Preference iof the recombination sites involved in the formation of extrachromosomal copies of the human alphoid Sau3A repat family

Abstract

The human alphoid Sau3A repetitive family DNA is one of the DNA species that are actively amplified to formextrachromosomal circular DNA in several cell lines. The drcularization takes place between two of the five -170 bp subunits wtth an average of 73.1% homology as well as between identical subunits. To investigate the nature of the recombination reaction, we cloned and analyzed the subunits containing recombination junctions. Analysis of a total of 68 junctions revealed that recombination had occurred preferentially at four positions 10-25 (A), 40-50 (B), 85-90 (C) and 135-160 (D) in the 170 bp subunit structure. Two regions (B and C) were overlapped with the regions with higher homology between subunits, while other two regions (A and D) cannot be explained solely by the regional homology between the subunits. These regions were located at both junctions of the nucleosomal and the linker region, and overlapped with the binding motifs for α protein and CENP-B. Approximately 90% of the recombination occurred between the subunits located next but one (±2 shift), although the frequency of recombination between the adjoining subunits (±1 shift) was ∼10%. © 1995 Oxford University Press.