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Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing.
- Source :
-
Cell [Cell] 2018 Mar 22; Vol. 173 (1), pp. 181-195.e18. Date of Electronic Publication: 2018 Mar 15. - Publication Year :
- 2018
-
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.<br /> (Copyright © 2018 Elsevier Inc. All rights reserved.)
- 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
Subjects
Details
- Language :
- English
- ISSN :
- 1097-4172
- Volume :
- 173
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Cell
- Publication Type :
- Academic Journal
- Accession number :
- 29551268
- Full Text :
- https://doi.org/10.1016/j.cell.2018.02.034