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

Sager J. Gosai, Shawn W. Foley, Dongxue Wang, Ian M. Silverman, Nur Selamoglu, Andrew D.L. Nelson, Mark A. Beilstein, Fevzi Daldal, Roger B. Deal, Brian D. Gregory

Research output: Contribution to journalArticlepeer-review

60 Scopus citations

Abstract

Posttranscriptional 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 nuclear RNAs has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP-binding site mapping approaches to globally profile these features in Arabidopsis seedling nuclei invivo. We reveal anticorrelated patterns of secondary structure and RBP binding throughout nuclear mRNAs that demarcate sites of 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, using these motifs, we find that the chloroplast RBP CP29A also interacts with nuclear mRNAs. In total, we provide a simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus.

Original languageEnglish (US)
Pages (from-to)376-388
Number of pages13
JournalMolecular cell
Volume57
Issue number2
DOIs
StatePublished - Jan 22 2015

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology

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