Chromophore-Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells.
Tao DingLiyuan ZhuYuxin FangYangluorong LiuWei TangPeng ZouPublished in: Angewandte Chemie (International ed. in English) (2020)
The spatial arrangement of chromosome within the nucleus is linked to genome function and gene expression regulation. Existing genome-wide mapping methods often rely on chemically crosslinking DNA with protein baits, which raises concerns of artifacts being introduced during cell fixation. By genetically targeting a photosensitizer protein to specific subnuclear locations, we achieved blue-light-activated labeling of local DNA with a bioorthogonal functional handle for affinity purification and sequence identification through next-generation sequencing. When applied to the nuclear lamina in human embryonic kidney 293T cells, it revealed lamina-associated domains (LADs) that cover 37.6 % of the genome. These LADs overlap with heterochromatin hallmarks and are depleted with CpG islands. This simple labeling method avoids the harsh treatment of chemical crosslinking and is generally applicable to the genome-wide high-resolution mapping of the spatial chromosome organization in living cells.
Keyphrases
- living cells
- genome wide
- single molecule
- copy number
- dna methylation
- high resolution
- circulating tumor
- fluorescent probe
- gene expression
- cell free
- single cell
- endothelial cells
- photodynamic therapy
- amino acid
- circulating tumor cells
- protein protein
- induced pluripotent stem cells
- mass spectrometry
- stem cells
- high density
- binding protein
- drug delivery
- cell therapy
- cancer therapy
- mesenchymal stem cells
- small molecule