An Intrachromosomal Repeating Unit Based on DNA Bending

Abstract

DNA bending has been observed in conjunction with transcription, replication, and recombination. Furthermore, nucleosomes in eukaryotic cells are positioned through DNA bending, suggesting an active role for DNA bending in the chromosome organization. We reported previously that DNA bend sites appear every 680 bp in the human e- and β-globin gene regions. Here we showed that these sites are present at an interval of roughly 700 bp in the ^Gγ-^Aγ-ψβ-globin gene region and that they divide the region into units. They were conserved in the promoter regions of nearly all β-like globin genes and between human β- and mouse β^maj-globin genes, although the periodicity of the sites was locally disturbed at the junctions of the duplicated ^Gγ- and ^Aγ-globin genes and in their second introns. This suggested that the periodicity is ranked lower in the hierarchy of genomic DNA organization than genome rearrangement and gene expression. A close inspection of one of the sites in the ^Aγ-globin gene region indicated that a 20-bp sequence containing periodic short (dA)_n tracts was partly responsible for the bending. This sequence was shown to phase nucleosomes in this region by preferential binding to the core histones.