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Author Notes:

Correspondence: bdgregor@sas.upenn.edu.

Authors' contributions are listed in the full article.

The authors thank Dr. Christian Schmitz-Linneweber for providing the α-CP29A antibody, Alsu Ibragimova for optimizing the RNA-affinity chromatography, Jennifer Nemhauser for providing the UBQ10p:NTF/ACT2p:BirA transgenic line, and members of the B.D.G. lab for helpful discussions.

The raw and processed data for PIP-seq and total RNA sequencing from our analyses have been deposited into the NCBI Gene Expression Omnibus (GEO) database under the accession number GSE58974.


Research Funding:

This work was funded by NSF grant MCB-1243947 to B.D.G. and NIGMS 5T32GM008216-26 to I.M.S.


  • Arabidopsis
  • Arabidopsis Proteins
  • Base Sequence
  • Binding Sites
  • Cell Nucleus
  • Chloroplast Proteins
  • Consensus Sequence
  • Gene Expression Regulation, Plant
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Transport
  • RNA Interference
  • RNA, Messenger
  • RNA, Plant
  • Ribonucleoproteins
  • Seedlings
  • Transcriptome

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

Journal Title:

Molecular Cell


Volume 57, Number 2


, Pages 376-388

Type of Work:

Article | Post-print: After Peer Review


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.

Copyright information:

© 2015 Elsevier Inc.

This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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