Higher-Order Organization Principles of Pre-translational mRNPs

Mihir Metkar; Hakan Ozadam; Bryan R Lajoie; Maxim Imakaev; Leonid A Mirny; Job Dekker; Melissa J Moore

doi:10.1016/j.molcel.2018.09.012

Higher-Order Organization Principles of Pre-translational mRNPs

Mol Cell. 2018 Nov 15;72(4):715-726.e3. doi: 10.1016/j.molcel.2018.09.012. Epub 2018 Nov 8.

Authors

Mihir Metkar¹, Hakan Ozadam², Bryan R Lajoie², Maxim Imakaev³, Leonid A Mirny³, Job Dekker⁴, Melissa J Moore⁵

Affiliations

¹ RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA.
² Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA.
³ Institute for Medical Engineering and Science and Department of Physics, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
⁴ Program in Systems Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA; Howard Hughes Medical Institute, USA. Electronic address: job.dekker@umassmed.edu.
⁵ RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01655, USA; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA. Electronic address: melissa.moore@umassmed.edu.

Abstract

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.

Keywords: ChimeraTie; RIPPLiT; exon-junction complex; mRNA; mRNP structure; proximity ligation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Cell Nucleus
Exons
HEK293 Cells
Humans
Immunoprecipitation / methods
Protein Processing, Post-Translational
RNA Precursors / genetics
RNA Precursors / ultrastructure*
RNA Splicing
RNA Stability
RNA, Messenger / genetics
RNA, Messenger / ultrastructure
RNA, Untranslated
Ribonucleoproteins / genetics*
Ribonucleoproteins / ultrastructure*
Spliceosomes
Transcription, Genetic

Substances

RNA Precursors
RNA, Messenger
RNA, Untranslated
Ribonucleoproteins
messenger ribonucleoprotein

Abstract

Publication types

MeSH terms

Substances

Grants and funding