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Gurskaya NG, Pereverzev AP, Staroverov DB, Markina NM, Lukyanov KA. Analysis of Nonsense-Mediated mRNA Decay at the Single-Cell Level Using Two Fluorescent Proteins. Methods Enzymol 2016; 572:291-314. [PMID: 27241760 DOI: 10.1016/bs.mie.2016.02.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nonsense-mediated mRNA decay (NMD) is an evolutionarily conserved mechanism of specific degradation of transcripts with a premature stop codon. NMD eliminates aberrant mRNAs arising from mutations, alternative splicing, and other events in cells. In addition, many normal transcripts undergo NMD. Recent studies demonstrated that NMD activity is specifically regulated and that NMD can play a role of global regulator of gene expression. Recently, we developed dual-color fluorescent protein-based reporters for quantification of NMD activity using fluorescence microscopy and flow cytometry (Pereverzev, Gurskaya, et al., 2015). Due to ratiometric fluorescence response, these reporters make it possible to assess NMD activity in live cells at the single-cell level and to reveal otherwise hidden heterogeneity of cells in respect of NMD activity. Here we provide a detailed description of applications of the NMD reporters in mammalian cell lines.
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Affiliation(s)
- N G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - A P Pereverzev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - D B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - N M Markina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.
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Gurskaya NG, Staroverov DB, Lukyanov KA. Fluorescent Protein-Based Quantification of Alternative Splicing of a Target Cassette Exon in Mammalian Cells. Methods Enzymol 2016; 572:255-68. [PMID: 27241758 DOI: 10.1016/bs.mie.2016.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Alternative splicing is an important mechanism of regulation of gene expression and expansion of proteome complexity. Recently we developed a new fluorescence reporter for quantitative analysis of alternative splicing of a target cassette exon in live cells (Gurskaya et al., 2012). It consists of a specially designed minigene encoding red and green fluorescent proteins (Katushka and TagGFP2) and a fragment of the target gene between them. Skipping or inclusion of the alternative exon induces a frameshift; ie, alternative exon length must not be a multiple of 3. Finally, red and green fluorescence intensities of cells expressing this reporter are used to estimate the percentage of alternative (exon-skipped) and normal (exon-retained) transcripts. Here, we provide a detailed description of design and application of the fluorescence reporter of a target alternative exon splicing in mammalian cell lines.
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Affiliation(s)
- N G Gurskaya
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - D B Staroverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - K A Lukyanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia; Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia.
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Hogue IB, Bosse JB, Engel EA, Scherer J, Hu JR, Del Rio T, Enquist LW. Fluorescent Protein Approaches in Alpha Herpesvirus Research. Viruses 2015; 7:5933-61. [PMID: 26610544 PMCID: PMC4664988 DOI: 10.3390/v7112915] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 10/12/2015] [Accepted: 10/14/2015] [Indexed: 12/28/2022] Open
Abstract
In the nearly two decades since the popularization of green fluorescent protein (GFP), fluorescent protein-based methodologies have revolutionized molecular and cell biology, allowing us to literally see biological processes as never before. Naturally, this revolution has extended to virology in general, and to the study of alpha herpesviruses in particular. In this review, we provide a compendium of reported fluorescent protein fusions to herpes simplex virus 1 (HSV-1) and pseudorabies virus (PRV) structural proteins, discuss the underappreciated challenges of fluorescent protein-based approaches in the context of a replicating virus, and describe general strategies and best practices for creating new fluorescent fusions. We compare fluorescent protein methods to alternative approaches, and review two instructive examples of the caveats associated with fluorescent protein fusions, including describing several improved fluorescent capsid fusions in PRV. Finally, we present our future perspectives on the types of powerful experiments these tools now offer.
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Affiliation(s)
- Ian B Hogue
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Jens B Bosse
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Esteban A Engel
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Julian Scherer
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Jiun-Ruey Hu
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Tony Del Rio
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
| | - Lynn W Enquist
- Department of Molecular Biology & Princeton Neuroscience Institute, Princeton University, Princeton, NJ 08544, USA.
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Pereverzev AP, Markina NM, Ianushevich IG, Gorodnicheva TV, Minasian BE, Luk'ianov KA, Gurskaia NG. [Intron 2 of human beta-globin in 3'-untranslated region enhances expression of chimeric genes]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2015; 40:293-6. [PMID: 25898735 DOI: 10.1134/s106816201403011x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Possibility to enhance heterologous gene expression in mammalian cells by introduction of an intron in 3' untranslated region (UTR) was investigated. To this end, a fragment of human beta-globin gene with intron 2 and flanked exon regions was introduced into vector encoding green fluorescent protein TagGFP2 after the TagGFP2 stop-codon (Int+). The distance between the stop-codon and the exonjunction was 35 nucleotides. It ensured that Int+ mRNA was resistant to degradation by nonsense mediated decay (NMD) machinery. A control vector Int- contained corresponding intronless sequence of the beta-globin mRNA. On the same plasmid, the second gene encoded far-red fluorescent protein Katushka was used to normalize fluorescence for transfection efficiency and expression level in individual cells. Transiently transfected HEK293T cells were analysed by flow cytometry. It was shown that cells transfected with plasmid carrying the Int+ gene possess 1.8 ± 0.2 fold higher green fluorescence compared to Int- cells. The observed effect was used to enhance expression of destabilized variants of yellow fluorescent protein TurboYFP-dest with high degradation rate in mammalian cells. We believe that introduction of beta-globin intron in the 3'-UTR of the chimeric gene can be used to enhance its expression and may be advantageous in some cases when usage of 5'-UTR intron is inappropriate.
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Luker K, Pata P, Shemiakina I, Pereverzeva A, Stacer A, Shcherbo D, Pletnev V, Skolnaja M, Lukyanov K, Luker G, Pata I, Chudakov D. Comparative study reveals better far-red fluorescent protein for whole body imaging. Sci Rep 2015; 5:10332. [PMID: 26035795 PMCID: PMC4603699 DOI: 10.1038/srep10332] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 04/08/2015] [Indexed: 11/10/2022] Open
Abstract
Genetically encoded far-red and near-infrared fluorescent proteins enable efficient imaging in studies of tumorigenesis, embryogenesis, and inflammation in model animals. Here we report comparative testing of available GFP-like far-red fluorescent proteins along with a modified protein, named Katushka2S, and near-infrared bacterial phytochrome-based markers. We compare fluorescence signal and signal-to-noise ratio at various excitation wavelength and emission filter combinations using transiently transfected cell implants in mice, providing a basis for rational choice of optimal marker(s) for in vivo imaging studies. We demonstrate that the signals of various far-red fluorescent proteins can be spectrally unmixed based on different signal-to-noise ratios in different channels, providing the straightforward possibility of multiplexed imaging with standard equipment. Katushka2S produced the brightest and fastest maturing fluorescence in all experimental setups. At the same time, signal-to-noise ratios for Katushka2S and near-infrared bacterial phytochrome, iRFP720 were comparable in their optimal channels. Distinct spectral and genetic characteristics suggest this pair of a far-red and a near-infrared fluorescent protein as an optimal combination for dual color, whole body imaging studies in model animals.
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Affiliation(s)
- K.E. Luker
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - P. Pata
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - I.I. Shemiakina
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Evrogen JSC, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A. Pereverzeva
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - A.C. Stacer
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - D.S. Shcherbo
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Evrogen JSC, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - V.Z. Pletnev
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
| | - M. Skolnaja
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - K.A. Lukyanov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia
| | - G.D. Luker
- Department of Radiology, University of Michigan Medical School, Ann Arbor, MI48109-2200, USA
| | - I. Pata
- Tallinn University of Technology, Department of Gene Technology. 15 Akadeemia St, Tallinn 12618, Estonia
| | - D.M. Chudakov
- Shemiakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Miklukho-Maklaya 16/10, 117997, Moscow, Russia
- CEITEC MU, Masaryk University, Brno, Czech republic
- Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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Gurskaya NG, Staroverov DB, Zhang L, Fradkov AF, Markina NM, Pereverzev AP, Lukyanov KA. Analysis of alternative splicing of cassette exons at single-cell level using two fluorescent proteins. Nucleic Acids Res 2012; 40:e57. [PMID: 22259036 PMCID: PMC3333876 DOI: 10.1093/nar/gkr1314] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/18/2011] [Accepted: 12/22/2011] [Indexed: 12/03/2022] Open
Abstract
Alternative splicing plays a major role in increasing proteome complexity and regulating gene expression. Here, we developed a new fluorescent protein-based approach to quantitatively analyze the alternative splicing of a target cassette exon (skipping or inclusion), which results in an open-reading frame shift. A fragment of a gene of interest is cloned between red and green fluorescent protein (RFP and GFP)-encoding sequences in such a way that translation of the normally spliced full-length transcript results in expression of both RFP and GFP. In contrast, alternative exon skipping results in the synthesis of RFP only. Green and red fluorescence intensities can be used to estimate the proportions of normal and alternative transcripts in each cell. The new method was successfully tested for human PIG3 (p53-inducible gene 3) cassette exon 4. Expected pattern of alternative splicing of PIG3 minigene was observed, including previously characterized effects of UV light irradiation and specific mutations. Interestingly, we observed a broad distribution of normal to alternative transcript ratio in individual cells with at least two distinct populations with ∼45% and >95% alternative transcript. We believe that this method is useful for fluorescence-based quantitative analysis of alternative splicing of target genes in a variety of biological models.
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