Polymorphisms and genomic organization of repetitive DNA from centromeric regions of Arabidopsis chromosomes

A highly abundant repetitive DNA sequence family of Arabidopsis, AtCon, is composed of 178-bp tandemly repealed units and is located at the centromere s of all five chromosome pairs. Analysis of multiple copies of AtCon showed 95% conservation of nucleotides, with some alternative bases, and revealed two boxes, 30 and 24 bp long, that are 99% conserved. Sequences at the 3' end of these boxes showed similarity to yeast CDEI and human CENP-B DNA-pro tein binding motifs. When oligonucleotides from less conserved regions of A tCon were hybridized in situ and visualized by using primer extension, they were detected on specific chromosomes. When used for polymerase chain reac tion with genomic DNA, single primers or primer pairs oriented in the same direction showed negligible amplification, indicating a head-to-tail repeat unit organization. Most primer pairs facing in opposite directions gave se veral strong bands corresponding to their positions within AtCon. However, consistent with the primer extension results, some primer pairs showed no a mplification, indicating that there are chromosome-specific variants of AtC on. The results are significant because they elucidate the organization, mo de of amplification, dispersion, and evolution of one of the major repeated sequence families of Arabidopsis. The evidence presented here suggests tha t AtCon, like human alpha satellites, plays a role in Arabidopsis centromer e organization and function.