morphogenesis. EMBO J 2020; 39:e106003. [PMID: 32946121 PMCID: PMC7604621 DOI: 10.15252/embj.2020106003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/08/2020] [Accepted: 08/14/2020] [Indexed: 02/06/2023] Open
Abstract
Polarised targeting of diverse mRNAs to cellular protrusions is a hallmark of cell migration. Although a widespread phenomenon, definitive functions for endogenous targeted mRNAs and their relevance to modulation of in vivo tissue dynamics remain elusive. Here, using single-molecule analysis, gene editing and zebrafish live-cell imaging, we report that mRNA polarisation acts as a molecular compass that orients motile cell polarity and spatially directs tissue movement. Clustering of protrusion-derived RNAseq datasets defined a core 192-nt localisation element underpinning precise mRNA targeting to sites of filopodia formation. Such targeting of the small GTPase RAB13 generated tight spatial coupling of mRNA localisation, translation and protein activity, achieving precise subcellular compartmentalisation of RAB13 protein function to create a polarised domain of filopodia extension. Consequently, genomic excision of this localisation element and perturbation of RAB13 mRNA targeting-but not translation-depolarised filopodia dynamics in motile endothelial cells and induced mispatterning of blood vessels in zebrafish. Hence, mRNA polarisation, not expression, is the primary determinant of the site of RAB13 action, preventing ectopic functionality at inappropriate subcellular loci and orienting tissue morphogenesis.
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Affiliation(s)
- Guilherme Costa
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,Wellcome-Wolfson Institute for Experimental Medicine, Queen's University of Belfast, Belfast, UK
| | - Joshua J Bradbury
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Nawseen Tarannum
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Shane P Herbert
- Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
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14
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Lim HYG, Alvarez YD, Gasnier M, Wang Y, Tetlak P, Bissiere S, Wang H, Biro M, Plachta N. Keratins are asymmetrically inherited fate determinants in the mammalian embryo. Nature 2020; 585:404-409. [PMID: 32848249 DOI: 10.1038/s41586-020-2647-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/30/2020] [Indexed: 11/08/2022]
Abstract
To implant in the uterus, the mammalian embryo first specifies two cell lineages: the pluripotent inner cell mass that forms the fetus, and the outer trophectoderm layer that forms the placenta1. In many organisms, asymmetrically inherited fate determinants drive lineage specification2, but this is not thought to be the case during early mammalian development. Here we show that intermediate filaments assembled by keratins function as asymmetrically inherited fate determinants in the mammalian embryo. Unlike F-actin or microtubules, keratins are the first major components of the cytoskeleton that display prominent cell-to-cell variability, triggered by heterogeneities in the BAF chromatin-remodelling complex. Live-embryo imaging shows that keratins become asymmetrically inherited by outer daughter cells during cell division, where they stabilize the cortex to promote apical polarization and YAP-dependent expression of CDX2, thereby specifying the first trophectoderm cells of the embryo. Together, our data reveal a mechanism by which cell-to-cell heterogeneities that appear before the segregation of the trophectoderm and the inner cell mass influence lineage fate, via differential keratin regulation, and identify an early function for intermediate filaments in development.
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Affiliation(s)
- Hui Yi Grace Lim
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yanina D Alvarez
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Maxime Gasnier
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | - Yiming Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Science, Beijing, China
| | - Piotr Tetlak
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore
| | | | - Hongmei Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Science, Beijing, China
| | - Maté Biro
- EMBL Australia, Single Molecule Science Node, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Nicolas Plachta
- Institute of Molecular and Cell Biology, ASTAR, Singapore, Singapore.
- Department of Cell and Developmental Biology and Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Mofatteh M. mRNA localization and local translation in neurons. AIMS Neurosci 2020; 7:299-310. [PMID: 32995487 PMCID: PMC7519968 DOI: 10.3934/neuroscience.2020016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 08/05/2020] [Indexed: 12/15/2022] Open
Abstract
The spatial and temporal regulation of gene expression in neurons is an important step in creating functional and structural neuronal networks. The complexity of neurons require differential expression of various proteins in different compartments. Highly polarised cells, such as neurons, respond rapidly to different external stimuli by changing their local protein abundance and composition. Neurons can have extensions up to a meter away from their cell body in humans, so it is easy to envisage why they need to manage the synthesis of new proteins locally and on-demand. Recent research has demonstrated that neurons can control the expression of different proteins by localising translationally silent mRNAs, followed by subsequent translation. Neurons use mRNA localization and local translation to achieve different purposes during their life cycle. While developing neurons rely on mRNA localization for axon guidance and synaptogenesis, mature neurons can use mRNA localization for maintenance of essential physiological processes. mRNA localization also plays a role in response to neuron injury to regenerate and restore neuronal connections. Recent microscopic imaging techniques such as live imaging of fluorescently tagged molecules combined with genetic and biochemical studies in neurons have illustrated evolutionarily conserved mechanisms for targeting mRNAs into their correct compartments. This review provides an overview of mRNA localization and local translation in vertebrate and invertebrate neurons and discusses the mechanism by which mRNAs are trafficked into axons. Furthermore, the role of mRNA localization in synaptic activation, as well as axonal injury is explored.
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Affiliation(s)
- Mohammad Mofatteh
- Lincoln College, University of Oxford, Turl Street, Oxford, OX1 3DR, United Kingdom.,Merton College, University of Oxford, Merton Street, Oxford, OX1 4DJ, United Kingdom.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, United Kingdom
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16
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Casser E, Wdowik S, Israel S, Witten A, Schlatt S, Nordhoff V, Boiani M. Differences in blastomere totipotency in 2-cell mouse embryos are a maternal trait mediated by asymmetric mRNA distribution. Mol Hum Reprod 2020; 25:729-744. [PMID: 31504820 PMCID: PMC6884417 DOI: 10.1093/molehr/gaz051] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 07/05/2019] [Accepted: 08/14/2019] [Indexed: 12/13/2022] Open
Abstract
It is widely held that the first two blastomeres of mammalian embryos are equally totipotent and that this totipotency belongs to the group of regulative properties. However, this interpretation neglects an important aspect: evidence only came from successful monozygotic twins which can speak only for those pairs of half-embryos that are able to regulate in the first place. Are the frequently occurring incomplete pairs simply an artefact, or do they represent a real difference, be it in the imperfect blastomere's ability to regulate growth or in the distribution of any compound X that constrains regulation? Using the model system of mouse embryos bisected at the 2-cell stage after fertilization, we present evidence that the interblastomere differences evade regulation by external factors and are already latent in oocytes. Specifically, an interblastomere imbalance of epiblast production persists under the most diverse culture conditions and applies to the same extent in parthenogenetic counterparts. As a result, cases in which twin blastocysts continued to develop in only one member account for 65 and 57% of zygotic and parthenogenetic pairs, respectively. The interblastomere imbalance is related to the subcellular distribution of gene products, as documented for the epiblast-related gene Cops3, using mRNA FISH in super-resolution mode confocal microscopy. Blastomere patterns of Cops3 mRNA distribution are α-amanitin-resistant. Thus, the imbalance originates not from de novo transcription, but from influences which are effective before fertilisation. These data expose previously unrecognized limits of regulative capacities of 2-cell stage blastomeres and point to aspects of cytoplasmic organization of the mouse oocyte that segregate unequally to blastomeres during cleavage.
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Affiliation(s)
- E Casser
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - S Wdowik
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - S Israel
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
| | - A Witten
- Core Genomic Facility, University Hospital Muenster, Muenster, Germany
| | - S Schlatt
- Centre for Reproductive Medicine and Andrology, University Hospital Muenster, Muenster, Germany
| | - V Nordhoff
- Centre for Reproductive Medicine and Andrology, University Hospital Muenster, Muenster, Germany
| | - M Boiani
- Max Planck Institute for Molecular Biomedicine, Muenster, Germany
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17
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Sending messages in moving cells: mRNA localization and the regulation of cell migration. Essays Biochem 2020; 63:595-606. [PMID: 31324705 DOI: 10.1042/ebc20190009] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 07/05/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
Cell migration is a fundamental biological process involved in tissue formation and homeostasis. The correct polarization of motile cells is critical to ensure directed movement, and is orchestrated by many intrinsic and extrinsic factors. Of these, the subcellular distribution of mRNAs and the consequent spatial control of translation are key modulators of cell polarity. mRNA transport is dependent on cis-regulatory elements within transcripts, which are recognized by trans-acting proteins that ensure the efficient delivery of certain messages to the leading edge of migrating cells. At their destination, translation of localized mRNAs then participates in regional cellular responses underlying cell motility. In this review, we summarize the key findings that established mRNA targetting as a critical driver of cell migration and how the characterization of polarized mRNAs in motile cells has been expanded from just a few species to hundreds of transcripts. We also describe the molecular control of mRNA trafficking, subsequent mechanisms of local protein synthesis and how these ultimately regulate cell polarity during migration.
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18
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Cawte AD, Unrau PJ, Rueda DS. Live cell imaging of single RNA molecules with fluorogenic Mango II arrays. Nat Commun 2020; 11:1283. [PMID: 32152311 PMCID: PMC7062757 DOI: 10.1038/s41467-020-14932-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/30/2020] [Indexed: 01/19/2023] Open
Abstract
RNA molecules play vital roles in many cellular processes. Visualising their dynamics in live cells at single-molecule resolution is essential to elucidate their role in RNA metabolism. RNA aptamers, such as Spinach and Mango, have recently emerged as a powerful background-free technology for live-cell RNA imaging due to their fluorogenic properties upon ligand binding. Here, we report a novel array of Mango II aptamers for RNA imaging in live and fixed cells with high contrast and single-molecule sensitivity. Direct comparison of Mango II and MS2-tdMCP-mCherry dual-labelled mRNAs show marked improvements in signal to noise ratio using the fluorogenic Mango aptamers. Using both coding (β-actin mRNA) and long non-coding (NEAT1) RNAs, we show that the Mango array does not affect cellular localisation. Additionally, we can track single mRNAs for extended time periods, likely due to bleached fluorophore replacement. This property makes the arrays readily compatible with structured illumination super-resolution microscopy.
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Affiliation(s)
- Adam D Cawte
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Rd, London, UK
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Rd, London, UK
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC, Canada.
| | - David S Rueda
- Single Molecule Imaging Group, MRC London Institute of Medical Sciences, Du Cane Rd, London, UK.
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, Du Cane Rd, London, UK.
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19
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Optogenetic control of mRNA localization and translation in live cells. Nat Cell Biol 2020; 22:341-352. [PMID: 32066905 DOI: 10.1038/s41556-020-0468-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 01/13/2020] [Indexed: 02/06/2023]
Abstract
Despite efforts to visualize the spatio-temporal dynamics of single messenger RNAs, the ability to precisely control their function has lagged. This study presents an optogenetic approach for manipulating the localization and translation of specific mRNAs by trapping them in clusters. This clustering greatly amplified reporter signals, enabling endogenous RNA-protein interactions to be clearly visualized in single cells. Functionally, this sequestration reduced the ability of mRNAs to access ribosomes, markedly attenuating protein synthesis. A spatio-temporally resolved analysis indicated that sequestration of endogenous β-actin mRNA attenuated cell motility through the regulation of focal-adhesion dynamics. These results suggest a mechanism highlighting the indispensable role of newly synthesized β-actin protein for efficient cell migration. This platform may be broadly applicable for use in investigating the spatio-temporal activities of specific mRNAs in various biological processes.
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20
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Chen X, Zhang D, Su N, Bao B, Xie X, Zuo F, Yang L, Wang H, Jiang L, Lin Q, Fang M, Li N, Hua X, Chen Z, Bao C, Xu J, Du W, Zhang L, Zhao Y, Zhu L, Loscalzo J, Yang Y. Visualizing RNA dynamics in live cells with bright and stable fluorescent RNAs. Nat Biotechnol 2019; 37:1287-1293. [PMID: 31548726 DOI: 10.1038/s41587-019-0249-1] [Citation(s) in RCA: 175] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 08/02/2019] [Indexed: 12/15/2022]
Abstract
Fluorescent RNAs (FRs), aptamers that bind and activate fluorescent dyes, have been used to image abundant cellular RNA species. However, limitations such as low brightness and limited availability of dye/aptamer combinations with different spectral characteristics have limited use of these tools in live mammalian cells and in vivo. Here, we develop Peppers, a series of monomeric, bright and stable FRs with a broad range of emission maxima spanning from cyan to red. Peppers allow simple and robust imaging of diverse RNA species in live cells with minimal perturbation of the target RNA's transcription, localization and translation. Quantification of the levels of proteins and their messenger RNAs in single cells suggests that translation is governed by normal enzyme kinetics but with marked heterogeneity. We further show that Peppers can be used for imaging genomic loci with CRISPR display, for real-time tracking of protein-RNA tethering, and for super-resolution imaging. We believe these FRs will be useful tools for live imaging of cellular RNAs.
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Affiliation(s)
- Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Dasheng Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Ni Su
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Bingkun Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Xin Xie
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Fangting Zuo
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Lipeng Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Hui Wang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Li Jiang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Qiuning Lin
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Mengyue Fang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Ningfeng Li
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Xin Hua
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Zhengda Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Chunyan Bao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China
| | - Jinjin Xu
- Key Laboratory of Advanced Control and Optimization for Chemical Processed of Ministry of Education, School of information Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Wenli Du
- Key Laboratory of Advanced Control and Optimization for Chemical Processed of Ministry of Education, School of information Science and Engineering, East China University of Science and Technology, Shanghai, China
| | - Lixin Zhang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China
| | - Yuzheng Zhao
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China.,School of Pharmacy, East China University of Science and Technology, Shanghai, China
| | - Linyong Zhu
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, China.
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, Shanghai, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China. .,School of Pharmacy, East China University of Science and Technology, Shanghai, China.
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21
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Kim SH, Vieira M, Shim JY, Choi H, Park HY. Recent progress in single-molecule studies of mRNA localization in vivo. RNA Biol 2019; 16:1108-1118. [PMID: 30336727 PMCID: PMC6693552 DOI: 10.1080/15476286.2018.1536592] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 08/28/2018] [Accepted: 10/08/2018] [Indexed: 12/26/2022] Open
Abstract
From biogenesis to degradation, mRNA goes through diverse types of regulation and interaction with other biomolecules. Uneven distribution of mRNA transcripts and the diverse isoforms and modifications of mRNA make us wonder how cells manage the complexity and keep the functional integrity for the normal development of cells and organisms. Single-molecule microscopy tools have expanded the scope of RNA research with unprecedented spatiotemporal resolution. In this review, we highlight the recent progress in the methods for labeling mRNA targets and analyzing the quantitative information from fluorescence images of single mRNA molecules. In particular, the MS2 system and its various applications are the main focus of this article. We also review how recent studies have addressed biological questions related to the significance of mRNA localization in vivo. Efforts to visualize the dynamics of single mRNA molecules in live cells will push forward our knowledge on the nature of heterogeneity in RNA sequence, structure, and distribution as well as their molecular function and coordinated interaction with RNA binding proteins.
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Affiliation(s)
- Songhee H. Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
| | - Melissa Vieira
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
| | - Jae Youn Shim
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hongyoung Choi
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, Korea
- Institute of Applied Physics, Seoul National University, Seoul, Korea
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22
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Visualization of Single mRNAs in Live Neurons. Methods Mol Biol 2019. [PMID: 31407277 DOI: 10.1007/978-1-4939-9674-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Transcription and post-transcriptional regulations are critical in gene expression. To study the spatiotemporal regulation of RNA inside a cell, techniques for high-resolution imaging of RNA have been developed. In this chapter, we describe RNA fluorescent labeling methods using MS2 and PP7 systems to detect single RNA molecules in live neurons. We use hippocampal neurons cultured from knock-in mouse models in which β-actin or Arc mRNAs are tagged with MS2 or PP7 stem-loops. Adeno-associated virus (AAV) or lentiviral vectors are used to express MS2 or PP7 capsid proteins fused with GFP in those neurons. Then, GFP-labeled RNAs in live neurons can be detected by epifluorescence microscopy, and their moving pathways can be analyzed using single-particle tracking software. For these processes, we introduce protocols for neuron culture, transfection, imaging, and particle tracking methods.
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Abstract
The molecular function and fate of mRNAs are controlled by RNA-binding proteins (RBPs). Identification of the interacting proteome of a specific mRNA in vivo remains very challenging, however. Based on the widely used technique of RNA tagging with MS2 aptamers for RNA visualization, we developed a RNA proximity biotinylation (RNA-BioID) technique by tethering biotin ligase (BirA*) via MS2 coat protein at the 3' UTR of endogenous MS2-tagged β-actin mRNA in mouse embryonic fibroblasts. We demonstrate the dynamics of the β-actin mRNA interactome by characterizing its changes on serum-induced localization of the mRNA. Apart from the previously known interactors, we identified more than 60 additional β-actin-associated RBPs by RNA-BioID. Among these, the KH domain-containing protein FUBP3/MARTA2 has been shown to be required for β-actin mRNA localization. We found that FUBP3 binds to the 3' UTR of β-actin mRNA and is essential for β-actin mRNA localization, but does not interact with the characterized β-actin zipcode element. RNA-BioID provides a tool for identifying new mRNA interactors and studying the dynamic view of the interacting proteome of endogenous mRNAs in space and time.
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24
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Stueland M, Wang T, Park HY, Mili S. RDI Calculator: An Analysis Tool to Assess RNA Distributions in Cells. Sci Rep 2019; 9:8267. [PMID: 31164708 PMCID: PMC6547641 DOI: 10.1038/s41598-019-44783-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 05/20/2019] [Indexed: 11/17/2022] Open
Abstract
Localization of RNAs to various subcellular destinations has emerged as a widely used mechanism that regulates a large proportion of transcripts in polarized cells. A number of methodologies have been developed that allow detection and imaging of RNAs at single-molecule resolution. However, methodologies to quantitatively describe RNA distributions are limited. Such approaches usually rely on the identification of cytoplasmic and nuclear boundaries which are used as reference points. Here, we describe an automated, interactive image analysis program that facilitates the accurate generation of cellular outlines from single cells and the subsequent calculation of metrics that quantify how a population of RNA molecules is distributed in the cell cytoplasm. We apply this analysis to mRNAs in mouse and human cells to demonstrate how these metrics can highlight differences in the distribution patterns of distinct RNA species. We further discuss considerations for the practical use of this tool. This program provides a way to facilitate and expedite the analysis of subcellular RNA localization for mechanistic and functional studies.
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Affiliation(s)
- Michael Stueland
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Tianhong Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, Korea
| | - Stavroula Mili
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
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25
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Kim SH, Vieira M, Kim HJ, Kesawat MS, Park HY. MS2 Labeling of Endogenous Beta-Actin mRNA Does Not Result in Stabilization of Degradation Intermediates. Mol Cells 2019; 42:356-362. [PMID: 30841028 PMCID: PMC6530646 DOI: 10.14348/molcells.2019.2398] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 01/17/2019] [Accepted: 02/05/2019] [Indexed: 11/27/2022] Open
Abstract
The binding of MS2 bacteriophage coat protein (MCP) to MS2 binding site (MBS) RNA stem-loop sequences has been widely used to label mRNA for live-cell imaging at single-molecule resolution. However, concerns have been raised recently from studies with budding yeast showing aberrant mRNA metabolism following the MS2-GFP labeling. To investigate the degradation pattern of MS2-GFP-labeled mRNA in mammalian cells and tissues, we used Northern blot analysis of β-actin mRNA extracted from the Actb-MBS knock-in and MBS×MCP hybrid mouse models. In the immortalized mouse embryonic cell lines and various organ tissues derived from the mouse models, we found no noticeable accumulation of decay products of β-actin mRNA compared with the wild-type mice. Our results suggest that accumulation of MBS RNA decay fragments does not always happen depending on the mRNA species and the model organisms used.
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Affiliation(s)
- Songhee H. Kim
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
| | - Melissa Vieira
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 08826,
Korea
| | - Hye-Jin Kim
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
| | - Mahipal Singh Kesawat
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul 08826,
Korea
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul 08826,
Korea
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul 08826,
Korea
- Institute of Applied Physics, Seoul National University, Seoul 08826,
Korea
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26
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Rodriguez A, Kashina A. Posttranscriptional and Posttranslational Regulation of Actin. Anat Rec (Hoboken) 2018; 301:1991-1998. [PMID: 30312009 DOI: 10.1002/ar.23958] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 04/12/2018] [Accepted: 04/14/2018] [Indexed: 12/14/2022]
Abstract
Actin is one of the most abundant intracellular proteins, essential in every eukaryotic cell type. Actin plays key roles in tissue morphogenesis, cell adhesion, muscle contraction, and developmental reprogramming. Most actin studies have focused on its regulation at the protein level, either directly or through differential interactions with over a hundred intracellular binding partners. However, numerous studies emerging in recent years demonstrate specific types of nucleotide-level regulation that strongly affect non-muscle actins during cell migration and adhesion and are potentially applicable to other members of the actin family. This regulation involves zipcode-mediated actin mRNA targeting to the cell periphery, proposed to mediate local synthesis of actin at the cell leading edge, as well as the recently discovered N-terminal arginylation that specifically targets non-muscle β-actin via a nucleotide-dependent mechanism. Moreover, a study published this year suggests that actin's essential roles at the organismal level may be entirely nucleotide-dependent. This review summarizes the emerging data on actin's nucleotide-level regulation. Anat Rec, 301:1991-1998, 2018. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Alexis Rodriguez
- Department of Biological Sciences, Rutgers University, Newark, New Jersey
| | - Anna Kashina
- Department of Biomedical Sciences, University of Pennsylvania, School of Veterinary Medicine, Philadelphia, Pennsylvania
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27
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Li Y, Ke K, Spitale RC. Biochemical Methods To Image and Analyze RNA Localization: From One to Many. Biochemistry 2018; 58:379-386. [DOI: 10.1021/acs.biochem.8b01087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Fan X, Ashraf UM, Drummond CA, Shi H, Zhang X, Kumarasamy S, Tian J. Characterization of a Long Non-Coding RNA, the Antisense RNA of Na/K-ATPase α1 in Human Kidney Cells. Int J Mol Sci 2018; 19:ijms19072123. [PMID: 30037072 PMCID: PMC6073804 DOI: 10.3390/ijms19072123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 07/17/2018] [Accepted: 07/19/2018] [Indexed: 01/19/2023] Open
Abstract
Non-coding RNAs are important regulators of protein-coding genes. The current study characterized an antisense long non-coding RNA, ATP1A1-AS1, which is located on the opposite strand of the Na/K-ATPase α1 gene. Our results show that four splice variants are expressed in human adult kidney cells (HK2 cells) and embryonic kidney cells (HEK293 cells). These variants can be detected in both cytosol and nuclear fractions. We also found that the inhibition of DNA methylation has a differential effect on the expression of ATP1A1-AS1 and its sense gene. To investigate the physiological role of this antisense gene, we overexpressed the ATP1A1-AS1 transcripts, and examined their effect on Na/K-ATPase expression and related signaling function in human kidney cells. The results showed that overexpression of the ATP1A1-AS1-203 transcript in HK2 cells reduced the Na/K-ATPase α1 (ATP1A1) gene expression by approximately 20% (p < 0.05), while reducing the Na/K-ATPase α1 protein synthesis by approximately 22% (p < 0.05). Importantly, overexpression of the antisense RNA transcript attenuated ouabain-induced Src activation in HK2 cells. It also inhibited the cell proliferation and potentiated ouabain-induced cell death. These results demonstrate that the ATP1A1-AS1 gene is a moderate negative regulator of Na/K-ATPase α1, and can modulate Na/K-ATPase-related signaling pathways in human kidney cells.
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Affiliation(s)
- Xiaoming Fan
- Department of Medicine, University of Toledo, Toledo, OH 43614, USA.
| | - Usman M Ashraf
- Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine, University of Toledo, Toledo, OH 43614, USA.
| | - Christopher A Drummond
- Department of Medicine, University of Toledo, Toledo, OH 43614, USA.
- MPI Research, Mattawan, MI 49071, USA.
| | - Huilin Shi
- Department of Medicine, University of Toledo, Toledo, OH 43614, USA.
| | - Xiaolu Zhang
- Department of Medicine, University of Toledo, Toledo, OH 43614, USA.
| | - Sivarajan Kumarasamy
- Department of Physiology and Pharmacology, Center for Hypertension and Personalized Medicine, University of Toledo, Toledo, OH 43614, USA.
| | - Jiang Tian
- Department of Medicine, University of Toledo, Toledo, OH 43614, USA.
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29
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Chen J, McSwiggen D, Ünal E. Single Molecule Fluorescence In Situ Hybridization (smFISH) Analysis in Budding Yeast Vegetative Growth and Meiosis. J Vis Exp 2018. [PMID: 29889208 PMCID: PMC6101419 DOI: 10.3791/57774] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Single molecule fluorescence in situ hybridization (smFISH) is a powerful technique to study gene expression in single cells due to its ability to detect and count individual RNA molecules. Complementary to deep sequencing-based methods, smFISH provides information about the cell-to-cell variation in transcript abundance and the subcellular localization of a given RNA. Recently, we have used smFISH to study the expression of the gene NDC80 during meiosis in budding yeast, in which two transcript isoforms exist and the short transcript isoform has its entire sequence shared with the long isoform. To confidently identify each transcript isoform, we optimized known smFISH protocols and obtained high consistency and quality of smFISH data for the samples acquired during budding yeast meiosis. Here, we describe this optimized protocol, the criteria that we use to determine whether high quality of smFISH data is obtained, and some tips for implementing this protocol in other yeast strains and growth conditions.
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Affiliation(s)
- Jingxun Chen
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley
| | - David McSwiggen
- Department of Molecular and Cell Biology, Li Ka Shing Center, University of California, Berkeley
| | - Elçin Ünal
- Department of Molecular and Cell Biology, Barker Hall, University of California, Berkeley;
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30
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IMP1, an mRNA binding protein that reduces the metastatic potential of breast cancer in a mouse model. Oncotarget 2018; 7:72662-72671. [PMID: 27655671 PMCID: PMC5341935 DOI: 10.18632/oncotarget.12083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 09/02/2016] [Indexed: 12/22/2022] Open
Abstract
Cells that are able to localize β-actin mRNA efficiently have decreased metastatic potential. Invasive carcinoma cells derived from primary mammary tumors have reduced levels of an RNA binding protein IMP1/ZBP1/IGF2BP1, required for β-actin mRNA localization. We showed previously that in human breast carcinoma cells in vitro, this protein suppresses invasion. In this work we examined whether its re-expression can suppress breast cancer metastasis in a breast cancer mouse model. We developed a mouse conditionally expressing IMP1-GFP (hereinafter referred to as the IMP1 transgene) specifically in the mammary gland of a PYMT breast cancer mouse. We found that mice conditionally expressing the IMP1 transgene showed little or no metastases to the lungs from the primary tumor in contrast to PYMT mice not expressing IMP1, which uniformly develop metastases at an early stage.
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31
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Tréfier A, Pellissier LP, Musnier A, Reiter E, Guillou F, Crépieux P. G Protein-Coupled Receptors As Regulators of Localized Translation: The Forgotten Pathway? Front Endocrinol (Lausanne) 2018; 9:17. [PMID: 29456523 PMCID: PMC5801404 DOI: 10.3389/fendo.2018.00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 01/15/2018] [Indexed: 12/31/2022] Open
Abstract
G protein-coupled receptors (GPCRs) exert their physiological function by transducing a complex signaling network that coordinates gene expression and dictates the phenotype of highly differentiated cells. Much is known about the gene networks they transcriptionally regulate upon ligand exposure in a process that takes hours before a new protein is synthesized. However, far less is known about GPCR impact on the translational machinery and subsequent mRNA translation, although this gene regulation level alters the cell phenotype in a strikingly different timescale. In fact, mRNA translation is an early response kinetically connected to signaling events, hence it leads to the synthesis of a new protein within minutes following receptor activation. By these means, mRNA translation is responsive to subtle variations of the extracellular environment. In addition, when restricted to cell subcellular compartments, local mRNA translation contributes to cell micro-specialization, as observed in synaptic plasticity or in cell migration. The mechanisms that control where in the cell an mRNA is translated are starting to be deciphered. But how an extracellular signal triggers such local translation still deserves extensive investigations. With the advent of high-throughput data acquisition, it now becomes possible to review the current knowledge on the translatome that some GPCRs regulate, and how this information can be used to explore GPCR-controlled local translation of mRNAs.
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Affiliation(s)
- Aurélie Tréfier
- Biologie et Bioinformatique des Systèmes de Signalisation, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Lucie P. Pellissier
- Déficit de Récompense, GPCR et sociabilité, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Astrid Musnier
- Biologie et Bioinformatique des Systèmes de Signalisation, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Eric Reiter
- Biologie et Bioinformatique des Systèmes de Signalisation, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Florian Guillou
- Plasticité Génomique et Expression Phénotypique, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
| | - Pascale Crépieux
- Biologie et Bioinformatique des Systèmes de Signalisation, INRA, UMR85, Physiologie de la Reproduction et des Comportements, Nouzilly, France
- CNRS, UMR7247, Nouzilly, France
- Université François Rabelais, Tours, France
- IFCE, Nouzilly, France
- *Correspondence: Pascale Crépieux,
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32
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Hotz M, Nelson WJ. Pumilio-dependent localization of mRNAs at the cell front coordinates multiple pathways required for chemotaxis. Nat Commun 2017; 8:1366. [PMID: 29118357 PMCID: PMC5678099 DOI: 10.1038/s41467-017-01536-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 09/27/2017] [Indexed: 12/26/2022] Open
Abstract
Chemotaxis is a specialized form of directed cell migration important for normal development, wound healing, and cancer metastasis. In the social amoeba Dictyostelium discoideum, four signaling pathways act synergistically to maintain directional cell migration. However, it is unknown how these pathways are coordinated in space and time to achieve persistent chemotaxis. Here, we show that the mRNAs and proteins of these four chemotaxis pathways and actin are preferentially enriched at the cell front during dynamic cell migration, which requires the Pumilio-related RNA-binding protein Puf118. Significantly, disruption of the Pumilio-binding sequence in chemotaxis pathway mRNAs, or mislocalization of Puf118 and its target mRNAs to the cell rear perturbs efficient chemotaxis in shallow cAMP gradients, without affecting the abundance of the mRNAs or encoded proteins. Thus, the polarized localization of Puf118-bound mRNAs coordinates the distribution of different chemotaxis pathway proteins in time and space, leading to cell polarization and persistent chemotaxis.
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Affiliation(s)
- Manuel Hotz
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - W James Nelson
- Department of Biology, Stanford University, Stanford, CA, 94305, USA. .,Molecular and Cellular Physiology, Stanford University, Stanford, CA, 94305, USA.
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33
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Extracellular matrix stiffness and cell contractility control RNA localization to promote cell migration. Nat Commun 2017; 8:896. [PMID: 29026081 PMCID: PMC5638855 DOI: 10.1038/s41467-017-00884-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 08/02/2017] [Indexed: 01/13/2023] Open
Abstract
Numerous RNAs are enriched within cellular protrusions, but the underlying mechanisms are largely unknown. We had shown that the APC (adenomatous polyposis coli) protein controls localization of some RNAs at protrusions. Here, using protrusion-isolation schemes and RNA-Seq, we find that RNAs localized in protrusions of migrating fibroblasts can be distinguished in two groups, which are differentially enriched in distinct types of protrusions, and are additionally differentially dependent on APC. APC-dependent RNAs become enriched in high-contractility protrusions and, accordingly, their localization is promoted by increasing stiffness of the extracellular matrix. Dissecting the underlying mechanism, we show that actomyosin contractility activates a RhoA-mDia1 signaling pathway that leads to formation of a detyrosinated-microtubule network, which in turn is required for localization of APC-dependent RNAs. Importantly, a competition-based approach to specifically mislocalize APC-dependent RNAs suggests that localization of the APC-dependent RNA subgroup is functionally important for cell migration.Adenomatous polyposis coli (APC) regulates the localization of some mRNAs at cellular protrusions but the underlying mechanisms and functional roles are not known. Here the authors show that APC-dependent RNAs are enriched in contractile protrusions, via detyrosinated microtubules, and enhance cell migration.
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34
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Das S, Parker JM, Guven C, Wang W, Kriebel PW, Losert W, Larson DR, Parent CA. Adenylyl cyclase mRNA localizes to the posterior of polarized DICTYOSTELIUM cells during chemotaxis. BMC Cell Biol 2017; 18:23. [PMID: 28545392 PMCID: PMC5445419 DOI: 10.1186/s12860-017-0139-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/09/2017] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND In Dictyostelium discoideum, vesicular transport of the adenylyl cyclase A (ACA) to the posterior of polarized cells is essential to relay exogenous 3',5'-cyclic adenosine monophosphate (cAMP) signals during chemotaxis and for the collective migration of cells in head-to-tail arrangements called streams. RESULTS Using fluorescence in situ hybridization (FISH), we discovered that the ACA mRNA is asymmetrically distributed at the posterior of polarized cells. Using both standard estimators and Monte Carlo simulation methods, we found that the ACA mRNA enrichment depends on the position of the cell within a stream, with the posterior localization of ACA mRNA being strongest for cells at the end of a stream. By monitoring the recovery of ACA-YFP after cycloheximide (CHX) treatment, we observed that ACA mRNA and newly synthesized ACA-YFP first emerge as fluorescent punctae that later accumulate to the posterior of cells. We also found that the ACA mRNA localization requires 3' ACA cis-acting elements. CONCLUSIONS Together, our findings suggest that the asymmetric distribution of ACA mRNA allows the local translation and accumulation of ACA protein at the posterior of cells. These data represent a novel functional role for localized translation in the relay of chemotactic signal during chemotaxis.
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Affiliation(s)
- Satarupa Das
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA.,Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Joshua M Parker
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Can Guven
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Weiye Wang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA
| | - Paul W Kriebel
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA
| | - Wolfgang Losert
- Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, NCI, NIH, Bethesda, MD, 20892, USA
| | - Carole A Parent
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, 37 Convent Drive, Bldg.37/Rm2066, NCI, NIH, Bethesda, MD, 20892-4256, USA. .,Institute for Physical Science and Technology, Department of Physics, University of Maryland, College Park, MD, 20742, USA.
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Vera M, Biswas J, Senecal A, Singer RH, Park HY. Single-Cell and Single-Molecule Analysis of Gene Expression Regulation. Annu Rev Genet 2017; 50:267-291. [PMID: 27893965 DOI: 10.1146/annurev-genet-120215-034854] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in single-cell and single-molecule imaging technologies have resolved biological processes in time and space that are fundamental to understanding the regulation of gene expression. Observations of single-molecule events in their cellular context have revealed highly dynamic aspects of transcriptional and post-transcriptional control in eukaryotic cells. This approach can relate transcription with mRNA abundance and lifetimes. Another key aspect of single-cell analysis is the cell-to-cell variability among populations of cells. Definition of heterogeneity has revealed stochastic processes, determined characteristics of under-represented cell types or transitional states, and integrated cellular behaviors in the context of multicellular organisms. In this review, we discuss novel aspects of gene expression of eukaryotic cells and multicellular organisms revealed by the latest advances in single-cell and single-molecule imaging technology.
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Affiliation(s)
- Maria Vera
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Jeetayu Biswas
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Adrien Senecal
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , ,
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, NY 10461; , , , .,Janelia Research Campus of the HHMI, Ashburn, Virginia 20147
| | - Hye Yoon Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, Korea; .,Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, Korea
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Abstract
Localization of mRNA is required for protein synthesis to occur within discrete intracellular compartments. Neurons represent an ideal system for studying the precision of mRNA trafficking because of their polarized structure and the need for synapse-specific targeting. To investigate this targeting, we derived a quantitative and analytical approach. Dendritic spines were stimulated by glutamate uncaging at a diffraction-limited spot, and the localization of single β-actin mRNAs was measured in space and time. Localization required NMDA receptor activity, a dynamic actin cytoskeleton, and the transacting RNA-binding protein, Zipcode-binding protein 1 (ZBP1). The ability of the mRNA to direct newly synthesized proteins to the site of localization was evaluated using a Halo-actin reporter so that RNA and protein were detected simultaneously. Newly synthesized Halo-actin was enriched at the site of stimulation, required NMDA receptor activity, and localized preferentially at the periphery of spines. This work demonstrates that synaptic activity can induce mRNA localization and local translation of β-actin where the new actin participates in stabilizing the expanding synapse in dendritic spines.
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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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Musser SM, Grünwald D. Deciphering the Structure and Function of Nuclear Pores Using Single-Molecule Fluorescence Approaches. J Mol Biol 2016; 428:2091-119. [PMID: 26944195 DOI: 10.1016/j.jmb.2016.02.023] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 01/05/2016] [Accepted: 02/17/2016] [Indexed: 01/06/2023]
Abstract
Due to its central role in macromolecular trafficking and nucleocytoplasmic information transfer, the nuclear pore complex (NPC) has been studied in great detail using a wide spectrum of methods. Consequently, many aspects of its architecture, general function, and role in the life cycle of a cell are well understood. Over the last decade, fluorescence microscopy methods have enabled the real-time visualization of single molecules interacting with and transiting through the NPC, allowing novel questions to be examined with nanometer precision. While initial single-molecule studies focused primarily on import pathways using permeabilized cells, it has recently proven feasible to investigate the export of mRNAs in living cells. Single-molecule assays can address questions that are difficult or impossible to answer by other means, yet the complexity of nucleocytoplasmic transport requires that interpretation be based on a firm genetic, biochemical, and structural foundation. Moreover, conceptually simple single-molecule experiments remain technically challenging, particularly with regard to signal intensity, signal-to-noise ratio, and the analysis of noise, stochasticity, and precision. We discuss nuclear transport issues recently addressed by single-molecule microscopy, evaluate the limits of existing assays and data, and identify open questions for future studies. We expect that single-molecule fluorescence approaches will continue to be applied to outstanding nucleocytoplasmic transport questions, and that the approaches developed for NPC studies are extendable to additional complex systems and pathways within cells.
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Affiliation(s)
- Siegfried M Musser
- Department of Molecular and Cellular Medicine, College of Medicine, The Texas A&M Health Science Center, 1114 TAMU, College Station, TX 77843, USA.
| | - David Grünwald
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Mapping translation 'hot-spots' in live cells by tracking single molecules of mRNA and ribosomes. eLife 2016; 5. [PMID: 26760529 PMCID: PMC4764586 DOI: 10.7554/elife.10415] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/29/2015] [Indexed: 11/13/2022] Open
Abstract
Messenger RNA localization is important for cell motility by local protein translation. However, while single mRNAs can be imaged and their movements tracked in single cells, it has not yet been possible to determine whether these mRNAs are actively translating. Therefore, we imaged single β-actin mRNAs tagged with MS2 stem loops colocalizing with labeled ribosomes to determine when polysomes formed. A dataset of tracking information consisting of thousands of trajectories per cell demonstrated that mRNAs co-moving with ribosomes have significantly different diffusion properties from non-translating mRNAs that were exposed to translation inhibitors. These data indicate that ribosome load changes mRNA movement and therefore highly translating mRNAs move slower. Importantly, β-actin mRNA near focal adhesions exhibited sub-diffusive corralled movement characteristic of increased translation. This method can identify where ribosomes become engaged for local protein production and how spatial regulation of mRNA-protein interactions mediates cell directionality.
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Affiliation(s)
- Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Salk Institute for Biological Studies, La Jolla, United States
| | - Brian P English
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Timothée Lionnet
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States
| | - Nilah Monnier
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Ben Ovryn
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
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Wu B, Buxbaum AR, Katz ZB, Yoon YJ, Singer RH. Quantifying Protein-mRNA Interactions in Single Live Cells. Cell 2015; 162:211-20. [PMID: 26140598 DOI: 10.1016/j.cell.2015.05.054] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 05/04/2015] [Accepted: 05/19/2015] [Indexed: 11/17/2022]
Abstract
Specific binding proteins are crucial for the correct spatiotemporal expression of mRNA. To understand this process, a method is required to characterize RNA-protein interactions in single living cells with subcellular resolution. We combined endogenous single RNA and protein detection with two-photon fluorescence fluctuation analysis to measure the average number of proteins bound to mRNA at specific locations within live cells. We applied this to quantify the known binding of zipcode binding protein 1 (ZBP1) and ribosomes to β-actin mRNA within subcellular compartments of primary fibroblasts and neurons. ZBP1-mRNA binding did not occur in nuclei, contrary to previous conclusions. ZBP1 interaction with β-actin mRNA was enhanced perinuclearly in neurons compared to fibroblasts. Cytoplasmic ZBP1 and ribosome binding to the mRNA were anti-correlated depending on their location in the cell. These measurements support a mechanism whereby ZBP1 inhibits translation of localizing mRNA until its release from the mRNA peripherally, allowing ribosome binding.
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Affiliation(s)
- Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Adina R Buxbaum
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Young J Yoon
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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41
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Maizels Y, Oberman F, Miloslavski R, Ginzach N, Berman M, Yisraeli JK. Localization of cofilin mRNA to the leading edge of migrating cells promotes directed cell migration. J Cell Sci 2015; 128:1922-33. [DOI: 10.1242/jcs.163972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 03/16/2015] [Indexed: 12/13/2022] Open
Abstract
ABSTRACT
mRNA trafficking, which enables the localization of mRNAs to particular intracellular targets, occurs in a wide variety of cells. The importance of the resulting RNA distribution for cellular functions, however, has been difficult to assess. We have found that cofilin-1 mRNA is rapidly localized to the leading edge of human lung carcinoma cells and that VICKZ family RNA-binding proteins help mediate this localization through specific interactions with the 3′UTR of cofilin mRNA. Using a phagokinetic assay for cell motility, we have been able to quantify the effect of mRNA localization on the rescue of lung carcinoma cells in which cofilin was knocked down by using short hairpin RNA (shRNA). Although restoring cofilin protein to normal endogenous levels rescues general lamellipodia formation around the periphery of the cell, only when the rescuing cofilin mRNA can localize to the leading edge is it capable of also fully rescuing directed cell movement. These results demonstrate that localization of an mRNA can provide an additional level of regulation for the function of its protein product.
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Affiliation(s)
- Yael Maizels
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Froma Oberman
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Rachel Miloslavski
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Nava Ginzach
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Malka Berman
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
| | - Joel K. Yisraeli
- Department of Developmental Biology and Cancer Research, IMRIC, Hebrew University – Hadassah Medical School, Jerusalem 91120, Israel
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42
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In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 2014; 16:95-109. [PMID: 25549890 DOI: 10.1038/nrm3918] [Citation(s) in RCA: 379] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The spatial regulation of protein translation is an efficient way to create functional and structural asymmetries in cells. Recent research has furthered our understanding of how individual cells spatially organize protein synthesis, by applying innovative technology to characterize the relationship between mRNAs and their regulatory proteins, single-mRNA trafficking dynamics, physiological effects of abrogating mRNA localization in vivo and for endogenous mRNA labelling. The implementation of new imaging technologies has yielded valuable information on mRNA localization, for example, by observing single molecules in tissues. The emerging movements and localization patterns of mRNAs in morphologically distinct unicellular organisms and in neurons have illuminated shared and specialized mechanisms of mRNA localization, and this information is complemented by transgenic and biochemical techniques that reveal the biological consequences of mRNA mislocalization.
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43
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Park HY, Lim H, Yoon YJ, Follenzi A, Nwokafor C, Lopez-Jones M, Meng X, Singer RH. Visualization of dynamics of single endogenous mRNA labeled in live mouse. Science 2014; 343:422-4. [PMID: 24458643 DOI: 10.1126/science.1239200] [Citation(s) in RCA: 213] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The transcription and transport of messenger RNA (mRNA) are critical steps in regulating the spatial and temporal components of gene expression, but it has not been possible to observe the dynamics of endogenous mRNA in primary mammalian tissues. We have developed a transgenic mouse in which all β-actin mRNA is fluorescently labeled. We found that β-actin mRNA in primary fibroblasts localizes predominantly by diffusion and trapping as single mRNAs. In cultured neurons and acute brain slices, we found that multiple β-actin mRNAs can assemble together, travel by active transport, and disassemble upon depolarization by potassium chloride. Imaging of brain slices revealed immediate early induction of β-actin transcription after depolarization. Studying endogenous mRNA in live mouse tissues provides insight into its dynamic regulation within the context of the cellular and tissue microenvironment.
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Affiliation(s)
- Hye Yoon Park
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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44
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Sinnamon JR, Czaplinski K. RNA detection in situ with FISH-STICs. RNA (NEW YORK, N.Y.) 2014; 20:260-266. [PMID: 24345395 PMCID: PMC3895277 DOI: 10.1261/rna.041905.113] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 10/31/2013] [Indexed: 06/03/2023]
Abstract
The ability to detect RNA molecules in situ has long had important applications for molecular biological studies. Enzyme or dye-labeled antisense in vitro runoff transcripts and synthetic oligodeoxynucleotides (ODN) both have a proven track record of success, but each of these also has scientific and practical drawbacks and limitations to its use. We devised a means to use commercially synthesized oligonucleotides as RNA-FISH probes without further modification and show that such probes work well for detection of RNA in cultured cells. This approach can bind a high concentration of fluorescent ODN to a short stretch of an RNA using commercial DNA synthesis outlets available to any laboratory. We call this approach for creating in situ hybridization probes Fluorescence In Situ Hybridization with Sequential Tethered and Intertwined ODN Complexes (FISH-STICs). We demonstrate that one FISH-STIC probe can detect mRNA molecules in culture, and that probe detection can be improved by the addition of multiple probes that can be easily adapted for robust mRNA quantification. Using FISH-STICs, we demonstrate a nonoverlapping distribution for β-actin and γ-actin mRNA in cultured fibroblasts, and the detection of neuron-specific transcripts within cultured primary hippocampal neurons.
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Affiliation(s)
- John R. Sinnamon
- Center for Nervous Systems Disorders, Centers for Molecular Medicine
- Program in Neuroscience, Department of Neurobiology and Behavior
| | - Kevin Czaplinski
- Center for Nervous Systems Disorders, Centers for Molecular Medicine
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11749, USA
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45
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Manipulation of RNA Using Engineered Proteins with Customized Specificity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:199-225. [DOI: 10.1007/978-1-4939-1221-6_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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46
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Abstract
The elaborate morphology of neurons together with the information processing that occurs in remote dendritic and axonal compartments makes the use of decentralized cell biological machines necessary. Recent years have witnessed a revolution in our understanding of signaling in neuronal compartments and the manifold functions of a variety of RNA molecules that regulate protein translation and other cellular functions. Here we discuss the view that mRNA localization and RNA-regulated and localized translation underlie many fundamental neuronal processes and highlight key issues for future experiments.
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47
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Wang Y, Wang Z, Tanaka Hall TM. Engineered proteins with Pumilio/fem-3 mRNA binding factor scaffold to manipulate RNA metabolism. FEBS J 2013; 280:3755-67. [PMID: 23731364 DOI: 10.1111/febs.12367] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 05/29/2013] [Accepted: 05/30/2013] [Indexed: 01/13/2023]
Abstract
Pumilio/fem-3 mRNA binding factor proteins are characterized by a sequence-specific RNA-binding domain. This unique single-stranded RNA recognition module, whose sequence specificity can be reprogrammed, has been fused with functional modules to engineer protein factors with various functions. We summarize the advances made with respect to developing RNA regulatory tools, as well as opportunities for the future.
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Affiliation(s)
- Yang Wang
- Department of Pharmacology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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48
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Eliscovich C, Buxbaum AR, Katz ZB, Singer RH. mRNA on the move: the road to its biological destiny. J Biol Chem 2013; 288:20361-8. [PMID: 23720759 DOI: 10.1074/jbc.r113.452094] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.
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Affiliation(s)
- Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
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49
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Skamagki M, Wicher KB, Jedrusik A, Ganguly S, Zernicka-Goetz M. Asymmetric localization of Cdx2 mRNA during the first cell-fate decision in early mouse development. Cell Rep 2013; 3:442-57. [PMID: 23375373 PMCID: PMC3607255 DOI: 10.1016/j.celrep.2013.01.006] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2012] [Revised: 06/01/2012] [Accepted: 01/07/2013] [Indexed: 11/08/2022] Open
Abstract
A longstanding question in mammalian development is whether the divisions that segregate pluripotent progenitor cells for the future embryo from cells that differentiate into extraembryonic structures are asymmetric in cell-fate instructions. The transcription factor Cdx2 plays a key role in the first cell-fate decision. Here, using live-embryo imaging, we show that localization of Cdx2 transcripts becomes asymmetric during development, preceding cell lineage segregation. Cdx2 transcripts preferentially localize apically at the late eight-cell stage and become inherited asymmetrically during divisions that set apart pluripotent and differentiating cells. Asymmetric localization depends on a cis element within the coding region of Cdx2 and requires cell polarization as well as intact microtubule and actin cytoskeletons. Failure to enrich Cdx2 transcripts apically results in a significant decrease in the number of pluripotent cells. We discuss how the asymmetric localization and segregation of Cdx2 transcripts could contribute to multiple mechanisms that establish different cell fates in the mouse embryo.
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Affiliation(s)
- Maria Skamagki
- The Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, United Kingdom
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50
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Katz ZB, Wells AL, Park HY, Wu B, Shenoy SM, Singer RH. β-Actin mRNA compartmentalization enhances focal adhesion stability and directs cell migration. Genes Dev 2012; 26:1885-90. [PMID: 22948660 DOI: 10.1101/gad.190413.112] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Directed cell motility is at the basis of biological phenomena such as development, wound healing, and metastasis. It has been shown that substrate attachments mediate motility by coupling the cell's cytoskeleton with force generation. However, it has been unclear how the persistence of cell directionality is facilitated. We show that mRNA localization plays an important role in this process, but the mechanism of action is still unknown. In this study, we show that the zipcode-binding protein 1 transports β-actin mRNA to the focal adhesion compartment, where it dwells for minutes, suggesting a means for associating its localization with motility through the formation of stable connections between adhesions and newly synthesized actin filaments. In order to demonstrate this, we developed an approach for assessing the functional consequences of β-actin mRNA and protein localization by tethering the mRNA to a specific location-in this case, the focal adhesion complex. This approach will have a significant impact on cell biology because it is now possible to forcibly direct any mRNA and its cognate protein to specific locations in the cell. This will reveal the importance of localized protein translation on various cellular processes.
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Affiliation(s)
- Zachary B Katz
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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