Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing

Cell. 2018 Mar 22;173(1):181-195.e18. doi: 10.1016/j.cell.2018.02.034. Epub 2018 Mar 15.


mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells. Nevertheless, mRNA structure remains similar between in-cell and cell-free environments, indicating broad potential for structure-mediated gene regulation. We find that the translation efficiency of endogenous genes is regulated by unfolding kinetics of structures overlapping the ribosome binding site. We discover conserved structured elements in 35% of UTRs, several of which we validate as novel protein binding motifs. RNA structure regulates every gene studied here in a meaningful way, implying that most functional structures remain to be discovered.

Keywords: RNA binding proteins; RNA structure; non-coding RNA; ribosomal proteins; translation efficiency; translation regulation; translational coupling.

Publication types

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

MeSH terms

  • Algorithms
  • Binding Sites
  • Cell-Free System
  • DNA Primers / metabolism
  • Electrophoretic Mobility Shift Assay
  • Entropy
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / chemistry
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Nucleic Acid Amplification Techniques / methods*
  • Nucleic Acid Conformation
  • Protein Biosynthesis
  • RNA Folding
  • RNA, Messenger / chemistry
  • RNA, Messenger / metabolism*
  • Recombinant Proteins / biosynthesis
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / isolation & purification
  • Ribosomes / chemistry
  • Ribosomes / metabolism
  • Untranslated Regions


  • DNA Primers
  • Escherichia coli Proteins
  • RNA, Messenger
  • Recombinant Proteins
  • Untranslated Regions