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Mol Cell. 2015 Jan 22;57(2):376-88. doi: 10.1016/j.molcel.2014.12.004. Epub 2014 Dec 31.

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

Author information

1
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
2
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
3
Department of Biology, Emory University, Atlanta, GA 30322, USA.
4
School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
5
Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA. Electronic address: bdgregor@sas.upenn.edu.

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 in vivo. 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.

PMID:
25557549
PMCID:
PMC4871124
DOI:
10.1016/j.molcel.2014.12.004
[Indexed for MEDLINE]
Free PMC Article

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