SFB 1551 Seminar Series Event – Prof. Dr. Dorothee Staiger

Partners in time – the RNA interactome of plant RNA-binding proteins

RNA-based regulation plays a key role in plant responses to endogenous cues and environmental stimuli. To provide insights into in vivo RNA-protein interactions shaping the transcriptome, we improved our previous protocol for individual nucleotide resolution crosslinking and immunoprecipitation and, in collaboration with Kathi Zarnack, established a bioinformatics pipeline to evaluate iCLIP-seq data (plant iCLIP2). We comprehensively profiled the binding landscape of Arabidopsis thaliana glycine-rich RNA binding protein 7 implicated in different steps of RNA processing and function. In the compendium of target transcripts, we delineated motifs preferentially associated with binding sites. Orthogonal transcriptomic data obtained from loss-of function mutants and plants overexpressing the RNA binding proteins provided insights into the mode of action how AtGRP7 affects its target transcripts. In particular, in collaboration with Martin Crespi we pursue the idea that long noncoding RNAs interacting with AtGRP7 and the splicing regulator NSRa serve as regulators of alternative splicing. In turn, we developed single mRNA interactome capture and identified ALBA4, a protein interacting with m⁶A readers, as an AtGRP7 interactor. Collectively, our data begin to shed light on the organisation of networks in posttranscriptional regulation in Arabidopsis.