nearBynding: A flexible pipeline characterizing protein binding to local RNA structure

Abstract

The etiology of diseases driven by dysregulated mRNA metabolism can be elucidated by characterizing the responsible RNA-binding proteins (RBPs). Although characterizations of RBPs have been mainly focused on their binding sequences, not much has been investigated about their preferences for RNA structures. We present nearBynding, an R/Bioconductor pipeline that incorporates RBP binding sites and RNA structure information to discern structural binding preferences for an RBP. nearBynding visualizes RNA structure at and proximal to sites of RBP binding transcriptome-wide, analyzes CLIP-seq data without peak-calling, and provides a flexible scaffold to study RBP binding preferences relative to diverse RNA structure data types.

RNA structure profiling at single-cell resolution reveals new determinants of cell identity

“…Figure 6b). We also confirmed that double-stranded regions are enriched for RBPs that are known to bind to double-stranded regions such as STAU2 30 , DDX3X 31 , UPF1 32 , and DDX55 33 (Supp. Figure 6b), confirming that our single-cell data captures known patterns from bulk cells.…”