1. Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.
- Author
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Mustoe AM, Busan S, Rice GM, Hajdin CE, Peterson BK, Ruda VM, Kubica N, Nutiu R, Baryza JL, and Weeks KM
- Subjects
- 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 Conformation, Protein Biosynthesis, RNA Folding, RNA, Messenger chemistry, Recombinant Proteins biosynthesis, Recombinant Proteins chemistry, Recombinant Proteins isolation & purification, Ribosomes chemistry, Ribosomes metabolism, Untranslated Regions, Nucleic Acid Amplification Techniques methods, RNA, Messenger metabolism
- Abstract
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., (Copyright © 2018 Elsevier Inc. All rights reserved.)
- Published
- 2018
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