Molecular Biology

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    Protocols in Current Issue
    Identification of RNase-sensitive LINE-1 Ribonucleoprotein Interactions by Differential Affinity Immobilization
    Authors:  Hua Jiang, Martin S. Taylor, Kelly R. Molloy, Ilya Altukhov and John LaCava, date: 04/05/2019, view: 607, Q&A: 0
    [Abstract] Long Interspersed Nuclear Element-1 (LINE-1, L1) constitutes a family of autonomous, self-replicating genetic elements known as retrotransposons. Although most are inactive, copious L1 sequences populate the human genome. L1s proliferate in a ‘copy-and-paste’ fashion through an RNA intermediate; a full-length L1 transcript is ~6,000 nucleotides ...
    RNA Immunoprecipitation Assay to Determine the Specificity of SRSF3 Binding to Nanog mRNA
    Authors:  Madara Ratnadiwakara and Minna-Liisa Änko, date: 11/05/2018, view: 1063, Q&A: 0
    [Abstract] Mammalian cells express hundreds of RNA binding proteins (RBPs) that are essential regulators of RNA metabolism. RBP activity plays a central role in the control of gene expression programs and identification of RNA-protein interactions is critical for comprehensive understanding of gene regulation in cells. In recent years, various tools and ...
    Detecting the Interaction of Double-stranded RNA Binding Protein, Viral Protein and Primary miRNA Transcript by Co-immunoprecipitation in planta
    Authors:  Lijia Zheng, Chao Zhang, Jianguo Wu and Yi Li, date: 05/05/2018, view: 1482, Q&A: 0
    [Abstract] MicroRNAs (miRNAs) play important roles in plant growth, development, and response to infection by microbes. Double-stranded RNA binding protein 1 (DRB1) facilitates the processing of primary miRNA transcripts into mature miRNAs. Recently, we found that NS3 protein encoded by rice stripe virus (RSV) associates with DRB1 and promotes miRNA ...
    Trimolecular Fluorescence Complementation (TriFC) Assay for Direct Visualization of RNA-Protein Interaction in planta
    Authors:  Jun Sung Seo and Nam-Hai Chua, date: 10/20/2017, view: 4545, Q&A: 0
    [Abstract] RNA-Protein interactions play important roles in various eukaryotic biological processes. Molecular imaging of subcellular localization of RNA/protein complexes in plants is critical for understanding these interactions. However, methods to image RNA-Protein interactions in living plants have not yet been developed until now. Recently, we have ...
    RNA-protein UV-crosslinking Assay
    Authors:  Dipak Kumar Poria and Partho Sarothi Ray, date: 03/20/2017, view: 6956, Q&A: 2
    [Abstract] RNA-protein interactions play a crucial role in every aspect of RNA metabolism, and also plays a major role in post-transcriptional gene regulation. RNA-binding proteins have been implicated in viral gene expression (Ray and Das, 2002) and microRNA-mediated gene regulation (Poria et al., 2016). Here we have described the protocol which ...
    Polysome Fractionation to Analyze mRNA Distribution Profiles
    Authors:  Amaresh C. Panda, Jennifer L. Martindale and Myriam Gorospe, date: 02/05/2017, view: 11449, Q&A: 2
    [Abstract] Eukaryotic cells adapt to changes in external or internal signals by precisely modulating the expression of specific gene products. The expression of protein-coding genes is controlled at the transcriptional and post-transcriptional levels. Among the latter steps, the regulation of translation is particularly important in cellular processes that ...
    Affinity Pulldown of Biotinylated RNA for Detection of Protein-RNA Complexes
    Authors:  Amaresh C Panda, Jennifer L. Martindale and Myriam Gorospe, date: 12/20/2016, view: 11622, Q&A: 0
    [Abstract] RNA-binding proteins (RBPs) have recently emerged as crucial players in the regulation of gene expression. The interactions of RBPs with target mRNAs control the levels of gene products by altering different regulatory steps, including pre-mRNA splicing and maturation, nuclear mRNA export, and mRNA stability and translation (Glisovic et al ...
    Identification of RNA-binding Proteins by RNA Ligand-based cDNA Expression Library Screening
    Authors:  Min Young Kim, Jong Joo Lee and Chul Geun Kim, date: 01/20/2016, view: 4406, Q&A: 0
    [Abstract] We previously reported when a portion of the Requiem (REQ/DPF2) messenger ribonucleic acid (mRNA) 3’ untranslated region (3’UTR), referred to as G8, was overexpressed in K562 cells, β-globin expression was induced, suggesting that the 3’UTR of REQ mRNA plays a physiological role (Kim et al., 2014). To identify trans-acting factors that ...
    RNA-binding Protein Immunoprecipitation (RIP) to Examine AUF1 Binding to Senescence-Associated Secretory Phenotype (SASP) Factor mRNA
    Authors:  Elise Alspach and Sheila A. Stewart, date: 05/20/2015, view: 8541, Q&A: 0
    [Abstract] Immunoprecipitation and subsequent isolation of nucleic acids allows for the investigation of protein:nucleic acid interactions. RNA-binding protein immunoprecipitation (RIP) is used for the analysis of protein interactions with mRNA. Combining RIP with quantitative real-time PCR (qRT-PCR) further enhances the RIP technique by allowing for the ...
    RNA Chromatin Immunoprecipitation (RNA-ChIP) in Caenorhabditis elegans
    Authors:  Germano Cecere and Alla Grishok, date: 12/20/2014, view: 8790, Q&A: 0
    [Abstract] The RNA chromatin immunoprecipitation assay (RNA-ChIP) allows detection and quantification of RNA–protein interactions using in vivo cross-linking with formaldehyde followed by immunoprecipitation of the RNA–protein complexes. Here we describe the RNA–ChIP protocol that we have adapted for Caenorhabditis elegans (C. elegans ...



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