Journal
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 67
Volume 67, Issue -, Pages 463-488Publisher
ANNUAL REVIEWS
DOI: 10.1146/annurev-arplant-043015-111754
Keywords
RNA secondary structure; RNA-binding proteins; posttranscriptional regulation; high-throughput sequencing; microRNAs; small interfering RNAs
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Funding
- Direct For Biological Sciences
- Div Of Biological Infrastructure [1444490] Funding Source: National Science Foundation
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1053846, 1243947] Funding Source: National Science Foundation
- NIGMS NIH HHS [T32 GM008216, T32 GM007229] Funding Source: Medline
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RNA transcripts fold into secondary structures via intricate patterns of base pairing. These secondary structures impart catalytic, ligand binding, and scaffolding functions to a wide array of RNAs, forming a critical node of biological regulation. Among their many functions, RNA structural elements modulate epigenetic marks, alter mRNA stability and translation, regulate alternative splicing, transduce signals, and scaffold large macromolecular complexes. Thus, the study of RNA secondary structure is critical to understanding the function and regulation of RNA transcripts. Here, we review the origins, form, and function of RNA secondary structure, focusing on plants. We then provide an overview of methods for probing secondary structure, from physical methods such as X-ray crystallography and nuclear magnetic resonance(NMR) imaging to chemical and nuclease probing methods. Combining these latter methods with high-throughput sequencing has enabled them to scale across whole transcriptomes, yielding tremendous new insights into the form and function of RNA secondary structure.
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