Characterization of human centromeric regions using restriction enzyme banding, alphoid DNA and structural...

Studies of banding induced by restriction enzymes may provide insight into banding mechanisms and chromosome structure. We examined whether or not the sizes of chromosome-specific alphoid DNA fragments created by digestion with various restriction enzymes relate to the presence or absence of C-like bands produced by these same enzymes. We sized alphoid DNA fragments from five different chromosomes, digested with each of six different restriction enzymes. There was no obvious correlation between the length of alphoid restriction fragments at specific human centromeric regions and the production of C-like bands. We used the enzyme AluI and traditional staining (CBG) techniques to band centromeres with conformational alterations. These included dicentric chromosomes, chromosomes from a patient with Roberts syndrome, and 5-azacytidine-treated prometaphase chromosomes. In all cases bands produced by AluI resembled CBG banding. We found that markedly decondensed portions of centromeric regions induced by 5-azacytidine did not band. Our studies demonstrate that restriction endonuclease C-like banding is not strictly related to the presence of restriction sites in alphoid DNA, and the condensed chromatin conformation at the centromeric region may play a role in banding.