In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Ding, Yiliang; Tang, Yin; Kwok, Chun Kit; Zhang, Yu; Bevilacqua, Philip C.; Assmann, Sarah M.

doi:10.1038/nature12756

Cited by 775RNA and protein synthesis mechanismsRNA Research and SplicingRNA regulation and disease

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Ding, Yiliang, Tang, Yin, Kwok, Chun Kit, Zhang, Yu, Bevilacqua, Philip C., Assmann, Sarah M.·2014·Nature

DOI 10.1038/nature12756

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Abstract

RNA structure has critical roles in processes ranging from ligand sensing to the regulation of translation, polyadenylation and splicing. However, a lack of genome-wide in vivo RNA structural data has limited our understanding of how RNA structure regulates gene expression in living cells. Here we present a high-throughput, genome-wide in vivo RNA structure probing method, structure-seq, in which dimethyl sulphate methylation of unprotected adenines and cytosines is identified by next-generation sequencing. Application of this method to Arabidopsis thaliana seedlings yielded the first in vivo genome-wide RNA structure map at nucleotide resolution for any organism, with quantitative structural information across more than 10,000 transcripts. Our analysis reveals a three-nucleotide periodic repeat pattern in the structure of coding regions, as well as a less-structured region immediately upstream of the start codon, and shows that these features are strongly correlated with translation efficiency. We also find patterns of strong and weak secondary structure at sites of alternative polyadenylation, as well as strong secondary structure at 5' splice sites that correlates with unspliced events. Notably, in vivo structures of messenger RNAs annotated for stress responses are poorly predicted in silico, whereas mRNA structures of genes related to cell function maintenance are well predicted. Global comparison of several structural features between these two categories shows that the mRNAs associated with stress responses tend to have more single-strandedness, longer maximal loop length and higher free energy per nucleotide, features that may allow these RNAs to undergo conformational changes in response to environmental conditions. Structure-seq allows the RNA structurome and its biological roles to be interrogated on a genome-wide scale and should be applicable to any organism.

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Some studies have shown that protein expression level drops if the 5′-end leader region has more secondary structure.
“Some studies have shown that protein expression level drops if the 5′-end leader region has more secondary structure5,50–53.”
From Algorithm for optimized mRNA design improves stability and immunogenicity (2023) · cites this paper as [50]
Highly structured 5' UTRs, such as dengue virus (DEN2), can support efficient translation, contrary to previous reports.
“Most surprising, in contrast to previous reports47–49, we found 5’ UTRs that are highly structured, such as the dengue virus (DEN2), can support efficient translation.”
From Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics (2022) · cites this paper as [48]

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Authors: Ding, Y., Tang, Y., Kwok, C. K., Zhang, Y., Bevilacqua, P. C., & Assmann, S. M.
Affiliations: Pennsylvania State University (US)
Corresponding author: Bevilacqua, Philip C.
Assmann, Sarah M.
ORCID: Ding, Yiliang
Tang, Yin
Kwok, Chun Kit
Zhang, Yu
Bevilacqua, Philip C.
Assmann, Sarah M.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2013-11-24
Volume: 505
Issue: 7485
Pages: 696-700
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature12756
OpenAlex: W2076091642
Cited by: 775
References: 37
Citations by year: 2026: 24 · 2025: 38 · 2024: 35 · 2023: 69 · 2022: 55 · 2021: 49 · 2020: 84 · 2019: 63 · 2018: 86 · 2017: 67 · 2016: 75 · 2015: 76 · 2014: 53 · 2013: 1
FWCI: 30.73
Type: journal article
Language: en
Open access: closed
Licence: www.springernature.com/gp/researchers/text-and-data-mining (tdm)
www.springernature.com/gp/researchers/text-and-data-mining (vor)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: National Science Foundation
Pennsylvania State University
Huck Institutes of the Life Sciences
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA regulation and disease
Keywords: RNA secondary structure, Arabidopsis thaliana, yeast, mammalian cells, single nucleotide variants, polyadenylation, splicing, stress response, translational regulation
MeSH terms: Base Sequence, Molecular Sequence Data, Nucleic Acid Conformation, Phylogeny, RNA, Messenger, RNA, Ribosomal, 18S, Stress, Physiological, Structure-Activity Relationship, Protein Biosynthesis, Arabidopsis, Sequence Analysis, RNA, Codon, Initiator, Genome, Plant, RNA, Plant, Computational Biology, RNA Splice Sites, Polyadenylation, Regulatory Sequences, Ribonucleic Acid

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In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

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