The Conservation and Function of RNA Secondary Structure in Plants
- PMID: 26865341
- PMCID: PMC5125251
- DOI: 10.1146/annurev-arplant-043015-111754
The Conservation and Function of RNA Secondary Structure in Plants
Abstract
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.
Keywords: RNA secondary structure; RNA-binding proteins; high-throughput sequencing; microRNAs; posttranscriptional regulation; small interfering RNAs.
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References
-
- Andersen J, Delihas N, Hanas JS, Wu CW. 5s rna structure and interaction with transcription factor a. 1. ribonuclease probe of the structure of 5s rna from xenopus laevis oocytes. Biochemistry (Mosc.) 1984;23(24):5752–5759. - PubMed
-
- Ares M, Igel AH. Lethal and temperature-sensitive mutations their suppressors identify an essential structural element in u2 small nuclear rna. Genes Dev. 1990;4(12A):2132–2145. - PubMed
-
- Backe PH, Messias AC, Ravelli RBG, Sattler M, Cusack S. X-ray crystallographic and nmr studies of the third kh domain of hnrnp k in complex with single-stranded nucleic acids. Structure. 2005;13(7):1055–1067. - PubMed
-
- Bai Y, Dai X, Harrison AP, Chen M. Rna regulatory networks in animals and plants: a long noncoding rna perspective. Brief. Funct. Genomics. 2015;14(2):91–101. - PubMed
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