The human genome is composed of large sequence segments with fairly homogeneous 
GC content, namely isochores, which have been linked to many important 
functions; biological implications of most isochore boundaries, however, remain 
elusive, partly due to the difficulty in determining these boundaries at high 
resolution. Using the segmentation algorithm based on the quadratic divergence, 
we re-determined all 79 boundaries of previously identified human isochores at 
single-nucleotide resolution, and then compared the boundary coordinates with 
other genome features. We found that 55.7% of isochore boundaries coincide with 
termini of repeat elements; 45.6% of isochore boundaries coincide with termini 
of highly conserved sequences based on alignment of 17 vertebrate genomes, i.e., 
the highly conserved genome sequence switches to a less or non-conserved one at 
the isochore boundary; some isochore boundaries coincide with abrupt change of 
CpG island distribution (note that one boundary can associate with more than one 
genome feature). In addition, sequences around isochore boundaries are highly 
conserved. It seems reasonable to deduce that the boundaries of all the 
isochores studied here would be replication timing sites in the human genome. 
These results suggest possible key roles of the isochore boundaries and may 
further our understanding of the human genome organization.