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Dasgupta S, Dayagi DY, Haimovich G, Wyler E, Olender T, Singer RH, Landthaler M, Gerst JE. Global analysis of contact-dependent human-to-mouse intercellular mRNA and lncRNA transfer in cell culture. eLife 2023; 12:83584. [PMID: 37249209 DOI: 10.7554/elife.83584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 05/29/2023] [Indexed: 05/31/2023] Open
Abstract
Full-length mRNAs transfer between adjacent mammalian cells via direct cell-to-cell connections called tunneling nanotubes (TNTs). However, the extent of mRNA transfer at the transcriptome-wide level (the 'transferome') is unknown. Here, we analyzed the transferome in an in vitro human-mouse cell co-culture model using RNA-sequencing. We found that mRNA transfer is non-selective, prevalent across the human transcriptome, and that the amount of transfer to mouse embryonic fibroblasts (MEFs) strongly correlates with the endogenous level of gene expression in donor human breast cancer cells. Typically, <1% of endogenous mRNAs undergo transfer. Non-selective, expression-dependent RNA transfer was further validated using synthetic reporters. RNA transfer appears contact-dependent via TNTs, as exemplified for several mRNAs. Notably, significant differential changes in the native MEF transcriptome were observed in response to co-culture, including the upregulation of multiple cancer and cancer-associated fibroblast-related genes and pathways. Together, these results lead us to suggest that TNT-mediated RNA transfer could be a phenomenon of physiological importance under both normal and pathogenic conditions.
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Affiliation(s)
- Sandipan Dasgupta
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Daniella Y Dayagi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gal Haimovich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Emanuel Wyler
- Berlin Institute of Medical Systems Biology and Systems Biology, Max Delbruck Center for Molecular Medicine, Zurich, Switzerland
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, New York, United States
| | - Markus Landthaler
- Berlin Institute for Medical Systems Biology, Max Delbruck Center for Molecular Medicine, Zurich, Switzerland
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Nair R, Haimovich G, Gerst J. An Aptamer-based mRNA Affinity Purification Procedure (RaPID) for the Identification of Associated RNAs (RaPID-seq) and Proteins (RaPID-MS) in Yeast. Bio Protoc 2022; 12:e4274. [DOI: 10.21769/bioprotoc.4274] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/15/2021] [Accepted: 10/18/2021] [Indexed: 11/02/2022] Open
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Haimovich G, Gerst JE. Detection of mRNA Transfer Between Mammalian Cells in Coculture by Single-Molecule Fluorescent In Situ Hybridization (smFISH). Methods Mol Biol 2019; 2038:109-129. [PMID: 31407281 DOI: 10.1007/978-1-4939-9674-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [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] [Indexed: 06/10/2023]
Abstract
In eukaryotic cells, a small percentage of mRNA molecules can undergo transfer from one cell to another. mRNA transfer occurs primarily via membrane nanotubes, which are long thin protrusions that are produced by numerous cell types and can connect cells that can be up to hundreds of microns apart. Potentially, mRNAs might also transfer via extracellular vesicles (EVs). Here we describe a method to detect transferred mRNA in cocultures of two different cell types and to distinguish between nanotube- and EVs-mediated transfer. This method uses single molecule fluorescent in situ hybridization (smFISH) to provide an accurate and quantitative detection of transferred mRNA molecules and their subcellular localization. Following the guidelines presented here will allow the user to investigate mRNA transfer of most transcripts in any co-culture system. In addition, we present modifications that improve nanotube preservation during the smFISH procedure.
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Affiliation(s)
- Gal Haimovich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Haimovich G, Gerst JE. Single-molecule Fluorescence in situ Hybridization (smFISH) for RNA Detection in Adherent Animal Cells. Bio Protoc 2018; 8:e3070. [PMID: 34532531 DOI: 10.21769/bioprotoc.3070] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 10/15/2018] [Accepted: 10/16/2018] [Indexed: 01/02/2023] Open
Abstract
Transcription and RNA decay play critical roles in the process of gene expression and the ability to accurately measure cellular mRNA levels is essential for understanding this regulation. Here, we describe a single-molecule fluorescent in situ hybridization (smFISH) method (as performed in Haimovich et al., 2017 ) that detects single RNA molecules in individual cells. This technique employs multiple single-stranded, fluorescent labeled, short DNA probes that hybridize to target RNAs in fixed cells, allowing for both the quantification and localization of cytoplasmic and nuclear RNAs at the single-cell level and single-molecule resolution. Analyzing smFISH data provides absolute quantitative data of the number of cytoplasmic ("mature") mRNAs, the number of nascent RNA molecules at distinct transcription sites, and the spatial localization of these RNAs in the cytoplasm and/or nucleoplasm.
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Affiliation(s)
- Gal Haimovich
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jeffrey E Gerst
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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Haimovich G, Zabezhinsky D, Haas B, Slobodin B, Purushothaman P, Fan L, Levin JZ, Nusbaum C, Gerst JE. Use of the MS2 aptamer and coat protein for RNA localization in yeast: A response to "MS2 coat proteins bound to yeast mRNAs block 5' to 3' degradation and trap mRNA decay products: implications for the localization of mRNAs by MS2-MCP system". RNA 2016; 22:660-6. [PMID: 26968626 PMCID: PMC4836641 DOI: 10.1261/rna.055095.115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/09/2016] [Indexed: 05/17/2023]
Abstract
The MS2 system has been extensively used to visualize single mRNA molecules in live cells and follow their localization and behavior. In their Letter to the Editor recently published, Garcia and Parker suggest that use of the MS2 system may yield erroneous mRNA localization results due to the accumulation of 3' decay products. Here we cite published works and provide new data which demonstrate that this is not a phenomenon general to endogenously expressed MS2-tagged transcripts, and that some of the results obtained in their study could have arisen from artifacts of gene expression.
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Affiliation(s)
- Gal Haimovich
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Dmitry Zabezhinsky
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Brian Haas
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Boris Slobodin
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | | | - Lin Fan
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Joshua Z Levin
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Jeffrey E Gerst
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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Haimovich G, Cohen-Zontag O, Gerst JE. A role for mRNA trafficking and localized translation in peroxisome biogenesis and function? Biochim Biophys Acta 2015; 1863:911-21. [PMID: 26367800 DOI: 10.1016/j.bbamcr.2015.09.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/08/2015] [Accepted: 09/09/2015] [Indexed: 02/03/2023]
Abstract
Peroxisomes are distinct membrane-enclosed organelles involved in the β-oxidation of fatty acids and synthesis of ether phospholipids (e.g. plasmalogens), as well as cholesterol and its derivatives (e.g. bile acids). Peroxisomes comprise a distinct and highly segregated subset of cellular proteins, including those of the peroxisome membrane and the interior matrix, and while the mechanisms of protein import into peroxisomes have been extensively studied, they are not fully understood. Here we will examine the potential role of RNA trafficking and localized translation on protein import into peroxisomes and its role in peroxisome biogenesis and function. Given that RNAs encoding peroxisome biogenesis (PEX) and matrix proteins have been found in association with the endoplasmic reticulum and peroxisomes, it suggests that localized translation may play a significant role in the import pathways of these different peroxisomal constituents.
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Affiliation(s)
- Gal Haimovich
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Osnat Cohen-Zontag
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Jeffrey E Gerst
- Dept. of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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Buxbaum AR, Haimovich G, Singer RH. Erratum: In the right place at the right time: visualizing and understanding mRNA localization. Nat Rev Mol Cell Biol 2015. [DOI: 10.1038/nrm4027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Haimovich G, Medina DA, Causse SZ, Garber M, Millán-Zambrano G, Barkai O, Chávez S, Pérez-Ortín JE, Darzacq X, Choder M. Gene expression is circular: factors for mRNA degradation also foster mRNA synthesis. Cell 2013; 153:1000-11. [PMID: 23706738 DOI: 10.1016/j.cell.2013.05.012] [Citation(s) in RCA: 246] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Revised: 01/03/2013] [Accepted: 05/07/2013] [Indexed: 01/14/2023]
Abstract
Maintaining proper mRNA levels is a key aspect in the regulation of gene expression. The balance between mRNA synthesis and decay determines these levels. We demonstrate that most yeast mRNAs are degraded by the cytoplasmic 5'-to-3' pathway (the "decaysome"), as proposed previously. Unexpectedly, the level of these mRNAs is highly robust to perturbations in this major pathway because defects in various decaysome components lead to transcription downregulation. Moreover, these components shuttle between the cytoplasm and the nucleus, in a manner dependent on proper mRNA degradation. In the nucleus, they associate with chromatin-preferentially ∼30 bp upstream of transcription start-sites-and directly stimulate transcription initiation and elongation. The nuclear role of the decaysome in transcription is linked to its cytoplasmic role in mRNA decay; linkage, in turn, seems to depend on proper shuttling of its components. The gene expression process is therefore circular, whereby the hitherto first and last stages are interconnected.
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Affiliation(s)
- Gal Haimovich
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 31096, Israel
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Harel-Sharvit L, Eldad N, Haimovich G, Barkai O, Duek L, Choder M. RNA polymerase II subunits link transcription and mRNA decay to translation. Cell 2010; 143:552-63. [PMID: 21074047 DOI: 10.1016/j.cell.2010.10.033] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 07/28/2010] [Accepted: 10/25/2010] [Indexed: 01/13/2023]
Abstract
Little is known about crosstalk between the eukaryotic transcription and translation machineries that operate in different cell compartments. The yeast proteins Rpb4p and Rpb7p represent one such link as they form a heterodimer that shuttles between the nucleus, where it functions in transcription, and the cytoplasm, where it functions in the major mRNA decay pathways. Here we show that the Rpb4/7 heterodimer interacts physically and functionally with components of the translation initiation factor 3 (eIF3), and is required for efficient translation initiation. Efficient translation in the cytoplasm depends on association of Rpb4/7 with RNA polymerase II (Pol II) in the nucleus, leading to a model in which Pol II remotely controls translation. Hence, like in prokaryotes, the eukaryotic translation is coupled to transcription. We propose that Rpb4/7, through its interactions at each step in the mRNA lifecycle, represents a class of factors, "mRNA coordinators," which integrate the various stages of gene expression into a system.
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Affiliation(s)
- Liat Harel-Sharvit
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, 31096, Israel
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Goler-Baron V, Selitrennik M, Barkai O, Haimovich G, Lotan R, Choder M. Transcription in the nucleus and mRNA decay in the cytoplasm are coupled processes. Genes Dev 2008; 22:2022-7. [PMID: 18676807 DOI: 10.1101/gad.473608] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Maintaining appropriate mRNAs levels is vital for any living cell. mRNA synthesis in the nucleus by RNA polymerase II core enzyme (Pol II) and mRNA decay by cytoplasmic machineries determine these levels. Yet, little is known about possible cross-talk between these processes. The yeast Rpb4/7 is a nucleo-cytoplasmic shuttling heterodimer that interacts with Pol II and with mRNAs and is required for mRNA decay in the cytoplasm. Here we show that interaction of Rpb4/7 with mRNAs and eventual decay of these mRNAs in the cytoplasm depends on association of Rpb4/7 with Pol II in the nucleus. We propose that, following its interaction with Pol II, Rpb4/7 functions in transcription, interacts with the transcript cotranscriptionally and travels with it to the cytoplasm to stimulate mRNA decay. Hence, by recruiting Rpb4/7, Pol II governs not only transcription but also mRNA decay.
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Affiliation(s)
- Vicky Goler-Baron
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion, Israel Institute of Technology, Haifa 31096, Israel
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Lotan R, Goler-Baron V, Duek L, Haimovich G, Choder M. The Rpb7p subunit of yeast RNA polymerase II plays roles in the two major cytoplasmic mRNA decay mechanisms. ACTA ACUST UNITED AC 2007; 178:1133-43. [PMID: 17875743 PMCID: PMC2064649 DOI: 10.1083/jcb.200701165] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The steady-state level of mRNAs is determined by the balance between their synthesis by RNA polymerase II (Pol II) and their decay. In the cytoplasm, mRNAs are degraded by two major pathways; one requires decapping and 5′ to 3′ exonuclease activity and the other involves 3′ to 5′ degradation. Rpb7p is a Pol II subunit that shuttles between the nucleus and the cytoplasm. Here, we show that Rpb7p is involved in the two mRNA decay pathways and possibly couples them. Rpb7p stimulates the deadenylation stage required for execution of both pathways. Additionally, Rpb7p is both an active component of the P bodies, where decapping and 5′ to 3′ degradation occur, and is capable of affecting the P bodies function. Moreover, Rpb7p interacts with the decapping regulator Pat1p in a manner important for the mRNA decay machinery. Rpb7p is also involved in the second pathway, as it stimulates 3′ to 5′ degradation. Our genetic analyses suggest that Rpb7p plays two distinct roles in mRNA decay, which can both be uncoupled from Rpb7p's role in transcription. Thus, Rpb7p plays pivotal roles in determining mRNA levels.
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Affiliation(s)
- Rona Lotan
- Department of Molecular Microbiology, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 31096, Israel
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Kamer I, Sarig R, Zaltsman Y, Niv H, Oberkovitz G, Regev L, Haimovich G, Lerenthal Y, Marcellus RC, Gross A. Proapoptotic BID Is an ATM Effector in the DNA-Damage Response. Cell 2005; 122:593-603. [PMID: 16122426 DOI: 10.1016/j.cell.2005.06.014] [Citation(s) in RCA: 179] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2004] [Revised: 05/03/2005] [Accepted: 06/13/2005] [Indexed: 10/25/2022]
Abstract
The "BH3-only" proapoptotic BCL-2 family members are sentinels of intracellular damage. Here, we demonstrated that the BH3-only BID protein partially localizes to the nucleus in healthy cells, is important for apoptosis induced by DNA damage, and is phosphorylated following induction of double-strand breaks in DNA. We also found that BID phosphorylation is mediated by the ATM kinase and occurs in mouse BID on two ATM consensus sites. Interestingly, BID-/- cells failed to accumulate in the S phase of the cell cycle following treatment with the topoisomerase II poison etoposide; reintroducing wild-type BID restored accumulation. In contrast, introducing a nonphosphorylatable BID mutant did not restore accumulation in the S phase and resulted in an increase in cellular sensitivity to etoposide-induced apoptosis. These results implicate BID as an ATM effector and raise the possibility that proapoptotic BID may also play a prosurvival role important for S phase arrest.
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Affiliation(s)
- Iris Kamer
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot 76100, Israel
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