Spatially resolved multi-bait mapping of stress granule and processing body transcriptome

Stress granules (SGs) are dynamic, membrane-less organelles containing complex RNA-protein networks. The RNA components of SGs have been profiled through various approaches, characterized as long, translation-repressed, and highly epigenetically modified. However, it remains unclear whether these RNAs are uniformly distributed within SGs. In this study, we used multiple SG core proteins to genetically target the photocatalyst protein miniSOG, which allows for comprehensive CAP-seq profiling of RNA components within SGs. We discovered that RNAs associated with different SG core proteins exhibit heterogeneous distribution and distinct intrinsic features. Furthermore, we applied CAP-seq to map the RNA components in processing bodies (PBs) under both unstressed conditions and arsenite stimulation. By comparing the SG and PB transcriptomes, our data revealed that m6A modification may promote the localization of RNAs to SGs, while higher AU content may facilitate the targeting of mRNAs to PBs. This suggests potential regulatory roles in determining the subcellular localization of mRNAs within membrane-less organelles.