Alus and LINEs (LINE1) are widespread classes of repeats that are very unevenly 
distributed in the human genome. The majority of GC-poor LINEs reside in the 
GC-poor isochores whereas GC-rich Alus are mostly present in GC-rich isochores. 
The discovery that LINES and Alus share similar target site duplication and a 
common AT-rich insertion site specificity raised the question as to why these 
two families of repeats show such a different distribution in the genome. This 
problem was investigated here by studying the isochore distributions of 
subfamilies of LINES and Alus characterized by different degrees of divergence 
from the consensus sequences, and of Alus, LINEs and pseudogenes located on 
chromosomes 21 and 22. Young Alus are more frequent in the GC-poor part of the 
genome than old Alus. This suggests that the gradual accumulation of Alus in 
GC-rich isochores has occurred because of their higher stability in 
compositionally matching chromosomal regions. Densities of Alus and LINEs 
increase and decrease, respectively, with increasing GC levels, except for the 
telomeric regions of the analyzed chromosomes. In addition to LINEs, processed 
pseudogenes are also more frequent in GC-poor isochores. Finally, the present 
results on Alu and LINE stability/exclusion predict significant losses of Alu 
DNA from the GC-poor isochores during evolution, a phenomenon apparently due to 
negative selection against sequences that differ from the isochore composition.