TSA-Seq measures chromosomal distances from specific nuclear compartments genome-wide but requires ≥100 million cells. We report 10-20-fold increased sensitivity using TSA-Seq 2.0 which deliberately saturates protein-labeling but preserves distance mapping by the still unsaturated DNA-labeling. Mapping nuclear speckle distances in four cell lines reveals highly transcriptionally active, conserved speckle-associated chromosome domains but relative shifts of a small fraction of the genome that highly correlates with changes in gene expression.