Systems Approaches to Map In Vivo RNA–Protein Interactions in Arabidopsis thaliana

Lewinski, Martin; Köster, Tino

doi:10.1007/978-3-319-92967-5_5

Cited by 2 publications

(2 citation statements)

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“…The in vitro approach involves the biosynthesis of RNA bait, the binding of the tagged-RNA to resin, the formation of a complex of ribonucleoproteins (RNPs), and the washing, purification, and elution of the RBPs that are bound with the tagged RNA [ 36 , 37 ]. The in vitro method is sensitive to a few challenges: in vitro transcribed RNAs have different structures and modifications from normal RNAs, the association of RBPs with RNA which might not occur due to the lack of posttranslational modifications, and the formation of an anomalous complex such as heterogeneous nuclear ribonucleoproteins (hnRNPs) [ 38 ].…”

Section: Experimental Approaches To Dissect the Rbpomementioning

confidence: 99%

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Ribonomics Approaches to Identify RBPome in Plants and Other Eukaryotes: Current Progress and Future Prospects

Haroon

Afzal

Zafar

et al. 2022

IJMS

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RNA-binding proteins (RBPs) form complex interactions with RNA to regulate the cell’s activities including cell development and disease resistance. RNA-binding proteome (RBPome) aims to profile and characterize the RNAs and proteins that interact with each other to carry out biological functions. Generally, RNA-centric and protein-centric ribonomic approaches have been successfully developed to profile RBPome in different organisms including plants and animals. Further, more and more novel methods that were firstly devised and applied in mammalians have shown great potential to unravel RBPome in plants such as RNA-interactome capture (RIC) and orthogonal organic phase separation (OOPS). Despise the development of various robust and state-of-the-art ribonomics techniques, genome-wide RBP identifications and characterizations in plants are relatively fewer than those in other eukaryotes, indicating that ribonomics techniques have great opportunities in unraveling and characterizing the RNA–protein interactions in plant species. Here, we review all the available approaches for analyzing RBPs in living organisms. Additionally, we summarize the transcriptome-wide approaches to characterize both the coding and non-coding RBPs in plants and the promising use of RBPome for booming agriculture.

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Section: Experimental Approaches To Dissect the Rbpomementioning

confidence: 99%

“…Despite the availability of several RNA-centric approaches, only the RIC RNA-centric approach was employed in Arabidopsis [ 22 , 37 , 49 , 56 , 57 , 58 , 59 , 60 ].…”

Section: Experimental Approaches To Dissect the Rbpomementioning

confidence: 99%