Multi-disciplinary methods to define RNA–protein interactions and regulatory networks

Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, United States.
Current opinion in genetics & development (Impact Factor: 7.57). 02/2013; 23(1). DOI: 10.1016/j.gde.2013.01.003
Source: PubMed


The advent of high-throughput technologies including deep-sequencing and protein mass spectrometry is facilitating the acquisition of large and precise data sets toward the definition of post-transcriptional regulatory networks. While early studies that investigated specific RNA-protein interactions in isolation laid the foundation for our understanding of the existence of molecular machines to assemble and process RNAs, there is a more recent appreciation of the importance of individual RNA-protein interactions that contribute to post-transcriptional gene regulation. The multitude of RNA-binding proteins (RBPs) and their many RNA targets has only been captured experimentally in recent times. In this review, we will examine current multidisciplinary approaches toward elucidating RNA-protein networks and their regulation.

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    • "These RNA structures can form motifs, which are frequently bound by an assortment of RNA-binding proteins (RBPs). In eukaryotic organisms, this provides a means to couple transcription with various levels of post-transcriptional gene regulation such as splicing, nuclear export, RNA localization, turnover, and translation (Dreyfuss et al., 2002; Keene, 2007; Dinger et al., 2011; Ascano et al., 2013; Mercer and Mattick, 2013). Researchers now regularly study these interactions by immunoprecipitating RNA-protein complexes (RNPs) and identifying the associated RNA cargo using genomic readouts including microarrays and more recently nextgeneration sequencing. "
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