ExperimentType TSA-seq

TSA sequencing (TSA-Seq), is a genomic method that allows the estimation of cytological distances of chromosome loci genome-wide relative to a particular nuclear compartment and can be used to infer chromosome trajectories from one compartment to another. This is a method for measuring distances on a scale of ~100-1000 nm.

TSA uses an antibody-coupled HRP in conjunction with an antibody targeting a specific protein or compartment to catalyze the formation of diffusible biotin-tyramide free radicals and create a free radical concentration gradient centered at the target in fixed nuclei. The TSA reaction is followed by the reversal of formaldehyde cross-linking, DNA isolation, pulldown of biotinylated DNA, and high-throughput sequencing. TSA labels DNA directly and the steady-state concentration of tyramide free radicals during the TSA reaction can be modeled by a simple exponential decay proportional to the distance from the target.

TSA enrichment genomic maps are generated by plotting the log2 ratio of the normalized pulldown read density versus the normalized read density of input DNA over a 20-kbp sliding window and can be visualized as normalized counts in 1D bigwig tracks.