A5043604566- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Cancer-related gene regulation
- Cancer-related molecular mechanisms research
University of Southern California
2020-2023
Abstract Direct determination of RNA structures and interactions in living cells is critical for understanding their functions normal physiology disease states. Here, we present PARIS2, a dramatically improved method duplex vivo with >4000-fold higher efficiency than previous methods. PARIS2 captures ribosome binding sites on mRNAs, reporting translation status transcriptome scale. Applying to the U8 snoRNA mutated neurological disorder LCC, discover network dynamic which are destabilized...
Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety biological processes. However, direct determination 3D vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present method, Spatial 2'-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers defined lengths measure distances between nucleotides cellular RNA. Integrating crosslinking, exonuclease (exo) trimming, proximity ligation,...
The dynamic balance between tRNA supply and codon usage demand is a fundamental principle in the cellular translation economy. However, regulation functional consequences of this remain unclear. Here, we use PARIS2 interactome capture, structure modeling, conservation analysis, RNA–protein interaction modification mapping to reveal targets hundreds snoRNAs, many which were previously considered orphans. We identify snoRNA–tRNA network that required for global modifications, including...
ABSTRACT Three-dimensional (3D) structures dictate the functions of RNA molecules in a wide variety biological processes. However, direct determination 3D vivo is difficult due to their large sizes, conformational heterogeneity, and dynamics. Here we present new method, Spatial 2’-Hydroxyl Acylation Reversible Crosslinking (SHARC), which uses chemical crosslinkers defined lengths measure distances between nucleotides cellular RNA. Integrating crosslinking, exonuclease (exo) trimming,...
SUMMARY snoRNAs are a large family of noncoding (nc)RNAs present across eukaryotes and archaea. While subset them guide 2’-O- methylation (Nm) pseudouridylation (Ψ) rRNAs snRNAs, targets most remain unknown. Here we used PARIS2 to map snoRNA targets, revealing an extensive conserved snoRNA-tRNA interaction network. Using optimized denatured RiboMeth-seq (dRMS), discovered snoRNA-guided Nm sites in ncRNAs, including tRNAs. Loss their associated 2’-O-methyltransferase FBL reduced tRNA...
SUMMARY Direct determination of RNA structures and interactions in living cells is critical for understanding their functions. Current crosslinking proximity-ligation approaches are fundamentally limited due to inefficient crosslinking, purification high-level photochemical damages. Here we present PARIS2 (psoralen analysis structures, second generation), a re-invented method capturing duplexes with three orders magnitude improved efficiency. captures ribosome small subunit (SSU) binding...