Vandivier Lee E, Anderson Stephen J, Foley Shawn W, Gregory Brian D
Department of Biology, School of Arts and Sciences, and.
Cell and Molecular Biology Graduate Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104; email:
Annu Rev Plant Biol. 2016 Apr 29;67:463-88. doi: 10.1146/annurev-arplant-043015-111754. Epub 2016 Feb 8.
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.
RNA转录本通过复杂的碱基配对模式折叠成二级结构。这些二级结构赋予了各种各样的RNA催化、配体结合和支架功能，形成了生物调控的关键节点。在其众多功能中，RNA结构元件可调节表观遗传标记、改变mRNA稳定性和翻译、调控可变剪接、转导信号以及搭建大型大分子复合物。因此，研究RNA二级结构对于理解RNA转录本的功能和调控至关重要。在这里，我们综述了RNA二级结构的起源、形式和功能，重点关注植物。然后，我们概述了探测二级结构的方法，从诸如X射线晶体学和核磁共振（NMR）成像等物理方法到化学和核酸酶探测方法。将这些后者的方法与高通量测序相结合，使它们能够扩展到整个转录组，从而对RNA二级结构的形式和功能产生了巨大的新见解。
