While nuclear compartmentalization is an essential feature of three-dimensional 
genome organization, no genomic method exists for measuring chromosome distances 
to defined nuclear structures. In this study, we describe TSA-Seq, a new mapping 
method capable of providing a "cytological ruler" for estimating mean 
chromosomal distances from nuclear speckles genome-wide and for predicting 
several Mbp chromosome trajectories between nuclear compartments without 
sophisticated computational modeling. Ensemble-averaged results in K562 cells 
reveal a clear nuclear lamina to speckle axis correlated with a striking spatial 
gradient in genome activity. This gradient represents a convolution of multiple 
spatially separated nuclear domains including two types of transcription "hot 
zones." Transcription hot zones protruding furthest into the nuclear interior 
and positioning deterministically very close to nuclear speckles have higher 
numbers of total genes, the most highly expressed genes, housekeeping genes, 
genes with low transcriptional pausing, and super-enhancers. Our results 
demonstrate the capability of TSA-Seq for genome-wide mapping of nuclear 
structure and suggest a new model for spatial organization of transcription and 
gene expression.