Parallel Proteomic and Transcriptomic Microenvironment Mapping (μMap) of Nuclear Condensates in Living Cells

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