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

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Mustoe, Anthony M., Busan, Steven, Rice, Greggory M., Hajdin, Christine E., Peterson, Brant K., Ruda, Vera M., Kubica, Neil, Nutiu, Razvan, Baryza, Jeremy L., Weeks, Kevin M.·2018·Cell

DOI 10.1016/j.cell.2018.02.034

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Abstract

SUMMARY Messenger RNAs (mRNAs) can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited 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 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 untranslated regions, 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.

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mRNA structure regulates protein expression through changes in functional half-life
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See all 258

Authors: Mustoe, A. M., Busan, S., Rice, G. M., Hajdin, C. E., Peterson, B. K., Ruda, V. M., Kubica, N., Nutiu, R., Baryza, J. L., & Weeks, K. M.
Venue: Cell
Publisher: Elsevier BV
Published: 2018-03
Volume: 173
Issue: 1
Pages: 181-195.e18
ISSN: 0092-8674 (ISSN-L)
DOI: 10.1016/j.cell.2018.02.034
OpenAlex: W2793097545
Cited by: 258
References: 115
FWCI: 11.93
Type: journal article
Language: en
Open access: bronze

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

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