Noncoding DNA in the human-mouse orthologous intergenic regions contains 
"islands" of conserved sequences, the functions of which remain largely unknown. 
We hypothesized that some of these regions might be matrix-scaffold attachment 
regions, MARs (or S/MARs). MARs comprise one of the few classes of eukaryotic 
noncoding DNA with an experimentally characterized function, being involved in 
the attachment of chromatin to the nuclear matrix, chromatin remodeling and 
transcription regulation. To test our hypothesis, we analyzed the co-occurrence 
of predicted MARs with highly conserved noncoding DNA regions in human-mouse 
genomic alignments. We found that 11% of the conserved noncoding DNA consists of 
predicted MARs. Conversely, more than half of the predicted MARs co-occur with 
one or more independently identified conserved sequence blocks. An excess of 
conserved predicted MARs is seen in intergenic regions preceding 5' ends of 
genes, suggesting that these MARs are primarily involved in transcriptional 
control.