J Cell Biol. 2018 Aug 28. pii: jcb.201807108. doi:10.1083/jcb.201807108

Chen Y, Zhang Y, Wang Y, Zhang L, Brinkman EK, Adam SA, Goldman R, van Steensel B, Ma J, Belmont AS.

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

Tyramide free radicals can label DNA directly. In TSA-Seq (Tyramide Signal Amplification-Sequencing), HRP is targeted on proteins of interest, biotinylated TSA labels neighboring DNA, and biotin-DNA complexes are purified and sequenced. Distances between chromosome domains and nuclear speckles is reproducible across experiments. Between peripheral lamina, marked by lamin A and B, and nuclear speckles (marked by SON), an increasing gradient of transcriptional activity is clearly visible.