Transcriptomics

Dataset Information

297

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


ABSTRACT: Post-transcriptional 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 RNAs in the nucleus has yet to be compiled for any organism. Here, we use our ribonuclease-mediated structure and RBP binding site mapping approach on Arabidopsis seedling nuclei in vivo to globally profile these features within the nuclear compartment. We reveal opposing patterns of secondary structure and RBP binding levels throughout native messenger RNAs that demarcate 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, we identify a nuclear role for the chloroplast RBP, CP29A. In total, we provide the first simultaneous view of the RNA secondary structure and RBP interaction landscapes in a eukaryotic nucleus. Protein interaction profile sequencing (PIP-seq) in Arabidopsis seedling nuclei. These are crosslinked with formaldehyde and treated with two RNases (ssRNase and dsRNase) with two replicates

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Shawn W Foley   Brian D Gregory  Sager Jayesh Gosai  Sager J Gosai 

PROVIDER: E-GEOD-58974 | ArrayExpress | 2014-12-16

SECONDARY ACCESSION(S): SRP043993GSE58974PRJNA254031

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

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

Gosai Sager J SJ   Foley Shawn W SW   Wang Dongxue D   Silverman Ian M IM   Selamoglu Nur N   Nelson Andrew D L AD   Beilstein Mark A MA   Daldal Fevzi F   Deal Roger B RB   Gregory Brian D BD  

Molecular cell 20141231 2


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  ...[more]

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