Parallel Proteomic\nand Transcriptomic Microenvironment\nMapping (μMap) of Nuclear Condensates in Living Cells

Cellular activity is spatially organized across different\norganelles.\nWhile several structures are well-characterized, many organelles have\nunknown roles. Profiling biomolecular composition is key to understanding\nfunction but is difficult to achieve in the context of small, dynamic\nstructures. Photoproximity labeling has emerged as a powerful tool\nfor mapping these interaction networks, yet maximizing catalyst localization\nand reducing toxicity remains challenging in live cell applications.\nHere, we disclose a new intracellular photocatalyst with minimal cytotoxicity\nand off-target binding, and we utilize this catalyst for HaloTag-based\nmicroenvironment-mapping (μMap) to spatially catalog subnuclear\ncondensates in living cells. We also specifically develop a novel\nRNA-focused workflow (μMap-seq) to enable parallel transcriptomic\nand proteomic profiling of these structures. After validating the\naccuracy of our approach, we generate a spatial map across the nucleolus,\nnuclear lamina, Cajal bodies, paraspeckles, and PML bodies. These\nresults provide potential new insights into RNA metabolism and gene\nregulation while significantly expanding the μMap platform for\nimproved live-cell proximity labeling in biological systems.