Current Protocols in Molecular Biology最新文献

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Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules 分析性超离心(AUC):荧光和吸光度AUC在生物大分子研究中的应用综述
Current Protocols in Molecular Biology Pub Date : 2020-12-22 DOI: 10.1002/cpmb.131
Garrett B. Edwards, Uma M. Muthurajan, Samuel Bowerman, Karolin Luger
{"title":"Analytical Ultracentrifugation (AUC): An Overview of the Application of Fluorescence and Absorbance AUC to the Study of Biological Macromolecules","authors":"Garrett B. Edwards,&nbsp;Uma M. Muthurajan,&nbsp;Samuel Bowerman,&nbsp;Karolin Luger","doi":"10.1002/cpmb.131","DOIUrl":"10.1002/cpmb.131","url":null,"abstract":"<p>The biochemical and biophysical investigation of proteins, nucleic acids, and the assemblies that they form yields essential information to understand complex systems. Analytical ultracentrifugation (AUC) represents a broadly applicable and information-rich method for investigating macromolecular characteristics such as size, shape, stoichiometry, and binding properties, all in the true solution-state environment that is lacking in most orthogonal methods. Despite this, AUC remains underutilized relative to its capabilities and potential in the fields of biochemistry and molecular biology. Although there has been a rapid development of computing power and AUC analysis tools in this millennium, fewer advancements have occurred in development of new applications of the technique, leaving these powerful instruments underappreciated and underused in many research institutes. With AUC previously limited to absorbance and Rayleigh interference optics, the addition of fluorescence detection systems has greatly enhanced the applicability of AUC to macromolecular systems that are traditionally difficult to characterize. This overview provides a resource for novices, highlighting the potential of AUC and encouraging its use in their research, as well as for current users, who may benefit from our experience. We discuss the strengths of fluorescence-detected AUC and demonstrate the power of even simple AUC experiments to answer practical and fundamental questions about biophysical properties of macromolecular assemblies. We address the development and utility of AUC, explore experimental design considerations, present case studies investigating properties of biological macromolecules that are of common interest to researchers, and review popular analysis approaches. © 2020 The Authors.</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38741109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA 用重组组蛋白和纯化DNA重组和纯化核小体
Current Protocols in Molecular Biology Pub Date : 2020-12-11 DOI: 10.1002/cpmb.130
Ilana M. Nodelman, Ashok Patel, Robert F. Levendosky, Gregory D. Bowman
{"title":"Reconstitution and Purification of Nucleosomes with Recombinant Histones and Purified DNA","authors":"Ilana M. Nodelman,&nbsp;Ashok Patel,&nbsp;Robert F. Levendosky,&nbsp;Gregory D. Bowman","doi":"10.1002/cpmb.130","DOIUrl":"10.1002/cpmb.130","url":null,"abstract":"<p>Nucleosomes are substrates for a broad range of factors, including those involved in transcription or chromosome maintenance/reorganization and enzymes that covalently modify histones. Given the heterogeneous nature of nucleosomes in vivo (i.e., varying histone composition, post-translational modifications, DNA sequence register), understanding the specificity and activities of chromatin-interacting factors has required in vitro studies using well-defined nucleosome substrates. Here, we provide detailed methods for large-scale PCR preparation of DNA, assembly of nucleosomes from purified DNA and histones, and purification of DNA and mononucleosomes. Such production of well-defined nucleosomes for biochemical and biophysical studies is key for studying numerous proteins and protein complexes that bind and/or alter nucleosomes and for revealing inherent characteristics of nucleosomes. © 2020 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Large-scale PCR amplification of DNA</p><p><b>Basic Protocol 2</b>: DNA and nucleosome purification using a Bio-Rad Mini Prep Cell/Prep Cell</p><p><b>Basic Protocol 3</b>: Nucleosome reconstitution via linear gradient salt dialysis</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-12-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.130","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38361753","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 12
Measuring Protein Synthesis in Cultured Cells and Mouse Tissues Using the Non-radioactive SUnSET Assay 用非放射性日落法测定培养细胞和小鼠组织中的蛋白质合成
Current Protocols in Molecular Biology Pub Date : 2020-11-20 DOI: 10.1002/cpmb.127
Venkatraman Ravi, Aditi Jain, Sneha Mishra, Nagalingam Ravi Sundaresan
{"title":"Measuring Protein Synthesis in Cultured Cells and Mouse Tissues Using the Non-radioactive SUnSET Assay","authors":"Venkatraman Ravi,&nbsp;Aditi Jain,&nbsp;Sneha Mishra,&nbsp;Nagalingam Ravi Sundaresan","doi":"10.1002/cpmb.127","DOIUrl":"10.1002/cpmb.127","url":null,"abstract":"<p>Changes in protein synthesis occur under diverse physiological and pathological conditions. For example, translation can increase in response to growth signals or decrease in response to pathological states. Such changes have traditionally been measured by tracking the incorporation of radiolabeled amino acids. However, use of radioactivity is increasingly disfavored, and a simple and efficient puromycin-based, non-radioactive method called the SUnSET assay has gained popularity for measuring protein synthesis in diverse cell types and tissues. Here, we describe the principles, procedures, and troubleshooting steps for measuring protein synthesis using the SUnSET assay in cultured cells and mouse tissues. © 2020 Wiley Periodicals LLC</p><p><b>Basic Protocol 1</b>: Measuring protein synthesis in cultured cells by western blotting</p><p><b>Support Protocol 1</b>: Ponceau staining</p><p><b>Support Protocol 2</b>: Testing the specificity of the anti-puromycin antibody</p><p><b>Basic Protocol 2</b>: Measuring protein synthesis in cultured cells by immunofluorescence</p><p><b>Basic Protocol 3</b>: Measuring protein synthesis in mouse tissues by western blotting</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.127","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38628477","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 10
Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines 在人类细胞中进行碱基编辑以产生单核苷酸变异克隆细胞系
Current Protocols in Molecular Biology Pub Date : 2020-11-05 DOI: 10.1002/cpmb.129
Carlos A. Vasquez, Quinn T. Cowan, Alexis C. Komor
{"title":"Base Editing in Human Cells to Produce Single-Nucleotide-Variant Clonal Cell Lines","authors":"Carlos A. Vasquez,&nbsp;Quinn T. Cowan,&nbsp;Alexis C. Komor","doi":"10.1002/cpmb.129","DOIUrl":"10.1002/cpmb.129","url":null,"abstract":"<p>Base-editing technologies enable the introduction of point mutations at targeted genomic sites in mammalian cells, with higher efficiency and precision than traditional genome-editing methods that use DNA double-strand breaks, such as zinc finger nucleases (ZFNs), transcription-activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated protein 9 (CRISPR-Cas9) system. This allows the generation of single-nucleotide-variant isogenic cell lines (i.e., cell lines whose genomic sequences differ from each other only at a single, edited nucleotide) in a more time- and resource-effective manner. These single-nucleotide-variant clonal cell lines represent a powerful tool with which to assess the functional role of genetic variants in a native cellular context. Base editing can therefore facilitate genotype-to-phenotype studies in a controlled laboratory setting, with applications in both basic research and clinical applications. Here, we provide optimized protocols (including experimental design, methods, and analyses) to design base-editing constructs, transfect adherent cells, quantify base-editing efficiencies in bulk, and generate single-nucleotide-variant clonal cell lines. © 2020 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Design and production of plasmids for base-editing experiments</p><p><b>Basic Protocol 2</b>: Transfection of adherent cells and harvesting of genomic DNA</p><p><b>Basic Protocol 3</b>: Genotyping of harvested cells using Sanger sequencing</p><p><b>Alternate Protocol 1</b>: Next-generation sequencing to quantify base editing</p><p><b>Basic Protocol 4</b>: Single-cell isolation of base-edited cells using FACS</p><p><b>Alternate Protocol 2</b>: Single-cell isolation of base-edited cells using dilution plating</p><p><b>Basic Protocol 5</b>: Clonal expansion to generate isogenic cell lines and genotyping of clones</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38570900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Preparation of Mammalian Nascent RNA for Long Read Sequencing 哺乳动物新生RNA的长读测序制备
Current Protocols in Molecular Biology Pub Date : 2020-10-21 DOI: 10.1002/cpmb.128
Kirsten A. Reimer, Karla M. Neugebauer
{"title":"Preparation of Mammalian Nascent RNA for Long Read Sequencing","authors":"Kirsten A. Reimer,&nbsp;Karla M. Neugebauer","doi":"10.1002/cpmb.128","DOIUrl":"10.1002/cpmb.128","url":null,"abstract":"<p>Long read sequencing technologies now allow high-quality sequencing of RNAs (or their cDNAs) that are hundreds to thousands of nucleotides long. Long read sequences of nascent RNA provide single-nucleotide-resolution information about co-transcriptional RNA processing events—e.g., splicing, folding, and base modifications. Here, we describe how to isolate nascent RNA from mammalian cells through subcellular fractionation of chromatin-associated RNA, as well as how to deplete poly(A)<sup>+</sup> RNA and rRNA, and, finally, how to generate a full-length cDNA library for use on long read sequencing platforms. This approach allows for an understanding of coordinated splicing status across multi-intron transcripts by revealing patterns of splicing or other RNA processing events that cannot be gained from traditional short read RNA sequencing. © 2020 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Subcellular fractionation</p><p><b>Basic Protocol 2</b>: Nascent RNA isolation and adapter ligation</p><p><b>Basic Protocol 3</b>: cDNA amplicon preparation</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.128","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38513392","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
Optimized Transgene Delivery Using Third-Generation Lentiviruses 利用第三代慢病毒优化转基因传递
Current Protocols in Molecular Biology Pub Date : 2020-09-28 DOI: 10.1002/cpmb.125
Katherine P. Gill, Mark Denham
{"title":"Optimized Transgene Delivery Using Third-Generation Lentiviruses","authors":"Katherine P. Gill,&nbsp;Mark Denham","doi":"10.1002/cpmb.125","DOIUrl":"10.1002/cpmb.125","url":null,"abstract":"<p>The lentivirus system enables efficient genetic modification of both dividing and non-dividing cells and therefore is a useful tool for elucidating developmental processes and disease pathogenesis. The development of third-generation lentiviruses has resulted in improved biosafety, low immunogenicity, and substantial packaging capabilities. However, because third-generation lentiviruses require successful co-transfection with four plasmids, this typically means that lower titers are attained. This is problematic, as it is often desirable to produce purified lentiviruses with high titers (&gt;1 × 10<sup>8</sup> TU/ml), especially for in vivo applications. The manufacturing process for lentiviruses involves several critical experimental factors that can influence titer, purity, and transduction efficiency. Here, we describe a straightforward, stepwise protocol for the reproducible manufacture of high-titer third-generation lentiviruses (1 × 10<sup>8</sup> to 1 × 10<sup>9</sup> TU/ml). This optimized protocol enhances transgene expression by use of Lipofectamine transfection and optimized serum replacement medium, a single ultracentrifugation step, use of a sucrose cushion, and addition of a histone deacetylation inhibitor. Furthermore, we provide alternate methods for titration analyses, including functional and genomic integration analyses, using common laboratory techniques such as FACS as well as genomic DNA extraction and qPCR. These optimized methods will be beneficial for investigating developmental processes and disease pathogenesis in vitro and in vivo. © 2020 The Authors.</p><p><b>Basic Protocol 1</b>: Lentivirus production</p><p><b>Support Protocol</b>: Lentivirus concentration</p><p><b>Basic Protocol 2</b>: Lentivirus titration</p><p><b>Alternate Protocol 1</b>: Determination of viral titration by FACS analysis</p><p><b>Alternate Protocol 2</b>: Determination of viral titration by genome integration analysis</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"133 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38428784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 8
Virion Display: A High-Throughput Method to Express Functional Membrane Proteins 病毒粒子展示:一种表达功能性膜蛋白的高通量方法
Current Protocols in Molecular Biology Pub Date : 2020-09-23 DOI: 10.1002/cpmb.126
Guan-Da Syu, Eric Johansen, Heng Zhu
{"title":"Virion Display: A High-Throughput Method to Express Functional Membrane Proteins","authors":"Guan-Da Syu,&nbsp;Eric Johansen,&nbsp;Heng Zhu","doi":"10.1002/cpmb.126","DOIUrl":"10.1002/cpmb.126","url":null,"abstract":"<p>Transmembrane proteins are responsible for many critical cellular functions and represent one of the largest families of drug targets. However, these proteins, especially multipass transmembrane proteins, are difficult to study because they must be embedded in a lipid bilayer to maintain their native conformations. The development of the virion display (VirD) technology enables transmembrane proteins to be integrated into the viral envelope of herpes simplex virus 1 (HSV-1). Combining high-throughput cloning, expression, and purification techniques, VirD technology has been applied to the largest set of human transmembrane proteins, namely G-protein-coupled receptors, and has allowed the identification of interactions that are both specific and functional. This article describes the procedures to integrate an open reading frame for any transmembrane protein into the HSV-1 genome and produce recombinant HSV-1 virus to ultimately generate pure VirD virions for biological and pharmaceutical studies. © 2020 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: Gateway cloning of transmembrane proteins</p><p><b>Support Protocol 1</b>: Ethanol precipitation of bacterial artificial chromosomal DNA</p><p><b>Support Protocol 2</b>: Preparation of competent cells</p><p><b>Basic Protocol 2</b>: Production of recombinant HSV-1 virions</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"132 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.126","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38411444","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels ARF-AID:一种快速诱导的蛋白质降解系统,可保持基础内源性蛋白质水平
Current Protocols in Molecular Biology Pub Date : 2020-08-05 DOI: 10.1002/cpmb.124
Kizhakke Mattada Sathyan, Thomas G. Scott, Michael J. Guertin
{"title":"ARF-AID: A Rapidly Inducible Protein Degradation System That Preserves Basal Endogenous Protein Levels","authors":"Kizhakke Mattada Sathyan,&nbsp;Thomas G. Scott,&nbsp;Michael J. Guertin","doi":"10.1002/cpmb.124","DOIUrl":"10.1002/cpmb.124","url":null,"abstract":"<p>Inducible degron systems are widely used to specifically and rapidly deplete proteins of interest in cell lines and organisms. An advantage of inducible degradation is that the biological system under study remains intact and functional until perturbation, a feature that necessitates that the endogenous levels of the protein are maintained. However, endogenous tagging of genes with auxin-inducible degrons (AID) can result in chronic, auxin-independent proteasome-mediated degradation. The ARF-AID (auxin-response factor–auxin-inducible degron) system is a re-engineered auxin-inducible protein degradation system. The additional expression of the ARF-PB1 domain prevents chronic, auxin-independent degradation of AID-tagged proteins while preserving rapid auxin-induced degradation of tagged proteins. Here, we describe the protocol for engineering human cell lines to implement the ARF-AID system for specific and inducible protein degradation. These methods are adaptable and can be extended from cell lines to organisms. © 2020 The Authors.</p><p><b>Basic Protocol 1</b>: Generation of ARF-P2A-TIR1 progenitor cells</p><p><b>Basic Protocol 2</b>: Designing, cloning, and testing of a gene-specific sgRNA</p><p><b>Basic Protocol 3</b>: Design and amplification of a homology-directed repair construct (C-terminal tagging)</p><p><b>Alternate Protocol 1</b>: Design and amplification of a homology-directed repair construct (N-terminal tagging)</p><p><b>Basic Protocol 4</b>: Tagging of a gene of interest with AID</p><p><b>Alternate Protocol 2</b>: Establishment of an ARF-AID clamp system</p><p><b>Basic Protocol 5</b>: Testing of auxin-mediated degradation of the AID-tagged protein</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"132 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-08-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.124","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38241685","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 6
High-Throughput Cellular RNA Sequencing (HiCAR-Seq): Cost-Effective, High-Throughput 3′ mRNA-Seq Method Enabling Individual Sample Quality Control 高通量细胞RNA测序(HiCAR-Seq):具有成本效益的高通量3 ' mRNA-Seq方法,可实现个体样品质量控制
Current Protocols in Molecular Biology Pub Date : 2020-07-31 DOI: 10.1002/cpmb.123
Yaligara Veeranagouda, Jean-Luc Zachayus, Jean-Claude Guillemot, Olivier Venier, Michel Didier
{"title":"High-Throughput Cellular RNA Sequencing (HiCAR-Seq): Cost-Effective, High-Throughput 3′ mRNA-Seq Method Enabling Individual Sample Quality Control","authors":"Yaligara Veeranagouda,&nbsp;Jean-Luc Zachayus,&nbsp;Jean-Claude Guillemot,&nbsp;Olivier Venier,&nbsp;Michel Didier","doi":"10.1002/cpmb.123","DOIUrl":"10.1002/cpmb.123","url":null,"abstract":"<p>High-throughput screening is one of the pillars of drug development. Unbiased transcriptome profiling is now widely used for a deeper understanding of a drug's mechanisms of action, off target effects, and cytotoxicity. Although currently available high-throughput RNA-Seq (HT RNA-Seq) methods such as PLATE-Seq, DRUG-Seq, and BRB-Seq serve these purposes, the inherent nature of these methods does not allow sample-wise sequencing library quality control. Here, we describe an HTR method called High-throughput CellulAr RNA Sequencing (HiCAR-Seq). HiCAR-Seq was optimized to work directly on cultured cells (as little as 1,000 cells) or 10 ng of total RNA. HiCAR-Seq involves reverse transcription from cultured cells or total RNA using oligo-dT primers followed by the PCR amplification of full-length cDNAs using sample-specific barcode primers in individual plate wells. Amplification of cDNA from every sample can be verified using Bioanalyzer. This step not only reveals cDNA amplification but also provides greater precision for pooling equal concentrations of cDNA from different samples. A single pooled cDNA library is made suitable for sequencing on Illumina sequencers using a tagmentation kit. Because HiCAR-Seq targets a small region at the 3′ of the mRNAs, as little as 3 to 4 million reads/sample are enough to infer changes in gene expression in human or mouse cells. We believe that HiCAR-Seq represents a robust and competitive addition to the existing set of transcriptome-based high-throughput screening methods. © 2020 Wiley Periodicals LLC.</p><p><b>Basic Protocol 1</b>: cDNA synthesis and barcoding/enrichment PCR</p><p><b>Basic Protocol 2</b>: Nextera tagmentation/amplification, quantification, and sequencing</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"132 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.123","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38214852","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Simultaneous Examination of Cellular Pathways using Multiplex Hextuple Luciferase Assaying. 使用多重六元荧光素酶测定同时检测细胞通路。
Current Protocols in Molecular Biology Pub Date : 2020-06-01 DOI: 10.1002/cpmb.122
Alejandro Sarrion-Perdigones, Lyra Chang, Yezabel Gonzalez, Tatiana Gallego-Flores, Damian W Young, Koen J T Venken
{"title":"Simultaneous Examination of Cellular Pathways using Multiplex Hextuple Luciferase Assaying.","authors":"Alejandro Sarrion-Perdigones,&nbsp;Lyra Chang,&nbsp;Yezabel Gonzalez,&nbsp;Tatiana Gallego-Flores,&nbsp;Damian W Young,&nbsp;Koen J T Venken","doi":"10.1002/cpmb.122","DOIUrl":"https://doi.org/10.1002/cpmb.122","url":null,"abstract":"<p><p>Multiplex experimentation that can assay multiple cellular signaling pathways in the same cells requires orthogonal genetically encoded reporters that report over large dynamic ranges. Luciferases are cost-effective, versatile candidates whose output signals can be sensitively detected in a multiplex fashion. Commonly used dual luciferase reporter assays detect one luciferase that is coupled to a single cellular pathway and a second that is coupled to a control pathway for normalization purposes. We have expanded this approach to multiplex hextuple luciferase assays that can report on five cellular signaling pathways and one control, each of which is encoded by a unique luciferase. Light emission by the six luciferases can be distinguished by the use of two distinct substrates, each specific for three luciferases, followed by spectral decomposition of the light emitted by each of the three luciferase enzymes with bandpass filters. Here, we present detailed protocols on how to perform multiplex hextuple luciferase assaying to monitor pathway fluxes through transcriptional response elements for five specific signaling pathways (i.e., c-Myc, NF-κβ, TGF-β, p53, and MAPK/JNK) using the constitutive CMV promoter as normalization control. Protocols are provided for preparing reporter vector plasmids for multiplex reporter assaying, performing cell culture and multiplex luciferase reporter vector plasmid transfection, executing multiplex luciferase assays, and analyzing and interpreting data obtained by a plate reader appropriately equipped to detect the different luminescences. © 2020 Wiley Periodicals LLC. Basic Protocol 1: Preparation of vectors for multiplex hextuple luciferase assaying Basic Protocol 2: Cell culture work for multiplex hextuple luciferase assays Basic Protocol 3: Transfection of luciferase reporter plasmids followed by drug and recombinant protein treatments Basic Protocol 4: Performing the multiplex hextuple luciferase assay.</p>","PeriodicalId":10734,"journal":{"name":"Current Protocols in Molecular Biology","volume":"131 1","pages":"e122"},"PeriodicalIF":0.0,"publicationDate":"2020-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpmb.122","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38044822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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