RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs

Gerber, André P.

doi:10.3390/ncrna7010011

Cited by 15 publications

(23 citation statements)

References 90 publications

(131 reference statements)

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“…RNA antisense purification (RAP) is a biochemical method first developed to understand the interaction of lncRNA with its target DNA. This method utilizes biotinylated antisense probes complementary to the target lncRNAs, that hybridizes with the lncRNA to capture the interacting target RNAs and proteins (Gerber, 2021). The biotinylated antisense probe is pulled down along with its interacting RNAs can then be identified using RNA-sequencing and quantitative PCR (Figure 3e).…”

Section: Rna Antisense Purification (Rap)mentioning

confidence: 99%

Detecting RNA–RNA interactome

2022

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The last decade has seen a robust increase in various types of novel RNA molecules and their complexity in gene regulation. RNA molecules play a critical role in cellular events by interacting with other biomolecules, including protein, DNA, and RNA. It has been established that RNA-RNA interactions play a critical role in several biological processes by regulating the biogenesis and function of RNA molecules. Interestingly, RNA-RNA interactions regulate the biogenesis of diverse RNA molecules, including mRNAs, microRNAs, tRNAs, and circRNAs, through splicing or backsplicing. Structured RNAs like rRNA, tRNA, and snRNAs achieve their functional conformation by intramolecular RNA-RNA interactions. In addition, functional consequences of many intermolecular RNA-RNA interactions have been extensively studied in the regulation of gene expression. Hence, it is essential to understand the mechanism and functions of RNA-RNA interactions in eukaryotes. Conventionally, RNA-RNA interactions have been identified through diverse biochemical methods for decades. The advent of high-throughput RNA-sequencing technologies has revolutionized the identification of global RNA-RNA interactome in cells and their importance in RNA structure and function in gene expression regulation. Although these technologies revealed tens of thousands of intramolecular and intermolecular RNA-RNA interactions, we further look forward to future unbiased and quantitative high-throughput technologies for detecting transcriptome-wide RNA-RNA interactions. With the ability to detect RNA-RNA interactome, we expect that future studies will reveal the higher-order structures of RNA molecules and multi-RNA hybrids impacting human health and diseases. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems

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Section: Rna Antisense Purification (Rap)mentioning

confidence: 99%

Detecting RNA–RNA interactome

2022

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“…The efficiency UV-based crosslinking is relatively low (∼5%) and shows some preference for uridine-rich single-stranded RNA regions, possibly adding a bias towards single-stranded RNA-binding proteins. In addition, we wish to note that UV-irradiation can also induce protein-protein and protein-DNA crosslinks - albeit at lower efficiency – but may lead to false positives through indirect interactors ( Gerber, 2021 ). Other types of crosslinking, such as the photoactivatable ribonucleoside-crosslinking (PAR-CL) ( Shchepachev et al., 2019 ) or the formaldehyde-based crosslinking (FA-CL) ( Na et al., 2021 ) may constitute suitable alternatives.…”

Section: Limitationsmentioning

confidence: 99%

Biochemical approach for isolation of polyadenylated RNAs with bound proteins from yeast

Matia-González¹,

Jabre²,

Gerber³

2021

STAR Protocols

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“…As important RNA regulators, RNA-binding proteins have attracted much attention [1][2][3][4]. Strategies for studying RNA protein interaction can be roughly divided into two categories: protein-centric methods and RNA-centric methods [5,6].…”

Section: Introductionmentioning

confidence: 99%

eCRUIS captures RNA-protein interaction in vitro and in vivo

Zhang

Liu

2022

Preprint

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As an information bridge between DNA and protein, RNA regulates cellular processes and gene expression in a variety of ways. From synthesis to degradation, RNA is associated with a series of RNA-binding proteins. Therefore, it is very important to develop innovative methods to study the interaction between RNA and protein. Previously, we developed an RNA-centric method, called CRISPR-based RNA-United Interacting System (CRUIS), to capture RNA-protein interaction in cells. On this basis, here we develop an enhanced CRUIS (eCRUIS) by combining the power of dCas13d and the engineered promiscuous ligase TurboID. The new version allows us to label RNA-binding proteins on the target RNA within 30 minutes, which may be used in vivo. By introducing bait-assay with exogenous RNA, we confirm that eCRUIS can effectively label RNA-binding proteins on bait RNA in a short time. eCRUIS provides a wider range of in vitro and in vivo applications.

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RNA-Centric Approaches to Profile the RNA–Protein Interaction Landscape on Selected RNAs

Cited by 15 publications

References 90 publications

Detecting RNA–RNA interactome

Detecting RNA–RNA interactome

Biochemical approach for isolation of polyadenylated RNAs with bound proteins from yeast

eCRUIS captures RNA-protein interaction in vitro and in vivo

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