Transcriptome-wide identification of single-stranded RNA binding proteins

RNA-protein interactions are precisely regulated by RNA secondary structures in various biological processes. Large-scale identification of proteins that interact with particular RNA structure is important to the RBPome. Herein, a kethoxal assisted single-stranded RNA interactome capture (KASRIC) strategy was developed to globally identify single-stranded RNA binding proteins (ssRBPs). This approach combines RNA secondary structure probing technology with the conventional method of RNA-binding proteins profiling, realizing the transcriptome-wide identification of ssRBPs. Applying KASRIC, we identified 3180 candidate RBPs and 244 candidate ssRBPs in HeLa cells. Importantly, the 244 candidate ssRBPs contained 55 previously reported ssRBPs and 189 novel ssRBPs. Function analysis of the candidate ssRBPs exhibited enrichment in cellular processes related to RNA splicing and RNA degradation. The KASRIC strategy will facilitate the investigation of RNA-protein interactions.

Automated summary

RNA-protein interactions are regulated by RNA secondary structures. The KASRIC strategy was developed to identify single-stranded RNA binding proteins (ssRBPs). Using KASRIC, 3180 candidate RBPs and 244 candidate ssRBPs were identified, including both previously reported and novel ssRBPs. Functional analysis of the candidate ssRBPs showed enrichment in RNA splicing and degradation processes. The KASRIC strategy facilitates the investigation of RNA-protein interactions.