1
|
Jing Y, Lv Y, Ye J, Yao L, Chen L, Mi L, Fei Y, Yu Y, Dong B, Lv H, Ma J. Quantifying tagged mRNA export flux via nuclear pore complexes in single live cells. Biochem Biophys Res Commun 2021; 545:138-144. [PMID: 33548627 DOI: 10.1016/j.bbrc.2021.01.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 02/08/2023]
Abstract
The mRNA export flux through nuclear pore complexes (NPC) changes under DNA manipulation and hence affects protein translation. However, monitoring the flux of a specific mRNA in single live cell is beyond reach of traditional techniques. We developed a fluorescence-based detection method for measuring the export flux of mRNA through NPC in single live cell using a snapshot image, which had been tested on exogenous genes' expression in HeLa cells, with transfection or infection, and endogenous genes' expression in yeast cells, during incubation and carbon catabolite repression. With its speediness, explicitness and noninvasiveness, we believe that it would be valuable in direct monitoring of gene behavior, and the understanding of gene regulation at a single cell level.
Collapse
Affiliation(s)
- Yueyue Jing
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yilin Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jingya Ye
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China
| | - Longfang Yao
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Liwen Chen
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Lan Mi
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Biao Dong
- National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Sichuan, 610041, China.
| | - Hong Lv
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, 200438, China; Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
| | - Jiong Ma
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Green Photoelectron Platform, Fudan University, Shanghai, China; Institute of Biomedical Engineering and Technology, Academy for Engineer and Technology, Fudan University, Shanghai, China; Shanghai Engineering Research Center of Industrial Microorganisms, Multiscale Research Institute of Complex Systems (MRICS), School of Life Sciences, Fudan University, Shanghai, China.
| |
Collapse
|
2
|
Koo CX, Kobiyama K, Shen YJ, LeBert N, Ahmad S, Khatoo M, Aoshi T, Gasser S, Ishii KJ. RNA polymerase III regulates cytosolic RNA:DNA hybrids and intracellular microRNA expression. J Biol Chem 2015; 290:7463-73. [PMID: 25623070 PMCID: PMC4367256 DOI: 10.1074/jbc.m115.636365] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
RNA:DNA hybrids form in the nuclei and mitochondria of cells as transcription-induced R-loops or G-quadruplexes, but exist only in the cytosol of virus-infected cells. Little is known about the existence of RNA:DNA hybrids in the cytosol of virus-free cells, in particular cancer or transformed cells. Here, we show that cytosolic RNA:DNA hybrids are present in various human cell lines, including transformed cells. Inhibition of RNA polymerase III (Pol III), but not DNA polymerase, abrogated cytosolic RNA:DNA hybrids. Cytosolic RNA:DNA hybrids bind to several components of the microRNA (miRNA) machinery-related proteins, including AGO2 and DDX17. Furthermore, we identified miRNAs that are specifically regulated by Pol III, providing a potential link between RNA:DNA hybrids and the miRNA machinery. One of the target genes, exportin-1, is shown to regulate cytosolic RNA:DNA hybrids. Taken together, we reveal previously unknown mechanism by which Pol III regulates the presence of cytosolic RNA:DNA hybrids and miRNA biogenesis in various human cells.
Collapse
Affiliation(s)
- Christine Xing'er Koo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456, the Laboratory of Adjuvant Innovation and
| | - Kouji Kobiyama
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Yu J Shen
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456
| | - Nina LeBert
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Shandar Ahmad
- the Laboratory of Bioinformatics, National Institute of Biomedical Innovation (NIBIO), Ibaraki, Osaka 567-0085, Japan, and
| | - Muznah Khatoo
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and
| | - Taiki Aoshi
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| | - Stephan Gasser
- From the Immunology Programme and Department of Microbiology, Centre for Life Sciences, and the NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117456,
| | - Ken J Ishii
- the Laboratory of Adjuvant Innovation and the Laboratory of Vaccine Science, World Premier International Immunology Frontier Research Center (iFREC), Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
3
|
Volkova NA, Fomina EG, Smolnikova VV, Zinovieva NA, Fomin IK. The U3 region of Moloney murine leukemia virus contains position-independent cis-acting sequences involved in the nuclear export of full-length viral transcripts. J Biol Chem 2014; 289:20158-69. [PMID: 24878957 DOI: 10.1074/jbc.m113.545855] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The distinguishing feature of self-inactivating (SIN) retroviral vectors is the deletion of the enhancer/promoter sequences in the U3 region of the 3' long terminal repeat. This design is used to overcome transcriptional interference and prevent downstream transcription from the 3' long terminal repeat. SIN vectors were derived from a number of different retroviruses. Studies of SIN vectors show that extensive U3 deletions in HIV-based vectors do not alter viral titers or the in vitro and in vivo properties of the vectors. However, deletion of the U3 sequences in γ- and α-retroviruses correlates with defects in 3' RNA processing and reduces viral titers by >10-fold. Here, we studied the steps in the retroviral life cycle that are affected by the deletion of sequences in the 3' U3 region of Moloney murine leukemia virus-derived retroviral vectors. The results show that the amounts of both full-length and internal RNA transcripts of U3-minus vectors are reduced in the nuclei of transfected cells, an effect that is probably due to a general defect in 3' RNA processing. Furthermore, full-length RNA transcripts were also defective in terms of nuclear export. This defect was complemented by transferring the U3 region to another position within the retroviral vector, indicating that the U3 region contains position-independent cis-acting sequences that are required for the transport of full-length viral transcripts. The results also suggest that the leader region of Moloney murine leukemia virus contains inhibitory/regulatory sequences, which prevent export and mediate nuclear retention of full-length viral RNA.
Collapse
Affiliation(s)
- Natalia A Volkova
- From the The Laboratory of Cellular Engineering, All-Russian State Research Institute of Animal Breeding, 142132 Moscow region, Russia
| | - Elena G Fomina
- The Laboratory for Biotechnology and Immunodiagnosis, The Republic Research and Practical Center for Epidemiology and Microbiology, 220114 Minsk, Belarus, and
| | - Viktoryia V Smolnikova
- The Republic Center of Hematology and Bone Marrow Transplantation, 220116 Minsk, Belarus
| | - Natalia A Zinovieva
- From the The Laboratory of Cellular Engineering, All-Russian State Research Institute of Animal Breeding, 142132 Moscow region, Russia,
| | - Igor K Fomin
- From the The Laboratory of Cellular Engineering, All-Russian State Research Institute of Animal Breeding, 142132 Moscow region, Russia,
| |
Collapse
|
4
|
Tonin Y, Heckel AM, Vysokikh M, Dovydenko I, Meschaninova M, Rötig A, Munnich A, Venyaminova A, Tarassov I, Entelis N. Modeling of antigenomic therapy of mitochondrial diseases by mitochondrially addressed RNA targeting a pathogenic point mutation in mitochondrial DNA. J Biol Chem 2014; 289:13323-34. [PMID: 24692550 PMCID: PMC4036341 DOI: 10.1074/jbc.m113.528968] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 03/20/2014] [Indexed: 12/24/2022] Open
Abstract
Defects in mitochondrial genome can cause a wide range of clinical disorders, mainly neuromuscular diseases. Presently, no efficient therapeutic treatment has been developed against this class of pathologies. Because most of deleterious mitochondrial mutations are heteroplasmic, meaning that wild type and mutated forms of mitochondrial DNA (mtDNA) coexist in the same cell, the shift in proportion between mutant and wild type molecules could restore mitochondrial functions. Recently, we developed mitochondrial RNA vectors that can be used to address anti-replicative oligoribonucleotides into human mitochondria and thus impact heteroplasmy level in cells bearing a large deletion in mtDNA. Here, we show that this strategy can be also applied to point mutations in mtDNA. We demonstrate that specifically designed RNA molecules containing structural determinants for mitochondrial import and 20-nucleotide sequence corresponding to the mutated region of mtDNA, are able to anneal selectively to the mutated mitochondrial genomes. After being imported into mitochondria of living human cells in culture, these RNA induced a decrease of the proportion of mtDNA molecules bearing a pathogenic point mutation in the mtDNA ND5 gene.
Collapse
Affiliation(s)
- Yann Tonin
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
| | - Anne-Marie Heckel
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
| | - Mikhail Vysokikh
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
| | - Ilya Dovydenko
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
- the Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia, and
| | - Mariya Meschaninova
- the Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia, and
| | - Agnès Rötig
- the Université Paris Descartes-Sorbonne Paris Cité, INSERM U781, Hôpital Necker-Enfants Malades, Paris 75015, France
| | - Arnold Munnich
- the Université Paris Descartes-Sorbonne Paris Cité, INSERM U781, Hôpital Necker-Enfants Malades, Paris 75015, France
| | - Alya Venyaminova
- the Laboratory of RNA Chemistry, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk 630090, Russia, and
| | - Ivan Tarassov
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
| | - Nina Entelis
- From the UMR 7156 Génétique Moléculaire, Génomique, Microbiologie (GMGM), Strasbourg University-CNRS, Strasbourg 67084, France
| |
Collapse
|
5
|
Genz C, Fundakowski J, Hermesh O, Schmid M, Jansen RP. Association of the yeast RNA-binding protein She2p with the tubular endoplasmic reticulum depends on membrane curvature. J Biol Chem 2013; 288:32384-32393. [PMID: 24056370 DOI: 10.1074/jbc.m113.486431] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Localization of mRNAs contributes to the generation and maintenance of cellular asymmetry in a wide range of organisms. In Saccharomyces cerevisiae, the so-called locasome complex with its core components Myo4p, She2p, and She3p localizes more than 30 mRNAs to the yeast bud tip. A significant fraction of these mRNAs encodes membrane or secreted proteins. Their localization requires, besides the locasome, a functional segregation apparatus of the cortical endoplasmic reticulum (ER), including the machinery that is involved in the movement of ER tubules into the bud. Colocalization of RNA-containing particles with these tubules suggests a coordinated transport of localized mRNAs and the cortical ER to the bud. Association of localized mRNAs to the ER requires the presence of the locasome component She2p. Here we report that She2p is not only an RNA-binding protein but can specifically bind to ER-derived membranes in a membrane curvature-dependent manner in vitro. Although it does not contain any known curvature recognizing motifs, the protein shows a binding preference for liposomes with a diameter resembling that of yeast ER tubules. In addition, membrane binding depends on tetramerization of She2p. In an in vivo membrane-tethering assay, She2p can target a viral peptide GFP fusion protein to the cortical ER, indicating that a fraction of She2p associates with the ER in vivo. Combining RNA- and membrane-binding features makes She2p an ideal coordinator of ER tubule and mRNA cotransport.
Collapse
Affiliation(s)
- Christian Genz
- From the Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Julia Fundakowski
- From the Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Orit Hermesh
- From the Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany
| | - Maria Schmid
- the Gene Center, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Ralf-Peter Jansen
- From the Interfaculty Institute of Biochemistry, Eberhard-Karls-Universität Tübingen, 72076 Tübingen, Germany.
| |
Collapse
|
6
|
Cui XA, Zhang Y, Hong SJ, Palazzo AF. Identification of a region within the placental alkaline phosphatase mRNA that mediates p180-dependent targeting to the endoplasmic reticulum. J Biol Chem 2013; 288:29633-41. [PMID: 24019514 DOI: 10.1074/jbc.m113.482505] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In both eukaryotic and prokaryotic cells, it has been recently established that mRNAs encoding secreted and membrane proteins can be localized to the surface of membranes via both translation-dependent and RNA element-mediated mechanisms. Previously, we showed that the placental alkaline phosphatase (ALPP) mRNA can be localized to the ER membrane independently of translation, and this localization is mediated by p180, an mRNA receptor present in the ER. In this article, we aimed to identify the cis-acting RNA element in ALPP. Using chimera constructs containing fragments of the ALPP mRNA, we demonstrate that the ER-localizing RNA element is present within the 3' end of the open reading frame and codes for a transmembrane domain. In addition, we show that this region requires p180 for efficient ER anchoring. Taken together, we provide the first insight into the nature of cis-acting ER-localizing RNA elements responsible for localizing mRNAs on the ER in mammalian cells.
Collapse
Affiliation(s)
- Xianying A Cui
- From the Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | | | | | | |
Collapse
|
7
|
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.
Collapse
Affiliation(s)
- Carolina Eliscovich
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine of Yeshiva University, Bronx, New York 10461, USA
| | | | | | | |
Collapse
|