Higher-Order Organization Principles of Pre-translational mRNPs

UMMS Affiliation

RNA Therapeutics Institute; Program in Systems Biology; Department of Biochemistry and Molecular Pharmacology; Graduate School of Biomedical Sciences

Publication Date


Document Type



Amino Acids, Peptides, and Proteins | Bioinformatics | Cell Biology | Cells | Computational Biology | Enzymes and Coenzymes | Molecular Biology | Nucleic Acids, Nucleotides, and Nucleosides | Structural Biology | Systems Biology


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 mRNA particles (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 ncRNPs, wherein strong locus-specific structures predominate, mRNPs behave more like flexible polymers. Polymer analysis of proximity ligation data for hundreds of mRNA species demonstrates that nascent and pre-translational mammalian mRNAs are compacted by their associated proteins into linear rod-like structures.

DOI of Published Version



Mol Cell. 2018 Nov 15;72(4):715-726.e3. doi: 10.1016/j.molcel.2018.09.012. Epub 2018 Nov 8. Link to article on publisher's site

Journal/Book/Conference Title

Molecular cell

Related Resources

Link to Article in PubMed

PubMed ID