1
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Chen F, Li X, Bai M, Zhao Y. Visualizing epigenetic modifications and their spatial proximities in single cells using three DNA-encoded amplifying FISH imaging strategies: BEA-FISH, PPDA-FISH and Cell-TALKING. Nat Protoc 2024:10.1038/s41596-024-01036-5. [PMID: 39232201 DOI: 10.1038/s41596-024-01036-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 06/11/2024] [Indexed: 09/06/2024]
Abstract
Epigenetic modifications and spatial proximities of nucleic acids and proteins play important roles in regulating physiological processes and disease progression. Currently available cell imaging methods, such as fluorescence in situ hybridization (FISH) and immunofluorescence, struggle to detect low-abundance modifications and their spatial proximities. Here we describe a step-by-step protocol for three DNA-encoded amplifying FISH-based imaging strategies to overcome these challenges for varying applications: base-encoded amplifying FISH (BEA-FISH), pairwise proximity-differentiated amplifying FISH (PPDA-FISH) and cellular macromolecules-tethered DNA walking indexing (Cell-TALKING). They all use the similar core principle of DNA-encoded amplification, which transforms different nonsequence molecular features into unique DNA barcodes for in situ rolling circle amplification and FISH analysis. This involves three key reactions in fixed cell samples: target labeling, DNA encoding and rolling circle amplification imaging. Using this protocol, these three imaging strategies achieve in situ counting of low-abundance modifications alone, the pairwise proximity-differentiated visualization of two modifications and the exploration of multiple modifications around one protein (one-to-many proximity), respectively. Low-abundance modifications, including 5-hydroxymethylcytosine, 5-formylcytosine, 5-hydroxymethyluracil and 5-formyluracil, are clearly visualized in single cells. Various combinatorial patterns of nucleic acid modifications and/or histone modifications are found. The whole protocol takes ~2-4 d to complete, depending on different imaging applications.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'An, P. R. China
| | - Xinyin Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'An, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'An, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'An, P. R. China.
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2
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Ren Y, Liu K, Yang H, Zhang Y, Deng S, Cao J, Xia X, Deng R. Multiplexing Imaging of Closely Located Single-Nucleotide Mutations in Single Cells via Encoded in situ PCR. ACS Sens 2024; 9:3549-3556. [PMID: 38982583 DOI: 10.1021/acssensors.4c00378] [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: 07/11/2024]
Abstract
Mutation accumulation in RNAs results in closely located single-nucleotide mutations (SNMs), which is highly associated with the drug resistance of pathogens. Imaging of SNMs in single cells has significance for understanding the heterogeneity of RNAs that are related to drug resistance, but the direct "see" closely located SNMs remains challenging. Herein, we designed an encoded ligation-mediated in situ polymerase chain reaction method (termed enPCR), which enabled the visualization of multiple closely located SNMs in bacterial RNAs. Unlike conventional ligation-based probes that can only discriminate a single SNM, this method can simultaneously image different SNMs at closely located sites with single-cell resolution using modular anchoring probes and encoded PCR primers. We tested the capacity of the method to detect closely located SNMs related to quinolone resistance in the gyrA gene of Salmonella enterica (S. enterica), and found that the simultaneous detection of the closely located SNMs can more precisely indicate the resistance of the S. enterica to quinolone compared to the detection of one SNM. The multiplexing imaging assay for SNMs can serve to reveal the relationship between complex cellular genotypes and phenotypes.
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Affiliation(s)
- Yao Ren
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Kerui Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hao Yang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, Liaoning 116600, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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3
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Shelansky R, Abrahamsson S, Brown CR, Doody M, Lenstra TL, Larson DR, Boeger H. Single gene analysis in yeast suggests nonequilibrium regulatory dynamics for transcription. Nat Commun 2024; 15:6226. [PMID: 39043639 PMCID: PMC11266658 DOI: 10.1038/s41467-024-50419-5] [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: 08/22/2023] [Accepted: 07/04/2024] [Indexed: 07/25/2024] Open
Abstract
Fluctuations in the initiation rate of transcription, the first step in gene expression, ensue from the stochastic behavior of the molecular process that controls transcription. In steady state, the regulatory process is often assumed to operate reversibly, i.e., in equilibrium. However, reversibility imposes fundamental limits to information processing. For instance, the assumption of equilibrium is difficult to square with the precision with which the regulatory process executes its task in eukaryotes. Here we provide evidence - from microscopic analyses of the transcription dynamics at a single gene copy of yeast - that the regulatory process for transcription is cyclic and irreversible (out of equilibrium). The necessary coupling to reservoirs of free energy occurs via sequence-specific transcriptional activators and the recruitment, in part, of ATP-dependent chromatin remodelers. Our findings may help explain how eukaryotic cells reconcile the dual but opposing requirements for fast regulatory kinetics and high regulatory specificity.
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Affiliation(s)
- Robert Shelansky
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Sara Abrahamsson
- Department of Electrical and Computer Engineering, University of California, Santa Cruz, CA, USA
| | - Christopher R Brown
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
- Korro Bio, Cambridge, MA, USA
| | - Michael Doody
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Tineke L Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, Amsterdam, The Netherlands
| | - Daniel R Larson
- Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Hinrich Boeger
- Department of Molecular Cell and Developmental Biology, University of California, Santa Cruz, CA, USA.
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4
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Liu X, Yang H, Liu J, Liu K, Jin L, Zhang Y, Khan MR, Zhong K, Cao J, He Q, Xia X, Deng R. In Situ Cas12a-Based Allele-Specific PCR for Imaging Single-Nucleotide Variations in Foodborne Pathogenic Bacteria. Anal Chem 2024; 96:2032-2040. [PMID: 38277772 DOI: 10.1021/acs.analchem.3c04532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2024]
Abstract
In situ profiling of single-nucleotide variations (SNVs) can elucidate drug-resistant genotypes with single-cell resolution. The capacity to directly "see" genetic information is crucial for investigating the relationship between mutated genes and phenotypes. Fluorescence in situ hybridization serves as a canonical tool for genetic imaging; however, it cannot detect subtle sequence alteration including SNVs. Herein, we develop an in situ Cas12a-based amplification refractory mutation system-PCR (ARMS-PCR) method that allows the visualization of SNVs related to quinolone resistance inside cells. The capacity of discriminating SNVs is enhanced by incorporating optimized mismatched bases in the allele-specific primers, thus allowing to specifically amplify quinolone-resistant related genes. After in situ ARMS-PCR, we employed a modified Cas12a/CRISPR RNA to tag the amplicon, thereby enabling specific binding of fluorophore-labeled DNA probes. The method allows to precisely quantify quinolone-resistant Salmonella enterica in the bacterial mixture. Utilizing this method, we investigated the survival competition capacity of quinolone-resistant and quinolone-sensitive bacteria toward antimicrobial peptides and indicated the enrichment of quinolone-resistant bacteria under colistin sulfate stress. The in situ Cas12a-based ARMS-PCR method holds the potential for profiling cellular phenotypes and gene regulation with single-nucleotide resolution at the single-cell level.
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Affiliation(s)
- Xinmiao Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Hao Yang
- School of Chemical Engineering, Sichuan University, Chengdu 610065, China
| | - Jun Liu
- Chengdu Customs Technology Center, Chengdu 610041, China
| | - Kerui Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Lulu Jin
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Yong Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Mohammad Rizwan Khan
- Department of Chemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Kai Zhong
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, Dalian Minzu University, Dalian, Liaoning 116600, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, China
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5
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Poveda C, Chen YL, Strych U. Generation and Characterization of In Vitro Transcribed mRNA. Methods Mol Biol 2024; 2786:147-165. [PMID: 38814393 DOI: 10.1007/978-1-0716-3770-8_6] [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: 05/31/2024]
Abstract
Here we describe the in vitro preparation of mRNA from DNA templates, including setting up the transcription reaction, mRNA capping, and mRNA labeling. We then describe methods used for mRNA characterization, including UV and fluorescence spectrophotometry, as well as gel electrophoresis. Moreover, characterization of the in vitro transcribed RNA using the Bioanalyzer instrument is described, allowing a higher resolution analysis of the target molecules. For the in vitro testing of the mRNA molecules, we include protocols for the transfection of various primary cell cultures and the confirmation of translation by intracellular staining and western blotting.
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Affiliation(s)
- Cristina Poveda
- Baylor College of Medicine, Department of Pediatrics, Division of Pediatric Tropical Medicine, Houston, TX, USA
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Yi-Lin Chen
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Ulrich Strych
- Baylor College of Medicine, Department of Pediatrics, Division of Pediatric Tropical Medicine, Houston, TX, USA.
- Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA.
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6
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A dynamical stochastic model of yeast translation across the cell cycle. Heliyon 2023; 9:e13101. [PMID: 36793957 PMCID: PMC9922973 DOI: 10.1016/j.heliyon.2023.e13101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 01/04/2023] [Accepted: 01/16/2023] [Indexed: 01/27/2023] Open
Abstract
Translation is a central step in gene expression, however its quantitative and time-resolved regulation is poorly understood. We developed a discrete, stochastic model for protein translation in S. cerevisiae in a whole-transcriptome, single-cell context. A "base case" scenario representing an average cell highlights translation initiation rates as the main co-translational regulatory parameters. Codon usage bias emerges as a secondary regulatory mechanism through ribosome stalling. Demand for anticodons with low abundancy is shown to cause above-average ribosome dwelling times. Codon usage bias correlates strongly both with protein synthesis rates and elongation rates. Applying the model to a time-resolved transcriptome estimated by combining data from FISH and RNA-Seq experiments, it could be shown that increased total transcript abundance during the cell cycle decreases translation efficiency at single transcript level. Translation efficiency grouped by gene function shows highest values for ribosomal and glycolytic genes. Ribosomal proteins peak in S phase while glycolytic proteins rank highest in later cell cycle phases.
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7
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Fu X, Patel HP, Coppola S, Xu L, Cao Z, Lenstra TL, Grima R. Quantifying how post-transcriptional noise and gene copy number variation bias transcriptional parameter inference from mRNA distributions. eLife 2022; 11:e82493. [PMID: 36250630 PMCID: PMC9648968 DOI: 10.7554/elife.82493] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Transcriptional rates are often estimated by fitting the distribution of mature mRNA numbers measured using smFISH (single molecule fluorescence in situ hybridization) with the distribution predicted by the telegraph model of gene expression, which defines two promoter states of activity and inactivity. However, fluctuations in mature mRNA numbers are strongly affected by processes downstream of transcription. In addition, the telegraph model assumes one gene copy but in experiments, cells may have two gene copies as cells replicate their genome during the cell cycle. While it is often presumed that post-transcriptional noise and gene copy number variation affect transcriptional parameter estimation, the size of the error introduced remains unclear. To address this issue, here we measure both mature and nascent mRNA distributions of GAL10 in yeast cells using smFISH and classify each cell according to its cell cycle phase. We infer transcriptional parameters from mature and nascent mRNA distributions, with and without accounting for cell cycle phase and compare the results to live-cell transcription measurements of the same gene. We find that: (i) correcting for cell cycle dynamics decreases the promoter switching rates and the initiation rate, and increases the fraction of time spent in the active state, as well as the burst size; (ii) additional correction for post-transcriptional noise leads to further increases in the burst size and to a large reduction in the errors in parameter estimation. Furthermore, we outline how to correctly adjust for measurement noise in smFISH due to uncertainty in transcription site localisation when introns cannot be labelled. Simulations with parameters estimated from nascent smFISH data, which is corrected for cell cycle phases and measurement noise, leads to autocorrelation functions that agree with those obtained from live-cell imaging.
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Affiliation(s)
- Xiaoming Fu
- Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and TechnologyShanghaiChina
- School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
- Center for Advanced Systems Understanding, Helmholtz-Zentrum Dresden-RossendorfGörlitzGermany
| | - Heta P Patel
- The Netherlands Cancer Institute, Oncode Institute, Division of Gene RegulationAmsterdamNetherlands
| | - Stefano Coppola
- The Netherlands Cancer Institute, Oncode Institute, Division of Gene RegulationAmsterdamNetherlands
| | - Libin Xu
- Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and TechnologyShanghaiChina
| | - Zhixing Cao
- Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and TechnologyShanghaiChina
| | - Tineke L Lenstra
- The Netherlands Cancer Institute, Oncode Institute, Division of Gene RegulationAmsterdamNetherlands
| | - Ramon Grima
- School of Biological Sciences, University of EdinburghEdinburghUnited Kingdom
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8
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Xu C, Zhao J, Chen S, Sakharov IY, Hu S, Zhao S. An ultrasensitive bunge bedstraw herb type DNA machine for absolute quantification of mRNA in single cell. Biosens Bioelectron 2022; 217:114702. [PMID: 36130443 DOI: 10.1016/j.bios.2022.114702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 11/30/2022]
Abstract
Messenger ribonucleic acids (mRNAs) comprise a class of small nucleic acids carrying genetic information, which exhibit very important role in medical research and diagnosis. If only the mean mRNA expression levels of the mRNA population are considered in medical research, important information linking mRNA expression and cellular function may be lost. Single-cell analysis provides valuable insights into studying its heterogeneity, signaling, and stochastic gene expression. In this study, a "bunge bedstraw herb"-type DNA machine based on DNAzyme catalyzing coupled clamping hybrid chain reaction (c-HCR) is presented. In the DNA machine, a bunge bedstraw herb-type DNA structure was first formed by hybridizing a core junction scaffold cruciform probe to a hairpin probe that can trigger the c-HCR via a target molecule in four directions. This approach can reduce the detection limit of mRNA to 5 × 10-15 M. Absolute quantification of survivin mRNA in individual cells was achieved using the DNA machine on a microfluidic chip electrophoresis platform. The reported method represents an unprecedented single-cell analysis platform for single-cell biology studies.
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Affiliation(s)
- Chunhuan Xu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Jingjin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
| | - Shengyu Chen
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Ivan Yu Sakharov
- Department of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory of Ecology of Rare and Endangered Species and Environmental Protection, Ministry of Education, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin, 541004, China.
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9
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Yang J, Dong C, Zhang A, Ren J. Quantification of mRNA in Single Cells Based on Dimerization-Induced Photoluminescence Nonblinking of Quantum Dots. Anal Chem 2022; 94:12407-12415. [PMID: 36050288 DOI: 10.1021/acs.analchem.2c02209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Photoluminescence (PL) intermittency (or "blinking") is a unique characteristic of single quantum dot (QD) emission. Here, we report a novel single-molecule detection strategy for the intracellular mRNA of interest using the mRNA-induced nonblinking QD dimers as probes. The working principle of the method is that the DNA hybrid of the target DNA (or mRNA) with a biotin-modified ssDNA probe can induce two blinking streptavidin-modified QDs (SAV-QDs) conjugated. The formed QD dimer as a bright spot showed a nonblinking emission property, observed with total inner reflection fluorescence microscopy (TIRFM). In theory, one nonblinking spot indicated a target DNA (or mRNA). The experimental results from single-spot fluorescence trajectory analysis and single-particle brightness analysis based on TIRFM and fluorescence correlation spectroscopy (FCS) techniques verified this dimerization process of QDs or its induced nonblinking emission. Employing a target DNA with the same base sequences to Survivin mRNA as a model, the detection strategy was used to detect the target DNA concentration based on the linear relationship between the percentage of the nonblinking spots and the target DNA concentration. This single-molecule detection strategy was also successfully used for determining Survivin mRNA in a single HeLa cell. The method can simplify the hybridization steps, eliminate self-quenching and photobleaching of fluorophores, and reduce the influence of unspecific binding on the detection.
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Affiliation(s)
- Jie Yang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Chaoqing Dong
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Aidi Zhang
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, State Key Laboratory of Metal Matrix Composites, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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10
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Rammohan J, Sarkar S, Ross D. Single-cell measurement quality in bits. PLoS One 2022; 17:e0269272. [PMID: 35951522 PMCID: PMC9371318 DOI: 10.1371/journal.pone.0269272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 05/17/2022] [Indexed: 11/18/2022] Open
Abstract
Single-cell measurements have revolutionized our understanding of heterogeneity in cellular response. However, there is no universally comparable way to assess single-cell measurement quality. Here, we show how information theory can be used to assess and compare single-cell measurement quality in bits, which provides a universally comparable metric for information content. We anticipate that the experimental and theoretical approaches we show here will generally enable comparisons of quality between any single-cell measurement methods.
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Affiliation(s)
- Jayan Rammohan
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - Swarnavo Sarkar
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
| | - David Ross
- National Institute of Standards and Technology, Gaithersburg, MD, United States of America
- * E-mail:
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11
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Wu Y, Xu W, Ma L, Yu Z, Wang Y, Yu CR. Robust and sensitive in situ RNA detection using Yn-situ. CELL REPORTS METHODS 2022; 2:100201. [PMID: 35497500 PMCID: PMC9046451 DOI: 10.1016/j.crmeth.2022.100201] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/25/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022]
Abstract
We describe a cost-effective, highly sensitive, and quantitative method for in situ detection of RNA molecules in tissue sections. This method, dubbed Yn-situ, standing for Y-branched probe in situ hybridization, uses a single-strand DNA preamplifier with multiple initiation sites that trigger a hybridization chain reaction (HCR) to detect polynucleotides. By characterizing the performance of this method, we show that the Yn-situ method, in conjunction with an improved fixation step, is sensitive enough to allow detection of RNA molecules using fewer probes targeting short nucleotide sequences than existing methods. A set of five probes can produce quantitative results with smaller puncta and higher signal-to-noise ratio than the 20-probe sets commonly required for HCR and RNAscope. We show that the high sensitivity and wide dynamic range allow quantification of genes expressed at different levels in the olfactory sensory neurons. We describe key steps of this method to enable broad utility by individual laboratories.
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Affiliation(s)
- Yunming Wu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Wenjing Xu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Limei Ma
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Zulin Yu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - Yongfu Wang
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
| | - C. Ron Yu
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
- Department of Anatomy and Cell Biology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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12
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Rensen E, Pietropaoli S, Mueller F, Weber C, Souquere S, Sommer S, Isnard P, Rabant M, Gibier JB, Terzi F, Simon-Loriere E, Rameix-Welti MA, Pierron G, Barba-Spaeth G, Zimmer C. Sensitive visualization of SARS-CoV-2 RNA with CoronaFISH. Life Sci Alliance 2022; 5:e202101124. [PMID: 34996842 PMCID: PMC8742873 DOI: 10.26508/lsa.202101124] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 12/22/2021] [Accepted: 12/22/2021] [Indexed: 01/22/2023] Open
Abstract
The current COVID-19 pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The positive-sense single-stranded RNA virus contains a single linear RNA segment that serves as a template for transcription and replication, leading to the synthesis of positive and negative-stranded viral RNA (vRNA) in infected cells. Tools to visualize vRNA directly in infected cells are critical to analyze the viral replication cycle, screen for therapeutic molecules, or study infections in human tissue. Here, we report the design, validation, and initial application of FISH probes to visualize positive or negative RNA of SARS-CoV-2 (CoronaFISH). We demonstrate sensitive visualization of vRNA in African green monkey and several human cell lines, in patient samples and human tissue. We further demonstrate the adaptation of CoronaFISH probes to electron microscopy. We provide all required oligonucleotide sequences, source code to design the probes, and a detailed protocol. We hope that CoronaFISH will complement existing techniques for research on SARS-CoV-2 biology and COVID-19 pathophysiology, drug screening, and diagnostics.
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Affiliation(s)
- Elena Rensen
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Stefano Pietropaoli
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Florian Mueller
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | - Christian Weber
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
| | | | - Sina Sommer
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Pierre Isnard
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Marion Rabant
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
- Service d'Anatomo-Pathologie, AP-HP, Hôpital Necker Enfants Malades, AP-HP Centre, Paris, France
| | - Jean-Baptiste Gibier
- Service d'Anatomo-Pathologie, Centre de Biologie Pathologie, CHU Lille, Lille, France
| | - Fabiola Terzi
- Université de Paris, INSERM U1151, CNRS UMR 8253, Institut Necker Enfants Malades, Département "Croissance et Signalisation," Paris, France
| | - Etienne Simon-Loriere
- Institut Pasteur, Université de Paris, G5 Evolutionary Genomics of RNA Viruses, Paris, France
| | - Marie-Anne Rameix-Welti
- Université Paris-Saclay, INSERM, Université de Versailles St. Quentin, UMR 1173 (2I), Montigny-le-Bretonneux, France
- AP-HP, Université Paris Saclay, Hôpital Ambroise Paré, Laboratoire de Microbiologie, Boulogne-Billancourt, France
| | | | - Giovanna Barba-Spaeth
- Institut Pasteur, Université de Paris, CNRS UMR 3569, Unité de Virologie Structurale, Paris, France
| | - Christophe Zimmer
- Institut Pasteur, Université de Paris, CNRS UMR 3691, Imaging and Modeling Unit, Paris, France
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13
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Tsirkas I, Dovrat D, Thangaraj M, Brouwer I, Cohen A, Paleiov Z, Meijler MM, Lenstra T, Aharoni A. Transcription-replication coordination revealed in single live cells. Nucleic Acids Res 2022; 50:2143-2156. [PMID: 35137218 PMCID: PMC8887460 DOI: 10.1093/nar/gkac069] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 01/04/2022] [Accepted: 01/25/2022] [Indexed: 11/23/2022] Open
Abstract
The coexistence of DNA replication and transcription during S-phase requires their tight coordination to prevent harmful conflicts. While extensive research revealed important mechanisms for minimizing these conflicts and their consequences, little is known regarding how the replication and transcription machinery are coordinated in real-time. Here, we developed a live-cell imaging approach for the real-time monitoring of replisome progression and transcription dynamics during a transcription-replication encounter. We found a wave of partial transcriptional repression ahead of the moving replication fork, which may contribute to efficient fork progression through the transcribed gene. Real-time detection of conflicts revealed their negative impact on both processes, leading to fork stalling or slowdown as well as lower transcription levels during gene replication, with different trade-offs observed in defined subpopulations of cells. Our real-time measurements of transcription-replication encounters demonstrate how these processes can proceed simultaneously while maintaining genomic stability, and how conflicts can arise when coordination is impaired.
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Affiliation(s)
- Ioannis Tsirkas
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Daniel Dovrat
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Manikandan Thangaraj
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amit Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Zohar Paleiov
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Michael M Meijler
- The Department of Chemistry and the National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
| | - Tineke Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute,1066CX Amsterdam, The Netherlands
| | - Amir Aharoni
- Department of Life Sciences, Ben-Gurion University of the Negev, Be'er Sheva 84105, Israel
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14
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Swaffer MP, Kim J, Chandler-Brown D, Langhinrichs M, Marinov GK, Greenleaf WJ, Kundaje A, Schmoller KM, Skotheim JM. Transcriptional and chromatin-based partitioning mechanisms uncouple protein scaling from cell size. Mol Cell 2021; 81:4861-4875.e7. [PMID: 34731644 PMCID: PMC8642314 DOI: 10.1016/j.molcel.2021.10.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 08/01/2021] [Accepted: 10/11/2021] [Indexed: 10/19/2022]
Abstract
Biosynthesis scales with cell size such that protein concentrations generally remain constant as cells grow. As an exception, synthesis of the cell-cycle inhibitor Whi5 "sub-scales" with cell size so that its concentration is lower in larger cells to promote cell-cycle entry. Here, we find that transcriptional control uncouples Whi5 synthesis from cell size, and we identify histones as the major class of sub-scaling transcripts besides WHI5 by screening for similar genes. Histone synthesis is thereby matched to genome content rather than cell size. Such sub-scaling proteins are challenged by asymmetric cell division because proteins are typically partitioned in proportion to newborn cell volume. To avoid this fate, Whi5 uses chromatin-binding to partition similar protein amounts to each newborn cell regardless of cell size. Disrupting both Whi5 synthesis and chromatin-based partitioning weakens G1 size control. Thus, specific transcriptional and partitioning mechanisms determine protein sub-scaling to control cell size.
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Affiliation(s)
| | - Jacob Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kurt M Schmoller
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Institute of Functional Epigenetics, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Jan M Skotheim
- Department of Biology, Stanford University, Stanford, CA 94305, USA.
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15
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Zhang Y, Zeng J, Huang C, Zhu B, Zhang Q, Chen D. Label-free detection of ssDNA base insertion and deletion mutations by surface-enhanced Raman spectroscopy. Anal Bioanal Chem 2021; 414:1461-1468. [PMID: 34825271 DOI: 10.1007/s00216-021-03799-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/09/2021] [Accepted: 11/19/2021] [Indexed: 11/28/2022]
Abstract
Surface-enhanced Raman spectroscopy (SERS), as a label-free, highly sensitive analytical method, has become an important tool for providing substance fingerprints. In this study, silver nanoparticles containing thiosulfate ions and calcium ions (Ag@SCNPs) have been used as an enhanced substrate to eliminate the interference of impurities on DNA signals. Intrinsic structural information on single-strand DNA (ssDNA) was directly obtained through SERS. The improved enhancement system was used to explore the base-stacking rules of ssDNA in a solution environment. For the first time, single-base insertion mutations and deletion mutations, as well as their exact mutation sites, were identified, and Raman spectra with high stability, repeatability, and high signal-to-noise ratio were obtained. The method is simple, fast, and accurate, and the detection process is nondestructive. It has potential to be applied in the fields of medical diagnosis and genetics research.
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Affiliation(s)
- Yufeng Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China
| | - Jiayu Zeng
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China
| | - Chao Huang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China
| | - Bixue Zhu
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China
| | - Qianjun Zhang
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China
| | - Dongmei Chen
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, Guizhou University, Guiyang City, 550025, Guizhou, China.
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16
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Patel HP, Brouwer I, Lenstra TL. Optimized protocol for single-molecule RNA FISH to visualize gene expression in S. cerevisiae. STAR Protoc 2021; 2:100647. [PMID: 34278333 PMCID: PMC8264745 DOI: 10.1016/j.xpro.2021.100647] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Single-molecule RNA fluorescence in situ hybridization (smFISH) allows subcellular visualization, localization, and quantification of endogenous RNA molecules in fixed cells. The spatial and intensity information of each RNA can be used to distinguish mature from nascent transcripts inside each cell, revealing both past and instantaneous transcriptional activity. Here, we describe an optimized protocol for smFISH in Saccharomyces cerevisiae with optimized lyticase digestion time and hybrization steps for more homogenous results. For complete details on the use and execution of this protocol, please refer to Donovan et al. (2019). Optimized protocol for single-molecule RNA FISH in S. cerevisiae Includes sample preparation, imaging setup, and image analysis Visualizes mature and nascent transcripts inside each cell
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Affiliation(s)
- Heta P. Patel
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
- Corresponding author
| | - Ineke Brouwer
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
| | - Tineke L. Lenstra
- Division of Gene Regulation, The Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands
- Corresponding author
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17
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Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 2021; 16:1647-1713. [PMID: 33619390 PMCID: PMC8525907 DOI: 10.1038/s41596-020-00478-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.
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18
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Gallardo P, Real-Calderón P, Flor-Parra I, Salas-Pino S, Daga RR. Acute Heat Stress Leads to Reversible Aggregation of Nuclear Proteins into Nucleolar Rings in Fission Yeast. Cell Rep 2020; 33:108377. [DOI: 10.1016/j.celrep.2020.108377] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 08/24/2020] [Accepted: 10/21/2020] [Indexed: 12/15/2022] Open
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19
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Mistry RM, Singh PK, Mancini MG, Stossi F, Mancini MA. Single Cell Analysis Of Transcriptionally Active Alleles By Single Molecule FISH. J Vis Exp 2020:10.3791/61680. [PMID: 33016938 PMCID: PMC8549401 DOI: 10.3791/61680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Gene transcription is an essential process in cell biology, and allows cells to interpret and respond to internal and external cues. Traditional bulk population methods (Northern blot, PCR, and RNAseq) that measure mRNA levels lack the ability to provide information on cell-to-cell variation in responses. Precise single cell and allelic visualization and quantification is possible via single molecule RNA fluorescence in situ hybridization (smFISH). RNA-FISH is performed by hybridizing target RNAs with labeled oligonucleotide probes. These can be imaged in medium/high throughput modalities, and, through image analysis pipelines, provide quantitative data on both mature and nascent RNAs, all at the single cell level. The fixation, permeabilization, hybridization and imaging steps have been optimized in the lab over many years using the model system described herein, which results in successful and robust single cell analysis of smFISH labeling. The main goal with sample preparation and processing is to produce high quality images characterized by a high signal-to-noise ratio to reduce false positives and provide data that are more accurate. Here, we present a protocol describing the pipeline from sample preparation to data analysis in conjunction with suggestions and optimization steps to tailor to specific samples.
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Affiliation(s)
- Ragini M Mistry
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine
| | - Pankaj K Singh
- GCC Center for Advanced Microscopy and Image Informatics; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University
| | - Maureen G Mancini
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine
| | - Fabio Stossi
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine;
| | - Michael A Mancini
- GCC Center for Advanced Microscopy and Image Informatics; Department of Molecular and Cellular Biology, Baylor College of Medicine; Center for Translational Cancer Research, Institute of Biosciences and Technology, Texas A&M University; Department of Pharmacology and Chemical Biology, Baylor College of Medicine
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20
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Depletion of the MFAP1/SPP381 Splicing Factor Causes R-Loop-Independent Genome Instability. Cell Rep 2020; 28:1551-1563.e7. [PMID: 31390568 PMCID: PMC6693559 DOI: 10.1016/j.celrep.2019.07.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 03/18/2019] [Accepted: 07/01/2019] [Indexed: 01/19/2023] Open
Abstract
THO/TREX is a conserved complex with a role in messenger ribonucleoprotein biogenesis that links gene expression and genome instability. Here, we show that human THO interacts with MFAP1 (microfibrillar-associated protein 1), a spliceosome-associated factor. Interestingly, MFAP1 depletion impairs cell proliferation and genome integrity, increasing γH2AX foci and DNA breaks. This phenotype is not dependent on either transcription or RNA-DNA hybrids. Mutations in the yeast orthologous gene SPP381 cause similar transcription-independent genome instability, supporting a conserved role. MFAP1 depletion has a wide effect on splicing and gene expression in human cells, determined by transcriptome analyses. MFAP1 depletion affects a number of DNA damage response (DDR) genes, which supports an indirect role of MFAP1 on genome integrity. Our work defines a functional interaction between THO and RNA processing and argues that splicing factors may contribute to genome integrity indirectly by regulating the expression of DDR genes rather than by a direct role.
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21
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Quintero-Cadena P, Lenstra TL, Sternberg PW. RNA Pol II Length and Disorder Enable Cooperative Scaling of Transcriptional Bursting. Mol Cell 2020; 79:207-220.e8. [DOI: 10.1016/j.molcel.2020.05.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 04/09/2020] [Accepted: 05/19/2020] [Indexed: 12/15/2022]
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22
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Trcek T, Douglas TE, Grosch M, Yin Y, Eagle WVI, Gavis ER, Shroff H, Rothenberg E, Lehmann R. Sequence-Independent Self-Assembly of Germ Granule mRNAs into Homotypic Clusters. Mol Cell 2020; 78:941-950.e12. [PMID: 32464092 DOI: 10.1016/j.molcel.2020.05.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 02/29/2020] [Accepted: 05/05/2020] [Indexed: 12/12/2022]
Abstract
mRNAs enriched in membraneless condensates provide functional compartmentalization within cells. The mechanisms that recruit transcripts to condensates are under intense study; however, how mRNAs organize once they reach a granule remains poorly understood. Here, we report on a self-sorting mechanism by which multiple mRNAs derived from the same gene assemble into discrete homotypic clusters. We demonstrate that in vivo mRNA localization to granules and self-assembly within granules are governed by different mRNA features: localization is encoded by specific RNA regions, whereas self-assembly involves the entire mRNA, does not involve sequence-specific, ordered intermolecular RNA:RNA interactions, and is thus RNA sequence independent. We propose that the ability of mRNAs to self-sort into homotypic assemblies is an inherent property of an messenger ribonucleoprotein (mRNP) that is augmented under conditions that increase RNA concentration, such as upon enrichment in RNA-protein granules, a process that appears conserved in diverse cellular contexts and organisms.
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Affiliation(s)
- Tatjana Trcek
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
| | - Tyler E Douglas
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Markus Grosch
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA
| | - Yandong Yin
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Whitby V I Eagle
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Elizabeth R Gavis
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Hari Shroff
- Section on High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, NIH, Bethesda, MD, USA
| | - Eli Rothenberg
- Department of Biochemistry and Pharmacology, NYU School of Medicine, New York, NY, USA
| | - Ruth Lehmann
- HHMI, Skirball Institute of Biomolecular Medicine, Department of Cell Biology, NYU School of Medicine, New York, NY, USA.
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23
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Jariani A, Vermeersch L, Cerulus B, Perez-Samper G, Voordeckers K, Van Brussel T, Thienpont B, Lambrechts D, Verstrepen KJ. A new protocol for single-cell RNA-seq reveals stochastic gene expression during lag phase in budding yeast. eLife 2020; 9:e55320. [PMID: 32420869 PMCID: PMC7259953 DOI: 10.7554/elife.55320] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Current methods for single-cell RNA sequencing (scRNA-seq) of yeast cells do not match the throughput and relative simplicity of the state-of-the-art techniques that are available for mammalian cells. In this study, we report how 10x Genomics' droplet-based single-cell RNA sequencing technology can be modified to allow analysis of yeast cells. The protocol, which is based on in-droplet spheroplasting of the cells, yields an order-of-magnitude higher throughput in comparison to existing methods. After extensive validation of the method, we demonstrate its use by studying the dynamics of the response of isogenic yeast populations to a shift in carbon source, revealing the heterogeneity and underlying molecular processes during this shift. The method we describe opens new avenues for studies focusing on yeast cells, as well as other cells with a degradable cell wall.
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Affiliation(s)
- Abbas Jariani
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Lieselotte Vermeersch
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Bram Cerulus
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Gemma Perez-Samper
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Karin Voordeckers
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
| | - Thomas Van Brussel
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Bernard Thienpont
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
- Laboratory for Functional Epigenetics, Department of Genetics, KU LeuvenLeuvenBelgium
| | - Diether Lambrechts
- Laboratory for Translational Genetics, Department of Human Genetics, KU LeuvenLeuvenBelgium
- VIB Center for Cancer Biology, VIBLeuvenBelgium
| | - Kevin J Verstrepen
- Laboratory for Systems Biology, VIB-KU Leuven Center for MicrobiologyLeuvenBelgium
- Laboratory of Genetics and Genomics, CMPG, Department M2S, KU LeuvenLeuvenBelgium
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24
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Size-Dependent Increase in RNA Polymerase II Initiation Rates Mediates Gene Expression Scaling with Cell Size. Curr Biol 2020; 30:1217-1230.e7. [DOI: 10.1016/j.cub.2020.01.053] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/01/2019] [Accepted: 01/16/2020] [Indexed: 12/19/2022]
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25
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Young AP, Jackson DJ, Wyeth RC. A technical review and guide to RNA fluorescence in situ hybridization. PeerJ 2020; 8:e8806. [PMID: 32219032 PMCID: PMC7085896 DOI: 10.7717/peerj.8806] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/25/2020] [Indexed: 12/20/2022] Open
Abstract
RNA-fluorescence in situ hybridization (FISH) is a powerful tool to visualize target messenger RNA transcripts in cultured cells, tissue sections or whole-mount preparations. As the technique has been developed over time, an ever-increasing number of divergent protocols have been published. There is now a broad selection of options available to facilitate proper tissue preparation, hybridization, and post-hybridization background removal to achieve optimal results. Here we review the technical aspects of RNA-FISH, examining the most common methods associated with different sample types including cytological preparations and whole-mounts. We discuss the application of commonly used reagents for tissue preparation, hybridization, and post-hybridization washing and provide explanations of the functional roles for each reagent. We also discuss the available probe types and necessary controls to accurately visualize gene expression. Finally, we review the most recent advances in FISH technology that facilitate both highly multiplexed experiments and signal amplification for individual targets. Taken together, this information will guide the methods development process for investigators that seek to perform FISH in organisms that lack documented or optimized protocols.
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Affiliation(s)
- Alexander P Young
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
| | - Daniel J Jackson
- Department of Geobiology, Georg-August Universität Göttingen, Göttingen, Germany
| | - Russell C Wyeth
- Department of Biology, St. Francis Xavier University, Antigonish, NS, Canada
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26
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Li X, Kim H, Litke JL, Wu J, Jaffrey SR. Fluorophore‐Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli‐Tagged mRNAs in Live Mammalian Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201914576] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Xing Li
- Department of PharmacologyWeill Cornell MedicineCornell University New York NY 10065 USA
| | - Hyaeyeong Kim
- Department of PharmacologyWeill Cornell MedicineCornell University New York NY 10065 USA
| | - Jacob L. Litke
- Department of PharmacologyWeill Cornell MedicineCornell University New York NY 10065 USA
| | - Jiahui Wu
- Department of PharmacologyWeill Cornell MedicineCornell University New York NY 10065 USA
| | - Samie R. Jaffrey
- Department of PharmacologyWeill Cornell MedicineCornell University New York NY 10065 USA
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27
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Sarkar S, Le P, Geng J, Liu Y, Han Z, Zahid MU, Nall D, Youn Y, Selvin PR, Smith AM. Short-Wave Infrared Quantum Dots with Compact Sizes as Molecular Probes for Fluorescence Microscopy. J Am Chem Soc 2020; 142:3449-3462. [PMID: 31964143 PMCID: PMC7335634 DOI: 10.1021/jacs.9b11567] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Materials with short-wave infrared (SWIR) emission are promising contrast agents for in vivo animal imaging, providing high-contrast and high-resolution images of blood vessels in deep tissues. However, SWIR emitters have not been developed as molecular labels for microscopy applications in the life sciences, which require optimized probes that are bright, stable, and small. Here, we design and synthesize semiconductor quantum dots (QDs) with SWIR emission based on HgxCd1-xSe alloy cores red shifted to the SWIR by epitaxial deposition of thin HgxCd1-xS shells with a small band gap. By tuning alloy composition alone, the emission can be shifted across the visible-to-SWIR (VIR) spectra while maintaining a small and equal size, allowing direct comparisons of molecular labeling performance across a broad range of wavelength. After coating with click-functional multidentate polymers, the VIR-QD spectral series has high quantum yield in the SWIR (14-33%), compact size (13 nm hydrodynamic diameter), and long-term stability in aqueous media during continuous excitation. We show that these properties enable diverse applications of SWIR molecular probes for fluorescence microscopy using conjugates of antibodies, growth factors, and nucleic acids. A broadly useful outcome is a 10-55-fold enhancement of the signal-to-background ratio at both the single-molecule level and the ensemble level in the SWIR relative to visible wavelengths, primarily due to drastically reduced autofluorescence. We anticipate that VIR-QDs with SWIR emission will enable ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluorescence.
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Affiliation(s)
- Suresh Sarkar
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Phuong Le
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Junlong Geng
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Beckman Institute for Advanced Science and Technology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yang Liu
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Zhiyuan Han
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Mohammad U Zahid
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Duncan Nall
- Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yeoan Youn
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Paul R Selvin
- Department of Physics , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for the Physics of Living Cells , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Center for Biophysics and Quantitative Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Andrew M Smith
- Department of Bioengineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Micro and Nanotechnology Laboratory , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carl R. Woese Institute for Genomic Biology , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
- Carle Illinois College of Medicine , Urbana , Illinois 61801 , United States
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28
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Kozlova NV, Pichon C, Rahmouni AR. mRNA with Mammalian Codon Bias Accumulates in Yeast Mutants with Constitutive Stress Granules. Int J Mol Sci 2020; 21:ijms21041234. [PMID: 32059599 PMCID: PMC7072924 DOI: 10.3390/ijms21041234] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/04/2020] [Accepted: 02/04/2020] [Indexed: 11/19/2022] Open
Abstract
Stress granules and P bodies are cytoplasmic structures assembled in response to various stress factors and represent sites of temporary storage or decay of mRNAs. Depending on the source of stress, the formation of these structures may be driven by distinct mechanisms, but several stresses have been shown to stabilize mRNAs via inhibition of deadenylation. A recent study identified yeast gene deletion mutants with constitutive stress granules and elevated P bodies; however, the mechanisms which trigger its formation remain poorly understood. Here, we investigate the possibility of accumulating mRNA with mammalian codon bias, which we termed the model RNA, in these mutants. We found that the model RNA accumulates in dcp2 and xrn1 mutants and in four mutants with constitutive stress granules overlapping with P bodies. However, in eight other mutants with constitutive stress granules, the model RNA is downregulated, or its steady state levels vary. We further suggest that the accumulation of the model RNA is linked to its protection from the main mRNA surveillance path. However, there is no obvious targeting of the model RNA to stress granules or P bodies. Thus, accumulation of the model RNA and formation of constitutive stress granules occur independently and only some paths inducing formation of constitutive stress granules will stabilize mRNA as well.
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Affiliation(s)
- Natalia V. Kozlova
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
| | - Chantal Pichon
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Colléguim Sciences et Techniques, Université d’Orléans, 45071 Orléans, France
| | - A. Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR 4301 du CNRS, Rue Charles Sadron, 45071 Orléans, France;
- Correspondence: (N.V.K.); (A.R.R.)
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29
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Li X, Kim H, Litke JL, Wu J, Jaffrey SR. Fluorophore-Promoted RNA Folding and Photostability Enables Imaging of Single Broccoli-Tagged mRNAs in Live Mammalian Cells. Angew Chem Int Ed Engl 2020; 59:4511-4518. [PMID: 31850609 DOI: 10.1002/anie.201914576] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Indexed: 11/11/2022]
Abstract
Spinach and Broccoli are fluorogenic RNA aptamers that bind DFHBI, a mimic of the chromophore in green fluorescent protein, and activate its fluorescence. Spinach/Broccoli-DFHBI complexes exhibit high fluorescence in vitro, but they exhibit lower fluorescence in mammalian cells. Here, computational screening was used to identify BI, a DFHBI derivative that binds Broccoli with higher affinity and leads to markedly higher fluorescence in cells compared to previous ligands. BI prevents thermal unfolding of Broccoli at 37 °C, leading to more folded Broccoli and thus more fluorescent Broccoli-BI complexes in cells. Broccoli-BI complexes are more photostable owing to impaired photoisomerization and rapid unbinding of photoisomerized cis-BI. These properties enable single mRNA containing 24 Broccoli aptamers to be imaged in live mammalian cells treated with BI. Small molecule ligands can thus promote RNA folding in cells, and thus allow single mRNA imaging with fluorogenic aptamers.
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Affiliation(s)
- Xing Li
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Hyaeyeong Kim
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Jacob L Litke
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Jiahui Wu
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
| | - Samie R Jaffrey
- Department of Pharmacology, Weill Cornell Medicine, Cornell University, New York, NY, 10065, USA
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30
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Li CC, Li Y, Zhang Y, Zhang CY. Single-molecule fluorescence resonance energy transfer and its biomedical applications. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.115753] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Estimating RNA numbers in single cells by RNA fluorescent tagging and flow cytometry. J Microbiol Methods 2019; 166:105745. [PMID: 31654657 DOI: 10.1016/j.mimet.2019.105745] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/11/2019] [Accepted: 10/15/2019] [Indexed: 12/13/2022]
Abstract
Estimating the statistics of single-cell RNA numbers has become a key source of information on gene expression dynamics. One of the most informative methods of in vivo single-RNA detection is MS2d-GFP tagging. So far, it requires microscopy and laborious semi-manual image analysis, which hampers the amount of collectable data. To overcome this limitation, we present a new methodology for quantifying the mean, standard deviation, and skewness of single-cell distributions of RNA numbers, from flow cytometry data on cells expressing RNA tagged with MS2d-GFP. The quantification method, based on scaling flow-cytometry data from microscopy single-cell data on integer-valued RNA numbers, is shown to readily produce precise, big data on in vivo single-cell distributions of RNA numbers and, thus, can assist in studies of transcription dynamics.
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32
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Qu Y, Jiang J, Liu X, Wei P, Yang X, Tang C. Cell Cycle Inhibitor Whi5 Records Environmental Information to Coordinate Growth and Division in Yeast. Cell Rep 2019; 29:987-994.e5. [PMID: 31644918 DOI: 10.1016/j.celrep.2019.09.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 04/28/2019] [Accepted: 09/11/2019] [Indexed: 01/16/2023] Open
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33
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Pizzinga M, Bates C, Lui J, Forte G, Morales-Polanco F, Linney E, Knotkova B, Wilson B, Solari CA, Berchowitz LE, Portela P, Ashe MP. Translation factor mRNA granules direct protein synthetic capacity to regions of polarized growth. J Cell Biol 2019; 218:1564-1581. [PMID: 30877141 PMCID: PMC6504908 DOI: 10.1083/jcb.201704019] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 11/12/2018] [Accepted: 02/28/2019] [Indexed: 12/22/2022] Open
Abstract
mRNA localization serves key functions in localized protein production, making it critical that the translation machinery itself is present at these locations. Here we show that translation factor mRNAs are localized to distinct granules within yeast cells. In contrast to many messenger RNP granules, such as processing bodies and stress granules, which contain translationally repressed mRNAs, these granules harbor translated mRNAs under active growth conditions. The granules require Pab1p for their integrity and are inherited by developing daughter cells in a She2p/She3p-dependent manner. These results point to a model where roughly half the mRNA for certain translation factors is specifically directed in granules or translation factories toward the tip of the developing daughter cell, where protein synthesis is most heavily required, which has particular implications for filamentous forms of growth. Such a feedforward mechanism would ensure adequate provision of the translation machinery where it is to be needed most over the coming growth cycle.
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Affiliation(s)
- Mariavittoria Pizzinga
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Christian Bates
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Jennifer Lui
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Gabriella Forte
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Fabián Morales-Polanco
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Emma Linney
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Barbora Knotkova
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Beverley Wilson
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Clara A Solari
- Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Luke E Berchowitz
- Department of Genetics and Development, Hammer Health Sciences Center, Columbia University Medical Center, New York, NY
| | - Paula Portela
- Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Mark P Ashe
- Division of Molecular and Cellular Function, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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34
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Abstract
In the postgenomic era, it is clear that the human genome encodes thousands of long noncoding RNAs (lncRNAs). Along the way, RNA imaging (e.g., RNA fluorescence in situ hybridization [RNA-FISH]) has been instrumental in identifying powerful roles for lncRNAs based on their subcellular localization patterns. Here, we explore how RNA imaging technologies have shed new light on how, when, and where lncRNAs may play functional roles. Specifically, we will synthesize the underlying principles of RNA imaging techniques by exploring several landmark lncRNA imaging studies that have illuminated key insights into lncRNA biology.
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Affiliation(s)
- Arjun Raj
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - John L Rinn
- Department of Biochemistry, University of Colorado Boulder and BioFrontiers Institute, Boulder, Colorado 80303
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35
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Tutucci E, Vera M, Singer RH. Single-mRNA detection in living S. cerevisiae using a re-engineered MS2 system. Nat Protoc 2018; 13:2268-2296. [DOI: 10.1038/s41596-018-0037-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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36
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Taylor SE, Taylor RD, Price J, Andreae LC. Single-molecule fluorescence in-situ hybridization reveals that human SHANK3 mRNA expression varies during development and in autism-associated SHANK3 heterozygosity. Stem Cell Res Ther 2018; 9:206. [PMID: 30064494 PMCID: PMC6069870 DOI: 10.1186/s13287-018-0957-3] [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] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 06/13/2018] [Accepted: 07/16/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Deletions and mutations in the SHANK3 gene are strongly associated with autism spectrum disorder and underlie the autism-associated disorder Phelan-McDermid syndrome. SHANK3 is a scaffolding protein found at the post-synaptic membrane of excitatory neurons. METHODS Single-molecule fluorescence in-situ hybridization (smFISH) allows the visualization of single mRNA transcripts in vitro. Here we perform and quantify smFISH in human inducible pluripotent stem cell (hiPSC)-derived cortical neurons, targeting the SHANK3 transcript. RESULTS Both smFISH and conventional immunofluorescence staining demonstrated a developmental increase in SHANK3 mRNA and protein, respectively, in control human cortical neurons. Analysis of single SHANK3 mRNA molecules in neurons derived from an autistic individual heterozygous for SHANK3 indicated that while the number of SHANK3 mRNA transcripts remained comparable with control levels in the cell soma, there was a 50% reduction within neuronal processes, suggesting that local, dendritic targeting of SHANK3 mRNA may be specifically affected in SHANK3 haploinsufficiency. CONCLUSION Human SHANK3 mRNA shows developmentally regulated dendritic localization in hiPSC-derived neurons, which is reduced in neurons generated from a haploinsufficient individual with autism. Although further replication is needed, given the importance of local mRNA translation in synaptic function, this could represent an important early abnormality.
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Affiliation(s)
- Samuel E Taylor
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Ruth D Taylor
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, UK.,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK
| | - Jack Price
- MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.,Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK
| | - Laura C Andreae
- Centre for Developmental Neurobiology, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE1 1UL, UK. .,MRC Centre for Neurodevelopmental Disorders, King's College London, London, UK.
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37
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Detection of single mRNAs in individual cells of the auditory system. Hear Res 2018; 367:88-96. [PMID: 30071403 DOI: 10.1016/j.heares.2018.07.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 05/23/2018] [Accepted: 07/16/2018] [Indexed: 01/17/2023]
Abstract
Gene expression analysis is essential for understanding the rich repertoire of cellular functions. With the development of sensitive molecular tools such as single-cell RNA sequencing, extensive gene expression data can be obtained and analyzed from various tissues. Single-molecule fluorescence in situ hybridization (smFISH) has emerged as a powerful complementary tool for single-cell genomics studies because of its ability to map and quantify the spatial distributions of single mRNAs at the subcellular level in their native tissue. Here, we present a detailed method to study the copy numbers and spatial localizations of single mRNAs in the cochlea and inferior colliculus. First, we demonstrate that smFISH can be performed successfully in adult cochlear tissue after decalcification. Second, we show that the smFISH signals can be detected with high specificity. Third, we adapt an automated transcript analysis pipeline to quantify and identify single mRNAs in a cell-specific manner. Lastly, we show that our method can be used to study possible correlations between transcriptional and translational activities of single genes. Thus, we have developed a detailed smFISH protocol that can be used to study the expression of single mRNAs in specific cell types of the peripheral and central auditory systems.
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38
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Transcriptional timing and noise of yeast cell cycle regulators-a single cell and single molecule approach. NPJ Syst Biol Appl 2018; 4:17. [PMID: 29844922 PMCID: PMC5962571 DOI: 10.1038/s41540-018-0053-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 12/12/2022] Open
Abstract
Gene expression is a stochastic process and its appropriate regulation is critical for cell cycle progression. Cellular stress response necessitates expression reprogramming and cell cycle arrest. While previous studies are mostly based on bulk experiments influenced by synchronization effects or lack temporal distribution, time-resolved methods on single cells are needed to understand eukaryotic cell cycle in context of noisy gene expression and external perturbations. Using smFISH, microscopy and morphological markers, we monitored mRNA abundances over cell cycle phases and calculated transcriptional noise for SIC1, CLN2, and CLB5, the main G1/S transition regulators in budding yeast. We employed mathematical modeling for in silico synchronization and for derivation of time-courses from single cell data. This approach disclosed detailed quantitative insights into transcriptional regulation with and without stress, not available from bulk experiments before. First, besides the main peak in G1 we found an upshift of CLN2 and CLB5 expression in late mitosis. Second, all three genes showed basal expression throughout cell cycle enlightening that transcription is not divided in on and off but rather in high and low phases. Finally, exposing cells to osmotic stress revealed different periods of transcriptional inhibition for CLN2 and CLB5 and the impact of stress on cell cycle phase duration. Combining experimental and computational approaches allowed us to precisely assess cell cycle progression timing, as well as gene expression dynamics.
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39
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Ishigaki Y, Sato K. Effects of Microchannel Shape and Ultrasonic Mixing on Microfluidic Padlock Probe Rolling Circle Amplification (RCA) Reactions. MICROMACHINES 2018; 9:mi9060272. [PMID: 30424205 PMCID: PMC6187661 DOI: 10.3390/mi9060272] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 05/22/2018] [Accepted: 05/29/2018] [Indexed: 01/17/2023]
Abstract
The fluorescence in situ hybridization (FISH)-based padlock probe and rolling circle amplification (RCA) method allows for the detection of point mutations. However, it requires multiple reaction steps and solution exchanges, making it costly, labor-intensive, and time-consuming. In this study, we aimed to improve the efficiency of padlock/RCA by determining the effects of microchannel shape and ultrasonic solution mixing. Using a circular-shaped microchamber and ultrasonic mixing, the efficiency of microfluidic padlock/RCA was improved, and the consumption of the expensive probe solution was reduced from 10 µL to approximately 3.5 µL. Moreover, the fluorescent probe hybridization time was reduced to 5 min, which is four times faster than that of the standard protocol. We used this method to successfully detect mitochondrial DNA and transcripts of β-actin and K-ras proto-oncogene codon 12 in cells. Our method offers improvements over current padlock/RCA methods and will be helpful in optimizing other microfluidics-based FISH-related analyses.
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Affiliation(s)
- Yuri Ishigaki
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo, Tokyo 112-8681, Japan.
| | - Kae Sato
- Department of Chemical and Biological Sciences, Faculty of Science, Japan Women's University, Bunkyo, Tokyo 112-8681, Japan.
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40
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Waminal NE, Pellerin RJ, Kim NS, Jayakodi M, Park JY, Yang TJ, Kim HH. Rapid and Efficient FISH using Pre-Labeled Oligomer Probes. Sci Rep 2018; 8:8224. [PMID: 29844509 PMCID: PMC5974128 DOI: 10.1038/s41598-018-26667-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 05/17/2018] [Indexed: 12/29/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is used to visualize the distribution of DNA elements within a genome. Conventional methods for FISH take 1-2 days. Here, we developed a simplified, rapid FISH technique using pre-labeled oligonucleotide probes (PLOPs) and tested the procedure using 18 PLOPs from 45S and 5S rDNA, Arabidopsis-type telomere, and newly-identified Panax ginseng-specific tandem repeats. The 16 developed rDNA PLOPs can be universally applied to plants and animals. The telomere PLOPs can be utilized in most plants with Arabidopsis-type telomeres. The ginseng-specific PLOP can be used to distinguish P. ginseng from related Panax species. Differential labeling of PLOPs allowed us to simultaneously visualize different target loci while reducing the FISH hybridization time from ~16 h to 5 min. PLOP-FISH is efficient, reliable, and rapid, making it ideal for routine analysis, especially of newly sequenced genomes using either universal or specific targets, such as novel tandem repeats identified from whole-genome sequencing data.
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Affiliation(s)
- Nomar Espinosa Waminal
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.,Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Remnyl Joyce Pellerin
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea
| | - Nam-Soo Kim
- Department of Molecular Biosciences, Kangwon National University, Chuncheon, 24341, Korea
| | - Murukarthick Jayakodi
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Korea.
| | - Hyun Hee Kim
- Chromosome Research Institute, Department of Life Science, Sahmyook University, Seoul, 01795, Korea.
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41
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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: 24] [Impact Index Per Article: 4.0] [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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42
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Jansova D, Tetkova A, Koncicka M, Kubelka M, Susor A. Localization of RNA and translation in the mammalian oocyte and embryo. PLoS One 2018. [PMID: 29529035 PMCID: PMC5846722 DOI: 10.1371/journal.pone.0192544] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The tight correlation between mRNA distribution and subsequent protein localization and function indicate a major role for mRNA localization within the cell. RNA localization, followed by local translation, presents a mechanism for spatial and temporal gene expression regulation utilized by various cell types. However, little is known about mRNA localization and translation in the mammalian oocyte and early embryo. Importantly, fully-grown oocyte becomes transcriptionally inactive and only utilizes transcripts previously synthesized and stored during earlier development. We discovered an abundant RNA population in the oocyte and early embryo nucleus together with RNA binding proteins. We also characterized specific ribosomal proteins, which contribute to translation in the oocyte and embryo. By applying selected markers to mouse and human oocytes, we found that there might be a similar mechanism of RNA metabolism in both species. In conclusion, we visualized the localization of RNAs and translation machinery in the oocyte, that could shed light on this terra incognita of these unique cell types in mouse and human.
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Affiliation(s)
- Denisa Jansova
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
- * E-mail: (DJ); (AS)
| | - Anna Tetkova
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Marketa Koncicka
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Michal Kubelka
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
| | - Andrej Susor
- Institute of Animal Physiology and Genetics, CAS, Libechov, Czech Republic
- * E-mail: (DJ); (AS)
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43
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Sikora G, Kepten E, Weron A, Balcerek M, Burnecki K. An efficient algorithm for extracting the magnitude of the measurement error for fractional dynamics. Phys Chem Chem Phys 2018; 19:26566-26581. [PMID: 28920611 DOI: 10.1039/c7cp04464j] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Modern live-imaging fluorescent microscopy techniques following the stochastic motion of labeled tracer particles, i.e. single particle tracking (SPT) experiments, have uncovered significant deviations from the laws of Brownian motion in a variety of biological systems. Accurately characterizing the anomalous diffusion for SPT experiments has become a central issue in biophysics. However, measurement errors raise difficulty in the analysis of single trajectories. In this paper, we introduce a novel surface calibration method based on a fractionally integrated moving average (FIMA) process as an effective tool for extracting both the magnitude of the measurement error and the anomalous exponent for autocorrelated processes of various origins. This method is developed using a toy model - fractional Brownian motion disturbed by independent Gaussian white noise - and is illustrated on both simulated and experimental biological data. We also compare this new method with the mean-squared displacement (MSD) technique, extended to capture the measurement noise in the toy model, which shows inferior results. The introduced procedure is expected to allow for more accurate analysis of fractional anomalous diffusion trajectories with measurement errors across different experimental fields and without the need for any calibration measurements.
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Affiliation(s)
- G Sikora
- Faculty of Pure and Applied Mathematics, Hugo Steinhaus Center, Wroclaw University of Science and Technology, Wyspianskiego 27, 50-370 Wroclaw, Poland.
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Reis M, Kromer JA, Klipp E. General solution of the chemical master equation and modality of marginal distributions for hierarchic first-order reaction networks. J Math Biol 2018; 77:377-419. [PMID: 29353313 PMCID: PMC6061068 DOI: 10.1007/s00285-018-1205-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 10/10/2017] [Indexed: 11/25/2022]
Abstract
Multimodality is a phenomenon which complicates the analysis of statistical data based exclusively on mean and variance. Here, we present criteria for multimodality in hierarchic first-order reaction networks, consisting of catalytic and splitting reactions. Those networks are characterized by independent and dependent subnetworks. First, we prove the general solvability of the Chemical Master Equation (CME) for this type of reaction network and thereby extend the class of solvable CME’s. Our general solution is analytical in the sense that it allows for a detailed analysis of its statistical properties. Given Poisson/deterministic initial conditions, we then prove the independent species to be Poisson/binomially distributed, while the dependent species exhibit generalized Poisson/Khatri Type B distributions. Generalized Poisson/Khatri Type B distributions are multimodal for an appropriate choice of parameters. We illustrate our criteria for multimodality by several basic models, as well as the well-known two-stage transcription–translation network and Bateman’s model from nuclear physics. For both examples, multimodality was previously not reported.
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Affiliation(s)
- Matthias Reis
- Institute of Biology, Theoretical Biophysics, Humboldt-Universität zu Berlin, 10117, Berlin, Germany
| | - Justus A Kromer
- Center for Advancing Electronics Dresden, Technische Universität Dresden, 01062, Dresden, Germany
| | - Edda Klipp
- Institute of Biology, Theoretical Biophysics, Humboldt-Universität zu Berlin, 10117, Berlin, Germany.
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Kocks C, Boltengagen A, Piwecka M, Rybak-Wolf A, Rajewsky N. Single-Molecule Fluorescence In Situ Hybridization (FISH) of Circular RNA CDR1as. Methods Mol Biol 2018; 1724:77-96. [PMID: 29322442 DOI: 10.1007/978-1-4939-7562-4_7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Individual mRNA molecules can be imaged in fixed cells by hybridization with multiple, singly labeled oligonucleotide probes, followed by computational identification of fluorescent signals. This approach, called single-molecule RNA fluorescence in situ hybridization (smRNA FISH), allows subcellular localization and absolute quantification of RNA molecules in individual cells. Here, we describe a simple smRNA FISH protocol for two-color imaging of a circular RNA, CDR1as, simultaneously with an unrelated messenger RNA. The protocol can be adapted to circRNAs that coexist with overlapping, noncircular mRNA isoforms produced from the same genetic locus.
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Affiliation(s)
- Christine Kocks
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
| | - Anastasiya Boltengagen
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Monika Piwecka
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Agnieszka Rybak-Wolf
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Nikolaus Rajewsky
- Systems Biology of Gene-Regulatory Elements, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center (MDC) for Molecular Medicine in the Helmholtz Association, Berlin, Germany
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46
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Abstract
Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.
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Affiliation(s)
- Tatjana Trcek
- Department of Cell Biology, Skirball Institute of Biomolecular Medicine, NYU School of Medicine, New York, NY, USA.
| | - Samir Rahman
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
| | - Daniel Zenklusen
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC, Canada
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47
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Wadsworth GM, Parikh RY, Choy JS, Kim HD. mRNA detection in budding yeast with single fluorophores. Nucleic Acids Res 2017; 45:e141. [PMID: 28666354 PMCID: PMC5587780 DOI: 10.1093/nar/gkx568] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 06/21/2017] [Indexed: 12/29/2022] Open
Abstract
Quantitative measurement of mRNA levels in single cells is necessary to understand phenotypic variability within an otherwise isogenic population of cells. Single-molecule mRNA Fluorescence In Situ Hybridization (FISH) has been established as the standard method for this purpose, but current protocols require a long region of mRNA to be targeted by multiple DNA probes. Here, we introduce a new single-probe FISH protocol termed sFISH for budding yeast, Saccharomyces cerevisiae using a single DNA probe labeled with a single fluorophore. In sFISH, we markedly improved probe specificity and signal-to-background ratio by using methanol fixation and inclined laser illumination. We show that sFISH reports mRNA changes that correspond to protein levels and gene copy number. Using this new FISH protocol, we can detect >50% of the total target mRNA. We also demonstrate the versatility of sFISH using FRET detection and mRNA isoform profiling as examples. Our FISH protocol with single-fluorophore sensitivity significantly reduces cost and time compared to the conventional FISH protocols and opens up new opportunities to investigate small changes in RNA at the single cell level.
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Affiliation(s)
- Gable M Wadsworth
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - Rasesh Y Parikh
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
| | - John S Choy
- Department of Biology, The Catholic University of America, 620 Michigan Avenue NE, Washington, DC 20064, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332-0430, USA
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48
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Baudrimont A, Voegeli S, Viloria EC, Stritt F, Lenon M, Wada T, Jaquet V, Becskei A. Multiplexed gene control reveals rapid mRNA turnover. SCIENCE ADVANCES 2017; 3:e1700006. [PMID: 28706991 PMCID: PMC5507631 DOI: 10.1126/sciadv.1700006] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 06/13/2017] [Indexed: 05/29/2023]
Abstract
The rates of mRNA synthesis and decay determine the mRNA expression level. The two processes are under coordinated control, which makes the measurements of these rates challenging, as evidenced by the low correlation among the methods of measurement of RNA half-lives. We developed a minimally invasive method, multiplexed gene control, to shut off expression of genes with controllable synthetic promoters. The method was validated by measuring the ratios of the nascent to mature mRNA molecules and by measuring the half-life with endogenous promoters that can be controlled naturally or through inserting short sequences that impart repressibility. The measured mRNA half-lives correlated highly with those obtained with the metabolic pulse-labeling method in yeast. However, mRNA degradation was considerably faster in comparison to previous estimates, with a median half-life of around 2 min. The half-life permits the estimation of promoter-dependent and promoter-independent transcription rates. The dynamical range of the promoter-independent transcription rates was larger than that of the mRNA half-lives. The rapid mRNA turnover and the broad adjustability of promoter-independent transcription rates are expected to have a major impact on stochastic gene expression and gene network behavior.
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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Size-Dependent Expression of the Mitotic Activator Cdc25 Suggests a Mechanism of Size Control in Fission Yeast. Curr Biol 2017; 27:1491-1497.e4. [PMID: 28479325 DOI: 10.1016/j.cub.2017.04.016] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 02/28/2017] [Accepted: 04/11/2017] [Indexed: 01/19/2023]
Abstract
Proper cell size is essential for cellular function. Nonetheless, despite more than 100 years of work on the subject, the mechanisms that maintain cell-size homeostasis are largely mysterious [1]. Cells in growing populations maintain cell size within a narrow range by coordinating growth and division. Bacterial and eukaryotic cells both demonstrate homeostatic size control, which maintains population-level variation in cell size within a certain range and returns the population average to that range if it is perturbed [1, 2]. Recent work has proposed two different strategies for size control: budding yeast has been proposed to use an inhibitor-dilution strategy to regulate size at the G1/S transition [3], whereas bacteria appear to use an adder strategy, in which a fixed amount of growth each generation causes cell size to converge on a stable average [4-6]. Here we present evidence that cell size in the fission yeast Schizosaccharomyces pombe is regulated by a third strategy: the size-dependent expression of the mitotic activator Cdc25. cdc25 transcript levels are regulated such that smaller cells express less Cdc25 and larger cells express more Cdc25, creating an increasing concentration of Cdc25 as cells grow and providing a mechanism for cells to trigger cell division when they reach a threshold concentration of Cdc25. Because regulation of mitotic entry by Cdc25 is well conserved, this mechanism may provide a widespread solution to the problem of size control in eukaryotes.
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