RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing - PubMed (original) (raw)

Review

RNA Regulations and Functions Decoded by Transcriptome-wide RNA Structure Probing

Meiling Piao et al. Genomics Proteomics Bioinformatics. 2017 Oct.

Abstract

RNA folds into intricate structures that are crucial for its functions and regulations. To date, a multitude of approaches for probing structures of the whole transcriptome, i.e., RNA structuromes, have been developed. Applications of these approaches to different cell lines and tissues have generated a rich resource for the study of RNA structure-function relationships at a systems biology level. In this review, we first introduce the designs of these methods and their applications to study different RNA structuromes. We emphasize their technological differences especially their unique advantages and caveats. We then summarize the structural insights in RNA functions and regulations obtained from the studies of RNA structuromes. And finally, we propose potential directions for future improvements and studies.

Keywords: RNA regulation; RNA secondary structure; RNA structure probing; RNA structurome; Structure–function relationship.

Copyright © 2017 The Author. Production and hosting by Elsevier B.V. All rights reserved.

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Figures

Figure 1

Figure 1

Experimental workflow of some representative high-throughput approaches for RNA structure probing PARS, parallel analysis of RNA structures; FragSeq, fragmentation sequencing; SHAPE, selective 2′ hydroxyl acylation analyzed by primer extension; icSHAPE, in vivo click SHAPE; SHAPE-MaP, SHAPE and mutational profiling; DMS-MaPseq, dimethyl sulfate mutational profiling with sequencing; LIGR-seq, ligation of interacting RNA and high-throughput sequencing; PARIS, psoralen Analysis of RNA interactions and structures; SPLASH, sequencing of psoralen crosslinked, ligated, and selected hybrids; DMS, dimethyl sulfide; NAI-N3, 2-methylnicotinic acid imidazolide-azide; AMT, 4′-aminomethyl trioxsalen.

Figure 2

Figure 2

Structural landscapes of RNA splicing and translation Structural landscapes of RNA splicing and translation are shown in panels A and B, respectively. Note that difference structural score metrics are used in different technologies. For PARS and structure scores, the higher score means the more secondary structures, while for DMS reactivity, the higher the score means the fewer secondary structures. The figure is adapted from , , , . PARS: parallel analysis of RNA structures; DMS: dimethyl sulfide.

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