An efficient C-to-U RNA recorder as a tool for profiling targets of RNA-binding proteins

Abstract

STAMP (Surveying Targets by APOBEC-Mediated Profiling) employed the fusion protein between an RBP and the C-to-U editing enzyme APOBEC1 to mark and determine RBP's target transcripts. It exhibited wonderful performance in mammals, however, it was confirmed not working in flies and unclear its generality. In this study, APOBEC1 in STAMP was replaced with an APOBEC1-H122L/D124N mutant (APO1m), so that the method HyperSTAMP was established here in flies. HyperSTAMP method effectively and semi-quantitatively uncovered the targets of both Hrp48 (Heterogeneous nuclear ribonucleoprotein 48) and Thor in S2 cells with good signal to noise ratio, reproducibility, and consistency with other methods. It also captured RBP-binding positions on mRNAs through editing clusters on target RNAs. This study filled in the gap of lacking C-to-U editing enzyme in insects and provided a good tool for the experiments of double labeling RNA when exploring multiple RBPs concurrently.

Keywords: APOBEC1 (APO1); Drosophila melanogaster; HyperSTAMP; RNA editing; RNA-binding protein (RBP).