Chromophore‐assisted proximity labeling of DNA reveals chromosomal organization in living cells

The spatial arrangement of chromosome within the nucleus is intimately linked to genome function and gene expression regulation. Existing genome-wide mapping methods to study chromosome organization often rely on chemically crosslinking DNA with protein baits, which raises concerns of introducing artefacts during cellular fixation. Herein, we developed a novel proximity-dependent DNA labeling method based on the chromophore-assisted nucleobase photooxidation. By genetically targeting a photosensitizer protein to specific subnuclear locations, we achieved blue light-activated labeling of local DNA with a bioorthogonal functional handle, which allowed subsequent affinity purification and sequence identification via next-generation sequencing. When applied to the nuclear lamina in human embryonic kidney 293T cells, our method revealed lamina-associated domains (LADs) that cover 37.6% of the genome. These LADs overlap with heterochromatin hallmarks including histone 3 lysine 9 dimethylation (H3K9me2) and are depleted with CpG islands. This simple labeling method avoids the harsh treatment of chemical crosslinking and is generally applicable for the genome-wide high-resolution mapping of the spatial chromosome organization in living cells.