Dnaase I Hypersensitive Site 3′ To The β-globin Gene Cluster Contains A Taa Insertion Specific For βs-benin Haplotype

Abstract

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 β-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 β 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 βs Benin chromosomes tested, but not in other βs haplotypes from the total of 380 βs chromosomes typed. Interpretation and Conclusions. SSCP analysis could easily distinguish sequence variations in the 3′AT-rich region of the β-globin cluster, and a TAA insertion in this region seems to be specific for the Benin-βs chromosome. ©2002, Ferrata Storti Foundation.873246249Cavalli-Sforza, L.L., Menozzi, P., Piazza, A., Genetic history of world populations. Area and time of origin of major mutants, with special attention to hemoglobins (1994) The history and geography of human genes, pp. 145-154. , L. Cavalli-Sforza, P. Menozzi, A Piazza, eds. Princeton: Princeton University PressLabie, D., Elion, J., Sequence polymorphisms of potential functional relevance in the β-globin gene locus (1996) Hemoglobin, 20, pp. 85-101Felsenfeld, G., Boyes, J., Chung, J., Clark, D., Studitsky, V., Chromatin structure and gene expression (1996) Proc Natl Acad Sci USA, 93, pp. 9384-9388Fleenor, D.E., Kaufman, R.E., Characterization of the DNase I hypersensitive site 3′of the human β globin gene domain (1993) Blood, 81, pp. 2781-2790Gonçalves, M.S., Nechtman, J.F., Figueiredo, M.S., Kerbauy, J., Arruda, V.R., Sonati, M.F., Sickle cell disease in a Brazilian population from Sao Paulo: A study of the βs haplotypes (1994) Hum Hered, 44, pp. 322-327Arruda, V.R., Von Zuben, P.M., Annichino-Bizzacehi, J.M., Costa, F.F., Rapid detection of factor V Leiden (FVQ506) by non-radioactive single strand conformation polymorphism (SSCP) (1996) Sangre, 41, pp. 379-381Gerhard, D.S., Kidd, K.K., Kidd, J.R., Egeland, J.A., Housman, D.E., Identification of a recent recombination event within the human β-globin gene cluster (1984) Proc Natl Acad Sci USA, 81, pp. 7875-7879Ofori-Acquah, S.F., Lalloz, M.R.A., Layton, D.M., Localization of cis-active determinants of fetal hemoglobin level in sickle cell anemia (1996) Blood, 88 (SUPPL. 1), p. 493. , abstractBordin, S., Crespi, V.G., Bassères, D.S., Different rates of recombination among polymorphic short tandem repeats of the β-globin gene cluster in βs chromosomes (1997) Blood, 90 (SUPPL. 1), p. 444. , abstractZago, M.A., Silva Jr., W.A., Dalle, B., Gualandro, S., Hutz, M.H., Lapoumeroulie, C., Atypical β(s) haplotypes are generated by diverse genetic mechanisms (2000) Am J Hematol, 63, pp. 79-84Zago, M.A., Silva Jr., W.A., Gualandro, S., Rearrangements of the beta-globin gene cluster in apparently typical betaS haplotypes (2001) Haematologica, 86, pp. 142-145Nagel, R.L., Steinberg, M.H., Genetics of the βs gene: Origins, genetic epidemiology, epistasis in sickle cell anemia (2001) Disorders of hemoglobin, , Steinberg MH, Forget BC, Higgs DR, Nagel RL, editors. Cambridge, UK, Cambridge University Pres