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Insights into RNA structure and function from genome-wide studies

Key Points

  • There has been a plethora of experimental approaches that combine traditional chemical probing techniques with next-generation sequencing. These methods have allowed the first glimpse of the 'RNA structurome'.

  • These studies have highlighted, on a genome-wide scale, how RNA structure controls functions and gene expression. It is now possible to identify structural motifs that affect both coding and non-coding RNA function.

  • Each step of protein translation is affected by RNA structure. Generally, the RNA surrounding the start and stops codons is poorly structured to allow ribosome regulation, and the coding region contains structured elements that can regulate protein expression.

  • Small-RNA-binding sites that regulate mRNA expression can be identified through degradome and immunoprecipitation studies to help to predict new small RNAs and their targets.

  • Recent in vivo studies indicate that RNA is less structured, or at least more structurally dynamic, in vivo than in vitro.

  • The future of this research field is likely to explore the structure of low-abundance RNAs, such as long non-coding RNAs, and tertiary RNA structure.

Abstract

A comprehensive understanding of RNA structure will provide fundamental insights into the cellular function of both coding and non-coding RNAs. Although many RNA structures have been analysed by traditional biophysical and biochemical methods, the low-throughput nature of these approaches has prevented investigation of the vast majority of cellular transcripts. Triggered by advances in sequencing technology, genome-wide approaches for probing the transcriptome are beginning to reveal how RNA structure affects each step of protein expression and RNA stability. In this Review, we discuss the emerging relationships between RNA structure and the regulation of gene expression.

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Figure 1: Structural motifs within the transcriptome.
Figure 2: Structure around start codons and translational efficiency.
Figure 3: RNA structure and stability under heat shock.
Figure 4: mRNA structure involved in the regulation of translation by small RNAs.

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Acknowledgements

The authors apologize to colleagues whose work was not cited owing to space limitation. They thank Y. Bai, R. Wilson, S. Floor, M. Hammond and members of J.A.D.'s laboratory for discussions; K. Weeks for sharing HIV-1 SHAPE data; and J. Ji for reading the manuscript. This work was supported in part by a grant from the US National Institutes of Health (to J.A.D.). J.A.D. is a Howard Hughes Medical Institute Investigator.

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Correspondence to Jennifer A. Doudna.

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Glossary

Secondary structures

Two-dimensional non-covalent interactions within an RNA molecule that consist of contiguous base pairs and loops. RNA molecules contain both canonical Watson–Crick base pairs and many non-canonical base pairs.

Tertiary structures

Non-covalent interactions of separate secondary structures within an RNA molecule. These interactions occur between the bases and 2′OH ribose to create precise three- dimensional structures.

Next-generation sequencing

(NGS). A high-throughput technology that simultaneously sequences millions of different DNA molecules by non-Sanger sequencing methods (most commonly sequencing by synthesis).

RNA structurome

The collective group of secondary and tertiary structures formed within the transcriptome of a given organism.

Shine–Dalgarno sequences

Ribosome-binding sites in bacterial mRNA. They are generally located eight bases upstream of the AUG start codon and contain the six-base consensus sequence AGGAGG.

Folding energies

The Gibbs free energies associated with particular RNA folds or structures.

Ribosome profiling

Qualitative and quantitative sequencing of the RNAs attached to ribosomes as a signature of RNAs that are being translated.

Signal peptide

A short peptide of 5–30 amino acids at the amino terminus of newly synthesized proteins in the secretory pathway.

RiboSNitches

Single-nucleotide variants that alter RNA structure and that potentially affect gene regulation.

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Mortimer, S., Kidwell, M. & Doudna, J. Insights into RNA structure and function from genome-wide studies. Nat Rev Genet 15, 469–479 (2014). https://doi.org/10.1038/nrg3681

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