Talk abstracts
Talk on Saturday 02:36-02:48pm submitted by Matthew R. Willmann
Global analysis of RNA-protein interaction site and RNA secondary structure dynamics in response to the plant hormone abscisic acid
Matthew R. Willmann (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA), Mengge Shan (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, and Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA), Fan Li (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, and Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA), Alsu Ibragimova (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA), Sarah Foster (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA), Brian D. Gregory (Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA, and Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA 19104, USA)
Abstract:
RNA-protein interactions are critical effectors throughout the life cycle of RNA molecules. In fact, transcription, pre-mRNA processing (splicing and polyadenylation), translation, subcellular localization, stability, and decay of RNAs are all driven by interactions with RNA-binding proteins (RBPs). Despite this fact, research into the global effect of RBPs on gene expression in plant transcriptomes has been lacking. Our lab has pioneered an RNase-mediated protein footprint sequencing method called protein interaction profile sequencing (PIP-seq) that allows for the global identification of RNA-protein interaction sites (protein-protected sites (PPSs)) and RNA secondary structure in eukaryotic transcriptomes. Here, we use this technique to simultaneously study the dynamics of these features in the moss Physcomitrella patens in response to the plant hormone abscisic acid (ABA). From this analysis, we identify hundreds of RBP interaction sites whose binding affinity changes within 30 and/or 60 minutes of ABA treatment. Several RNA sequence motifs are enriched among the differentially bound PPSs, suggesting that ABA is able to elicit some of its effects by changing the binding of one or more RBPs that regulate multiple mRNAs. Increased binding of at least one of these motifs by the cognate RBP seems to increase the stability of the RNA targets. In addition to changes in RNA-protein interactions and gene expression in response to ABA, we uncover the immediate early changes in RNA secondary structure, which correspond mostly to the formation of highly structured elements. Current research focuses on identifying the RBPs binding to the enriched sequence motifs, and studying the effect of ABA-induced differential binding by RBPs and RNA secondary structure on translation.
Keywords: RNA binding proteins, PIP-seq