There is so much amazing RNA research going on! We have a weekly journal club to talk about the latest publications. Here are the papers that we have been reading:
Upcoming 12/11/20: We are reading Rafael de Cesaris Araujo Tavares, et al.’s paper from Anna Marie Pyle’s lab about RNA structure across SAR-CoV2. This paper was recently published in the Journal of Virology – The global and local distribution of RNA structure throughout the SARS-CoV-2 genome.
12/4/20: We read Meredith Corley, et al.’s paper from Gene Yeo’s lab describing the fSHAPE protocol and its relevance. This paper was recently published in Molecular Cell – Footprinting SHAPE-eCLIP Reveals Transcriptome-wide Hydrogen Bonds at RNA-Protein Interfaces.
One interesting result we noticed in this paper was that RNA binding proteins generally interact with well structured regions (low Shannon entropy), but are more likely to directly contact accessible nucleotides within those structured regions. A question we would have liked to see more about in the discussion is how transcriptome-wide SHAPE protocols performed in the presence of proteins are influenced by protein protections and whether in-cell structure data is inaccurate or if eCLIP is necessary to see protein protection in standard SHAPE protocols.