Targeted ATAC-see (tATAC-see): A Visual Assay for Target-Specific Chromatin Profiling

We present Targeted ATAC-see (tATAC-see), a visual genomics assay for site-specific chromatin profiling. By integrating the in situ visualization of ATAC-see with antibody-tethered tagmentation, tATAC-see captures chromatin states at defined protein-occupied domains with the simplicity of standard immunofluorescence. Modulating the spatial interaction radius of Tn5 via salt titration enables extended tagmentation of target-proximal chromatin local environments. We validated this imaging-based method by capturing the expanded chromatin neighborhoods of active euchromatin (H3K27ac, H3K4me3) alongside the dense structural Lamina-Associated Domains (LADs) of Lamin A/C and Lamin B1. Utilizing an HDAC inhibitor, we test the assay’s sensitivity to detect dynamic structural remodeling. We not only tracked chromatin decompaction, but also demonstrated the robust structural resistance of LADs. As a proof of principle biological application, we applied tATAC-see to models of replicative, chronological, and pathological (Hutchinson-Gilford Progeria Syndrome) aging to assess its ability to detect well-characterized peripheral heterochromatin and LAD remodeling. We observed divergent chromatin trajectories at the nuclear envelope reflective of the Lamin’s distinct roles. Lamin B1 domains exhibited increased local accessibility consistent with age-associated heterochromatin erosion, while Lamin A/C-associated domains physically detach from their scaffold. Ultimately, tATAC-see provides a robust, accessible platform for mechanistic and population-level studies to uncover spatial epigenome dynamics natively in single cells.