Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus

Sager J. Gosai1,5, Shawn W. Foley1,2,5, Dongxue Wang3, Ian M. Silverman1,2, Nur Selamoglu1, Andrew D.L. Nelson4, Mark A. Beilstein4, Fevzi Daldal1, Roger B. Deal3, and Brian D. Gregory1,2s

1Department of Biology
2Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA USA
3Department of Biology, Emory University, Atlanta, GA USA
4School of Plant Sciences, University of Arizona, Tucson, AZ USA
5These authors contributed equally to this work.


Abstract

Post-transcriptional regulation in eukaryotes requires cis- and trans-acting features and factors including RNA secondary structure, and RNA-binding proteins (RBPs). However, a comprehensive view of the structural and RBP interaction landscape of RNAs in the nucleus has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP binding site mapping approach on Arabidopsis seedling nuclei in vivo to globally profile these features within the nuclear compartment. We reveal opposing patterns of secondary structure and RBP binding levels throughout native messenger RNAs that demarcate alternative splicing and polyadenylation. We also uncover a collection of protein bound sequence motifs, and identify their structural contexts, co-occurrences in transcripts encoding functionally related proteins, and interactions with putative RBPs. Finally, we identify a nuclear role for the chloroplast RBP, CP29A. In total, we provide the first simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.


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Description: These files contain enriched sequence motifs in protein-protected sites as identfied by MEME and HOMER. Modules of co-occuring sequence motifs identified by hierarchical clustering are also included.

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