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

ABSTRACT: RNA-binding proteins (RBPs) are essential regulators of RNA fate and function. A long-standing challenge in studying RBP regulation has been mapping RNA interactomes within the dynamic transcriptomic landscape, especially in single-cell contexts and primary tissues. Here we introduce MAPIT-seq (modification added to RBP interacting transcript-sequencing), which uses an antibody-directed editing strategy to map genome-wide in situ RBP–RNA interactions and gene expression concurrently. We demonstrate MAPIT-seq’s robustness across multiple RBPs and systematically analyze RNA substrates associated with core polycomb repressive complex 2 (PRC2) components. MAPIT-seq is also applicable to frozen tissue sections, enabling the mapping of RBP roles during brain development. Importantly, we develop high-throughput single-cell MAPIT-seq (scMAPIT-seq) to reveal cell stage-specific RBP regulation. In summary, MAPIT-seq expands multi-omics profiling, providing an effective framework to study post-transcriptional regulation in dynamic biological processes and clinically relevant scenarios. This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE278418 | 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 [scMAPIT-seq]

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