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 journalArticle

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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

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RNA-Binding Proteins
Arabidopsis
RNA
Proteins
Protein Binding
Chloroplast RNA
Chloroplast Proteins
Nuclear RNA
Messenger RNA
Polyadenylation
Trans-Activators
Alternative Splicing
Ribonucleases
Eukaryota
Seedlings
Binding Sites

ASJC Scopus subject areas

  • Molecular Biology
  • Cell Biology
  • Medicine(all)

Cite this

Gosai, S. J., Foley, S. W., Wang, D., Silverman, I. M., Selamoglu, N., Nelson, A. D. L., ... Gregory, B. D. (2015). Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the arabidopsis nucleus. Molecular Cell, 57(2), 376-388. https://doi.org/10.1016/j.molcel.2014.12.004

Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the arabidopsis nucleus. / Gosai, Sager J.; Foley, Shawn W.; Wang, Dongxue; Silverman, Ian M.; Selamoglu, Nur; Nelson, Andrew D L; Beilstein, Mark A; Daldal, Fevzi; Deal, Roger B.; Gregory, Brian D.

In: Molecular Cell, Vol. 57, No. 2, 22.01.2015, p. 376-388.

Research output: Contribution to journalArticle

Gosai, SJ, Foley, SW, Wang, D, Silverman, IM, Selamoglu, N, Nelson, ADL, Beilstein, MA, Daldal, F, Deal, RB & Gregory, BD 2015, 'Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the arabidopsis nucleus', Molecular Cell, vol. 57, no. 2, pp. 376-388. https://doi.org/10.1016/j.molcel.2014.12.004
Gosai, Sager J. ; Foley, Shawn W. ; Wang, Dongxue ; Silverman, Ian M. ; Selamoglu, Nur ; Nelson, Andrew D L ; Beilstein, Mark A ; Daldal, Fevzi ; Deal, Roger B. ; Gregory, Brian D. / Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the arabidopsis nucleus. In: Molecular Cell. 2015 ; Vol. 57, No. 2. pp. 376-388.
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