Active or potentially active gene loci are preferentially sensitive to DNAase I digestion. Cedar and colleagues used this DNAase I sensitivity to label active sequences preferentially by nick translation of nuclei and chromosomes. Using biotinylated nucleotides and immunofluorescence detection, we have looked for compartmentalization of DNAase I-sensitive sequences by nick translation of nuclei maintained as three-dimensional structures. Labeled sequences in mouse L cells are preferentially localized at the nuclear periphery in both permeabilized nuclei and frozen sections. In newt and chicken nucleated erythrocytes, labeled regions are at borders of condensed chromatin masses along interchromatin channels communicating with the nuclear periphery. Control experiments indicate that nick translation of nuclei preferentially labels highly expressed genes and that the preferential localization of DNAase-I sensitive regions is probably not a consequence of fixation artifacts or selective nuclear permeability to the labeling reagents.