Mesoscale proximity labeling at chromatin leads to identification of small molecule mechanism of action

Abstract

Proximity labeling typically identifies interactomes of single protein or RNA baits, limiting its use for mechanisms distributed across molecular systems. Here, we establish MesoMap, a chromatin-focused mesoscale proximity-labeling strategy that installs nanoscale photocatalysts on multiple histone baits to monitor drug-induced redistribution of proteins near chromatin. MesoMap captured HDAC inhibitor-induced remodeling of chromatin-associated proteins and, in a proof-of-concept de-orphaning application, prioritized a chromatin-proximal CLK/splicing axis for SR-1815, a phenotypically discovered SynGAP-restoring small molecule. Integration with kinase assays, splicing analysis, inhibitor comparisons, and published neuronal validation supports a model in which SR-1815 regulates SynGAP abundance through polypharmacological kinase modulation, including CLK-dependent effects on splicing. Together, these studies establish MesoMap as a complementary approach for resolving drug-induced protein redistribution near chromatin and accelerating mechanism-of-action studies for phenotypic chemical probes. The authors develop MesoMap, an extension of their previous proximity labeling system, which uses multiple baits on labeled histones to measure changes across chromatin rather than to a single specific protein.