Abstract
Ribonucleic acids (RNA) are associated with a multitude of RNA-binding proteins that regulate RNA. To identify in vivo targets of the RNA-binding protein AtGRP7, researchers from the University of Bielefeld have established individual nucleotide resolution crosslinking and immunoprecipitation (iCLIP) in plants. The use of high-affinity Nanobodies, i. e., the GFP-Trap®, enabled the purification of RNA-protein complexes from complex plant cell extracts and their subsequent analysis. They identified 858 AtGRP7 RNA targets and binding sites and showed that AtGRP7 modulates the circadian expression of its targets.
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Literatur
Reichel M, Liao Y, Rettel M et al. (2016) In Planta Determination of the mRNA-Binding Proteome of Arabidopsis Etiolated Seedlings. Plant Cell 28: 2435–2452
Köster T, Marondedze C, Meyer K, Staiger D (2017) RNA-Binding Proteins Revisited — The Emerging Arabidopsis mRNA Interactome. Trends Plant Sci 22: 512–526
Köster T, Meyer K (2018) Plant Ribonomics: Proteins in Search of RNA Partners. Trends Plant Sci 23: 325–365
Lewinski M, Köster T (2018) Systems Approaches to Map In Vivo RNA-Protein Interactions in Arabidopsis thaliana. In: Rajewsky N, Jurga S, Barciszewski J (Hrsg.) Systems Biology. Springer International Publishing, Cham, 77–95
König J, Zarnack K, Rot G et al. (2010) iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol 17: 909–915
Hafner M, Katsantoni M, Köster T et al. (2021) CLIP and complementary methods. Nat Rev Methods Primers 1: 20
Meyer K, Köster T, Nolte C et al. (2017) Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7. Genome Biol 18: 204
Köster T, Reichel M, Staiger D (2020) CLIP and RNA interactome studies to unravel genome-wide RNA-protein interactions in vivo in Arabidopsis thaliana. Methods 178: 63–71
Muyldermans S (2013) Nanobodies: Natural Single-Domain Antibodies. Ann Rev Biochem 82: 775–797
Heintzen C, Nater M, Apel K, Staiger D (1997) AtGRP7, a nuclear RNA-binding protein as a component of a circadian-regulated negative feedback loop in Arabidopsis thaliana. Proc Nat Acad Sci 94: 8515–8520
Schöning JC, Streitner C, Meyer IM et al. (2008) Reciprocal regulation of glycine-rich RNA-binding proteins via an interlocked feedback loop coupling alternative splicing to nonsense-mediated decay in Arabidopsis. Nucleic Acids Res 36: 6977–6987
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Köster, T., Sitte, A. Plant iCLIP — auf Spurensuche im Transkriptom der Pflanze. Biospektrum 29, 174–176 (2023). https://doi.org/10.1007/s12268-023-1871-5
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DOI: https://doi.org/10.1007/s12268-023-1871-5