Trends in Biochemical Sciences
ReviewGlobal Approaches in Studying RNA-Binding Protein Interaction Networks
Section snippets
From RNA-Binding Protein (RBP) Basics to RBP Networks
RBPs orchestrate most essential cellular processes. Some RBP–RNA interactions form stable ribonucleoprotein (RNP) (see Glossary) particles with defined roles, while other RBPs (and RNPs) interact transiently to process, regulate the function, and control the fate of virtually all RNAs in the cell. Importantly, RBPs are the key players in post-transcriptional regulation of both mRNAs and noncoding RNAs, encompassing RNA splicing, transport, modification, stability, and translation [1,2]. Many of
Approaches to Study Individual RBP Function
To illuminate the molecular mechanisms that underpin the cellular roles of RBPs, researchers have been systematically addressing several key questions about the binding and impact of individual RBPs and their interplay with the RNA landscape. For example, determining RBP effects on mRNA stability and splicing patterns is informative to their molecular modes of action. These measurements have typically involved knockdown/knockout/overexpression of an RBP of interest followed by RNA-sequencing
Tackling RBP–RBP Interactions
Finally, while the focus of most studies to date has been on the functional roles of individual RBPs, it is recognized that higher-order interactions between RBPs on specific mRNAs are common and these interactions mediate pervasive and complex regulatory outcomes. Throughout their lifecycles, mRNAs are continuously associated with large and dynamically changing sets of RBPs [2,47,48]. In addition, recent studies hint that RBPs form large regulatory networks that act to coordinate complex
Interaction Types and Mechanisms Gathered from Studies on Specific mRNAs
Examination of interactions between particular RBPs and/or miRNAs on specific mRNAs (typically using reporter assays, site-directed mutagenesis, manipulation of RBP levels, and co-IP) have delineated some of the mechanisms of such coregulatory events and their effects on expression outcomes, as detailed in recent reviews [54., 55., 56.]. The interactions can be cooperative, where the binding of one RBP leads to increased binding and/or activity of its partner RBP (for recent examples, see [57.,
Transcriptome-Wide Integrative Approaches to Detect and Characterize Interactions between RBPs
In recent years, global approaches have provided novel insights into the scope and complexity of combinatorial post-transcriptional regulation. These studies utilize various mixtures of computational and experimental methods, such as RNA-seq, RIP-chip/seq, CLIP-seq, and bioinformatics based on RBP-binding motifs, as described later (illustrated in Figure 3).
Meta-Analyses Support Higher-Order RBP Interaction Networks
Using the complex and potentially combinatorial RBP regulation on individual transcripts as a building block, RBPs establish broad regulatory networks with emerging principles of autoregulation, hierarchy, and functional coordination (Figure 4). Evidence for such interaction networks has been uncovered in large meta-analyses, where many global datasets characterizing RBP binding (typically from CLIP-seq experiments), RBP localization (by immunofluorescence), transcript abundance (from RNA-seq
Concluding Remarks
The RNA landscape is a crowded environment, making combinatorial interactions between RBPs and RNAs common. The overall regulatory interactions between RBPs and RNA span a spectrum of mechanisms and it is important to stress that RNAs and RBPs can simultaneously participate in several kinds of interactions and their combination dictates the full cellular response. On one side of the spectrum are the stronger, more binary interactions between RBPs and RNAs, which drive the binding at specific
Acknowledgments
The authors would like to thank members of the Karginov laboratory for stimulating discussion, as well as Dr Dorothee Dormann and Dr Saskia Hutten for comments on the manuscript.
Glossary
- Alternative splicing (AS)
- the process of producing different mature (spliced) transcript variants from the same pre-mRNA, mediated by RBPs that affect splice site selection.
- AU-rich elements (AREs)
- a type of RBP-binding motif, often found within the 3′ UTR; defined as a region with frequent adenine and uridine bases.
- m6A
- (N6-methyladenosine); methylation of the adenosine base at the nitrogen-6 position; an abundant internal modification in mRNA that affects its fate in several aspects.
- Membrane-less
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2023, Biochimica et Biophysica Acta - Gene Regulatory MechanismsInsights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases
2023, Biochimica et Biophysica Acta - Gene Regulatory MechanismsCitation Excerpt :This processing includes not only post-transcriptional modifications like splicing and polyadenylation, but also translocation, degradation, and translation. The interaction of pre-mRNA with RBPs could be complicated as one RNA can interact with multiple RBPs, and one RBP can have up to thousands of target RNAs [1,2]. RBPs can interact with various types of RNA, including mRNA, ncRNA, tRNA, snRNA, snoRNA, miRNA, and other proteins to form ribonucleoprotein (RNP) complexes [3].
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2022, Translational OncologyCitation Excerpt :These complex layers of bi-directional regulation associated with AGO-RBPs often make it impossible to neatly classify their involvement in the control of gene expression into oncogenic or tumor-suppressive. Despite the challenges surrounding the context dependent function of miRNA-AGO and RBPs, studies over the last few years measuring RNA-RNA and RNA-protein interactions, as well as mRNA secondary structures, enabled us to connect networks of post-transcriptional regulation involving miRNAs, RBPs and decipher their relevance for cancer initiation and progression [9,10,122] (Figs. 1–2). And yet, the data generated so far is mostly from cell lines such as HEK or HeLa, of which may not reflect the real time scenarios that occur during the stages of malignant transformation in vivo.
Methods to study post-transcriptional regulation of gene expression
2022, Post-transcriptional Gene Regulation in Human Disease: Volume 32Depletion of HNRNPA1 induces peroxisomal autophagy by regulating PEX1 expression
2021, Biochemical and Biophysical Research CommunicationsCitation Excerpt :Gene expression is regulated at the level of transcription and translation and post-transcriptional regulation of gene expression underlies many aspects of cell physiology. As a major group of post-transcriptional regulators, RNA-binding proteins (RBPs) regulate mRNA stability, splicing and transport of RNA, storage and translation of transcripts [12,13]. In the present study, we found that heterogeneous nuclear ribonucleoprotein A1 (HNRNPA1) is involved in the control of peroxisome degradation by regulating PEX1 mRNA.