title: Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus.
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.
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Sager J
authors.initials: SJ
authors.lastname: Gosai
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Shawn W
authors.initials: SW
authors.lastname: Foley
authors.affiliation: Department of Biology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Dongxue
authors.initials: D
authors.lastname: Wang
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA; Cell and Molecular Biology Graduate Group, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Ian M
authors.initials: IM
authors.lastname: Silverman
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Nur
authors.initials: N
authors.lastname: Selamoglu
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Andrew D L
authors.initials: AD
authors.lastname: Nelson
authors.affiliation: School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
authors.forename: Mark A
authors.initials: MA
authors.lastname: Beilstein
authors.affiliation: Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA.
authors.forename: Fevzi
authors.initials: F
authors.lastname: Daldal
authors.affiliation: Department of Biology, Emory University, Atlanta, GA 30322, USA.
authors.forename: Roger B
authors.initials: RB
authors.lastname: Deal
authors.affiliation: 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.
authors.forename: Brian D
authors.initials: BD
authors.lastname: Gregory
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001483:Base Sequence; D001665:Binding Sites; D002467:Cell Nucleus / Q000378:metabolism*; D060365:Chloroplast Proteins / Q000378:metabolism*; D016384:Consensus Sequence; D018506:Gene Expression Regulation, Plant; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D021381:Protein Transport; D034622:RNA Interference; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism*; D018749:RNA, Plant / Q000235:genetics / Q000378:metabolism*; D012261:Ribonucleoproteins / Q000378:metabolism*; D036226:Seedlings / Q000166:cytology / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D029681:Arabidopsis Proteins; D060365:Chloroplast Proteins; C529074:RBP29 protein, Arabidopsis; D012333:RNA, Messenger; D018749:RNA, Plant; D012261:Ribonucleoproteins