RNA-binding proteins (RBPs) are critical regulators of gene expression and RNA processing that are required for gene function. Yet the dynamics of RBP regulation in single cells is unknown. To address this gap in understanding, we developed STAMP (Surveying Targets by APOBEC-Mediated Profiling), which efficiently detects RBP–RNA interactions. STAMP does not rely on ultraviolet cross-linking or immunoprecipitation and, when coupled with single-cell capture, can identify RBP-specific and cell-type–specific RNA–protein interactions for multiple RBPs and cell types in single, pooled experiments. Pairing STAMP with long-read sequencing yields RBP target sites in an isoform-specific manner. Finally, Ribo-STAMP leverages small ribosomal subunits to measure transcriptome-wide ribosome association in single cells. STAMP enables the study of RBP–RNA interactomes and translational landscapes with unprecedented cellular resolution.

RNA 结合蛋白 (RBP) 是基因功能所需的基因表达和 RNA 加工的关键调节剂。然而，单细胞中 RBP 调节的动力学是未知的。为了解决这种理解上的差距，我们开发了 STAMP（通过 APOBEC 介导的分析来测量目标），它可以有效地检测 RBP-RNA 相互作用。STAMP 不依赖于紫外线交联或免疫沉淀，当与单细胞捕获相结合时，可以在单个合并实验中识别多种 RBP 和细胞类型的 RBP 特异性和细胞类型特异性 RNA-蛋白质相互作用。将 STAMP 与长读长测序配对，以异构体特异性方式产生 RBP 目标位点。最后，Ribo-STAMP 利用小的核糖体亚基来测量单细胞中转录组范围内的核糖体关联。