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Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues [bulk RNA-seq]

ABSTRACT: RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping their RNA interactomes within the dynamically changing transcriptomic landscape, especially in single-cell contexts and primary tissues. Here, we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), a versatile method that uses an antibody-directed editing strategy to map genome-wide in situ RBP-RNA interaction and gene expression simultaneously. We demonstrate the robustness and efficiency of MAPIT-seq across multiple RBPs and systematically analyze the RNA substrate associated with core components of polycomb repressive complex 2 (PRC2). Furthermore, MAPIT-seq can be readily applied to frozen tissue sections, highlighting its potential for studying clinical samples. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq), enabling the elucidation of cell stage-specific regulation of RBP. In summary, MAPIT-seq extends the dimensions of multi-omic profiling, offering deeper mechanistic insights into post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios.

ORGANISM(S): Homo sapiens

PROVIDER: GSE278255 | GEO | 2025/06/02

REPOSITORIES: GEO

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Co-profiling of in situ RNA-protein interactions and transcriptome in single cells and tissues

Project description:RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping their RNA interactomes within the dynamically changing transcriptomic landscape, especially in single-cell contexts and primary tissues. Here, we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), a versatile method that uses an antibody-directed editing strategy to map genome-wide in situ RBP-RNA interaction and gene expression simultaneously. We demonstrate the robustness and efficiency of MAPIT-seq across multiple RBPs and systematically analyze the RNA substrate associated with core components of polycomb repressive complex 2 (PRC2). Furthermore, MAPIT-seq can be readily applied to frozen tissue sections, highlighting its potential for studying clinical samples. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq), enabling the elucidation of cell stage-specific regulation of RBP. In summary, MAPIT-seq extends the dimensions of multi-omic profiling, offering deeper mechanistic insights into post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios. This SuperSeries is composed of the SubSeries listed below.

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