Study : Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Identification
Name
Global analysis of the RNA-protein interaction and RNA secondary structure landscapes of the Arabidopsis nucleus
Identifier
dXJuOkVWQS9zdHVkeS9QUkpOQTI1NDAzMQ==
Source
Description
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. Overall design: 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
Data files
- SRR1503848
- SRR1503849
- SRR1503850
- SRR1503851
- SRR1503852
- SRR1503853
- SRR1503854
- SRR1503855
- SRR1575168
- SRR1575169
- ERZ1125706
- ERZ272518
- ERZ307085
- ERZ509585
- ERZ1125697
- ERZ272516
- ERZ307083
- ERZ509587
- ERZ272515
- ERZ307082
- ERZ509588
- ERZ1125705
- ERZ272517
- ERZ307084
- ERZ509584
- ERZ1109598
- ERZ272513
- ERZ307080
- ERZ509586