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dc.contributor.authorTamburino, Alex M.
dc.contributor.authorKaymak, Ebru
dc.contributor.authorShrestha, Shaleen
dc.contributor.authorHoldorf, Amy D.
dc.contributor.authorRyder, Sean P.
dc.contributor.authorWalhout, Albertha J. M.
dc.date2022-08-11T08:08:23.000
dc.date.accessioned2022-08-23T15:53:19Z
dc.date.available2022-08-23T15:53:19Z
dc.date.issued2016-09-12
dc.date.submitted2018-06-20
dc.identifier.citation<p>bioRxiv 074823; doi: https://doi.org/10.1101/074823. <a href="https://doi.org/10.1101/074823" target="_blank">Link to preprint on bioRxiv service.</a></p>
dc.identifier.doi10.1101/074823
dc.identifier.urihttp://hdl.handle.net/20.500.14038/29329
dc.description.abstractInteractions between RNA binding protein (RBP) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest - in a 'gene-centered' manner, yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA 'bait' can be tested versus multiple RBP 'preys' in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-length Caenorhabditis elegans 3'UTRs. PRIMA faithfully recapitulates numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmed in vivo. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.
dc.language.isoen_US
dc.relation<p>Now published in <em>Translation</em> doi: <a href="http://dx.doi.org/10.1080/21690731.2017.1295130" target="_blank">10.1080/21690731.2017.1295130</a>.</p>
dc.rightsThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nd/4.0/
dc.subjectmolecular biology
dc.subjectProtein-RNA Interaction Mapping Assay
dc.subjectPRIMA
dc.subjectRNA binding protein
dc.subjectmRNA
dc.subjecttranslation-based assay
dc.subjectyeast cytoplasm
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectFungi
dc.subjectGenetic Phenomena
dc.subjectMolecular Biology
dc.subjectNucleic Acids, Nucleotides, and Nucleosides
dc.titlePRIMA: a gene-centered, RNA-to-protein method for mapping RNA-protein interactions [preprint]
dc.typePreprint
dc.source.journaltitlebioRxiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=2565&amp;context=faculty_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/1555
dc.identifier.contextkey12347261
refterms.dateFOA2022-08-23T15:53:19Z
html.description.abstract<p>Interactions between RNA binding protein (RBP) and mRNAs are critical to post-transcriptional gene regulation. Eukaryotic genomes encode thousands of mRNAs and hundreds of RBPs. However, in contrast to interactions between transcription factors (TFs) and DNA, the interactome between RBPs and RNA has been explored for only a small number of proteins and RNAs. This is largely because the focus has been on using 'protein-centered' (RBP-to-RNA) interaction mapping methods that identify the RNAs with which an individual RBP interacts. While powerful, these methods cannot as of yet be applied to the entire RBPome. Moreover, it may be desirable for a researcher to identify the repertoire of RBPs that can interact with an mRNA of interest - in a 'gene-centered' manner, yet few such techniques are available. Here, we present Protein-RNA Interaction Mapping Assay (PRIMA) with which an RNA 'bait' can be tested versus multiple RBP 'preys' in a single experiment. PRIMA is a translation-based assay that examines interactions in the yeast cytoplasm, the cellular location of mRNA translation. We show that PRIMA can be used with small RNA elements, as well as with full-length <em>Caenorhabditis elegans</em> 3'UTRs. PRIMA faithfully recapitulates numerous well-characterized RNA-RBP interactions and also identified novel interactions, some of which were confirmed <em>in vivo</em>. We envision that PRIMA will provide a complementary tool to expand the depth and scale with which the RNA-RBP interactome can be explored.</p>
dc.identifier.submissionpathfaculty_pubs/1555
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Molecular Medicine
dc.contributor.departmentProgram in Systems Biology


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The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.
Except where otherwise noted, this item's license is described as The copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-ND 4.0 International license.