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dc.contributor.authorMetkar, Mihir
dc.contributor.authorOzadam, Hakan
dc.contributor.authorLajoie, Bryan R.
dc.contributor.authorImakaev, Maxim
dc.contributor.authorMirny, Leonid A.
dc.contributor.authorDekker, Job
dc.contributor.authorMoore, Melissa J.
dc.date2022-08-11T08:08:23.000
dc.date.accessioned2022-08-23T15:53:01Z
dc.date.available2022-08-23T15:53:01Z
dc.date.issued2018-03-08
dc.date.submitted2018-06-04
dc.identifier.citation<p>bioRxiv 278747; doi: https://doi.org/10.1101/278747. <a href="https://doi.org/10.1101/278747" target="_blank">Link to preprint on bioRxiv service.</a></p>
dc.identifier.doi10.1101/278747
dc.identifier.urihttp://hdl.handle.net/20.500.14038/29266
dc.description.abstractCompared to noncoding RNAs (ncRNAs) such as rRNAs and ribozymes, for which high resolution structures abound, little is known about the tertiary structures of mRNAs. In eukaryotic cells, newly made mRNAs are packaged with proteins in highly compacted mRNPs, but the manner of this mRNA compaction is unknown. Here we developed and implemented RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), a transcriptome-wide method for probing the 3D conformations of RNAs stably-associated with defined proteins, in this case exon junction complex (EJC) core factors. EJCs multimerize with other mRNP components to form megadalton sized complexes that protect large swaths of newly synthesized mRNAs from endonuclease digestion. Unlike ncRNAs, mRNAs behave more like flexible polymers without strong locus-specific interactions. Polymer analysis of proximity ligation data for hundreds of mRNA species demonstrates that pre-translational mammalian mRNPs fold as linear rod-like structures with no strong propensity for 5' and 3' end interaction.
dc.language.isoen_US
dc.relationNow published in Molecular Cell doi: 10.1016/j.molcel.2018.09.012
dc.rightsThe copyright holder for this preprint (which was not peer-reviewed) is the author/funder. It is made available under a CC-BY-NC-ND 4.0 International license.
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/4.0/
dc.subjectmessenger ribonucleoprotein
dc.subjectmRNA
dc.subjectRNA ImmunoPrecipitation and Proximity Ligation in Tandem
dc.subjectprotein
dc.subjectexon junction complex core factors
dc.subjectmolecular biology
dc.subjectAmino Acids, Peptides, and Proteins
dc.subjectMolecular Biology
dc.subjectNucleic Acids, Nucleotides, and Nucleosides
dc.subjectStructural Biology
dc.titleHigher-Order Organization Principles of Pre-translational mRNPs [preprint]
dc.typePreprint
dc.source.journaltitlebioRxiv
dc.identifier.legacyfulltexthttps://escholarship.umassmed.edu/cgi/viewcontent.cgi?article=2500&amp;context=faculty_pubs&amp;unstamped=1
dc.identifier.legacycoverpagehttps://escholarship.umassmed.edu/faculty_pubs/1497
dc.identifier.contextkey12245850
refterms.dateFOA2022-08-23T15:53:01Z
html.description.abstract<p>Compared to noncoding RNAs (ncRNAs) such as rRNAs and ribozymes, for which high resolution structures abound, little is known about the tertiary structures of mRNAs. In eukaryotic cells, newly made mRNAs are packaged with proteins in highly compacted mRNPs, but the manner of this mRNA compaction is unknown. Here we developed and implemented RIPPLiT (RNA ImmunoPrecipitation and Proximity Ligation in Tandem), a transcriptome-wide method for probing the 3D conformations of RNAs stably-associated with defined proteins, in this case exon junction complex (EJC) core factors. EJCs multimerize with other mRNP components to form megadalton sized complexes that protect large swaths of newly synthesized mRNAs from endonuclease digestion. Unlike ncRNAs, mRNAs behave more like flexible polymers without strong locus-specific interactions. Polymer analysis of proximity ligation data for hundreds of mRNA species demonstrates that pre-translational mammalian mRNPs fold as linear rod-like structures with no strong propensity for 5' and 3' end interaction.</p>
dc.identifier.submissionpathfaculty_pubs/1497
dc.contributor.departmentDepartment of Biochemistry and Molecular Pharmacology
dc.contributor.departmentProgram in Systems Biology
dc.contributor.departmentRNA Therapeutics Institute


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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-NC-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-NC-ND 4.0 International license.