Abstract
RNAs transmit information from DNA to encode proteins that perform all cellular processes and regulate gene expression in multiple ways. From the time of synthesis to degradation, RNA molecules are associated with proteins called RNA-binding proteins (RBPs). The RBPs play diverse roles in many aspects of gene expression including pre-mRNA processing and post-transcriptional and translational regulation. In the last decade, the application of modern techniques to identify RNA–protein interactions with individual proteins, RNAs, and the whole transcriptome has led to the discovery of a hidden landscape of these interactions in plants. Global approaches such as RNA interactome capture (RIC) to identify proteins that bind protein-coding transcripts have led to the identification of close to 2000 putative RBPs in plants. Interestingly, many of these were found to be metabolic enzymes with no known canonical RNA-binding domains. Here, we review the methods used to analyze RNA–protein interactions in plants thus far and highlight the understanding of plant RNA–protein interactions these techniques have provided us. We also review some recent protein-centric, RNA-centric, and global approaches developed with non-plant systems and discuss their potential application to plants. We also provide an overview of results from classical studies of RNA–protein interaction in plants and discuss the significance of the increasingly evident ubiquity of RNA–protein interactions for the study of gene regulation and RNA biology in plants.
Highlights
DNA, the genetic blueprint of all organisms, controls all life processes through intermediate RNA molecules that dictate the types and levels of proteins made in cells
RNA–protein interactions are numerous, widespread, and play diverse biologically important roles in all organisms in many processes associated with gene regulation, including generation of coding and non-coding RNAs, transport, translation, and decay of RNAs, and control of diverse processes associated with development and disease
The proteins that interact with RNAs are collectively referred to as RNA-binding proteins (RBPs), a diverse class of proteins characterized by the presence of one or more RNA binding domains, usually alongside other catalytic or functional domains
Summary
DNA, the genetic blueprint of all organisms, controls all life processes through intermediate RNA molecules that dictate the types and levels of proteins made in cells. In plants, most research done in this field before ~10 years ago relied entirely on the use of indirect or in vitro methods to identify RNA and protein interaction, such as gel shift assay, mutant and knockout screening, nucleic acid-binding assay, and other classical genetics and cell biological techniques [2,11,12,13]. These techniques have contributed significantly to understanding the functions of RBPs in plant biology (see Section 3) but have since been superseded by the development of high throughput and global methods to analyze RNA and protein interactions. With the development of high throughput sequencing technologies, methodologies that used such sequencing platforms became known as RIP-seq [17]
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