DNAase I hypersensitive site 3' to the beta-globin gene cluster contains a TAA insertion specific for beta(S)-Benin haplotype

BACKGROUND AND OBJECTIVES. Analysis of DNA polymorphic sites is a powerful tool for detection of gene flow in human evolutionary studies and to trace genetic background associated with abnormal genes. The beta-globin locus contains more than 20 single-base restriction fragment length polymorphism (RFLP) sites spanning over 80 kb on chromosome 11. Far downstream of the expressed genes, there is a hypersensitive site (HS). The function of the 3'-HS remains unknown. As an approach to the understanding of the 3'-HS region in sickle cell anemia we searched for sequence polymorphism in the AT-rich region, using a non-radioactive polymerase chain reaction (PCR)-single strand conformational polymorphism (SSCP) technique. DESIGN AND METHODS. A 460 bp fragment located at the 3' of the b globin gene was amplified from patients (with sickle cell anemia and HbSC disease), and from AS individuals. Standard RFLP-haplotyping was performed and compared with the PCR-SSCP screening strategy. RESULTS. Two distinct band patterns were revealed by SSCP testing, each one in strict linkage disequilibrium with either Benin or Bantu haplotypes. Direct sequencing of the amplified segment revealed a TAA insertion in the AT-rich region, in all 121 beta(S) Benin chromosomes tested, but not in other beta(S) haplotypes from the total of 380 beta(S) chromosomes typed. INTERPRETATION AND CONCLUSIONS. SSCP analysis could easily distinguish sequence variations in the 3'AT-rich region of the beta-globin cluster, and a TAA insertion in this region seems to be specific for the Benin-beta(S) chromosome.