Gene density and chromosome territory shape

Despite decades of study of chromosome territories (CT) in the interphase nucleus of mammalian cells, our understanding of the global shape and 3-D organization of the individual CT remains very limited. Past microscopic analysis of CT suggested that while many of the CT appear to be very regular ellipsoid-like shapes, there were also those with more irregular shapes. We have undertaken a comprehensive analysis to determine the degree of shape regularity of different CT. To be representative of the whole human genome, 12 different CT (~41 % of the genome) were selected that ranged from the largest (CT 1) to the smallest (CT 21) in size and from the highest (CT 19) to lowest (CT Y) in gene density. Using both visual inspection and algorithms that measure the degree of shape ellipticity and regularity, we demonstrate a strong inverse correlation between the degree of regular CT shape and gene density for those CT that are most gene-rich (19, 17, 11) and gene-poor (18, 13, Y). CT more intermediate in gene density showed a strong negative correlation with shape regularity, but not with ellipticity. An even more striking correlation between gene density and CT shape was determined for the nucleolar-associated NOR-CT. Correspondingly, striking differences in shape between the X active and inactive CT implied that aside from gene density, the overall global level of gene transcription on individual CT is also an important determinant of chromosome territory shape.