Localisation ofcisRegulatory Elements at the β-Globin Locus: Analysis of Hybrid Haplotype Chromosomes

Abstract

Severalciselements at the β-globin gene cluster and the upstream locus control region (LCR) have been implicated in modulation of fetal haemoglobin (Hb F) level in β-globin disorders. To determine the role of elements at the LCR and the β-globin gene cluster on HbF level among sickle cell anaemia (SCA) patients, hybrid hapotype βSchromosomes exhibiting variation in the association of alleles of LCR hypersensitive site 2 (HS2) and the β-globin gene cluster restriction fragment length polymorphosim (RFLP) haplotypes were identified in an unselected population of 100 patients. On 15 chromosomes the polymorphic HS2 short tandem repeat(TA)xN10–12(TA)ycontaining a Hox2 binding motif differed from that typically associated with the corresponding β-globin gene cluster RFLP haplotype. Among patients homozygous for the Benin RFLP haplotype, in whom one chromosome carried the (TA)9N10(TA)10allele, no effect on HbF level was observed. Polymorphism of the pre-Gγ framework, an enhancer located 25 kb downstream of HS2 localised the breakpoint for each of these ‘hybrid’ haplotype chromosomes upstream of this element. Previously described hybrid haplotype chromosomes with the (TA)9N10(TA)10HS2 allele associated with raised HbF by contrast arise by recombination 1 kb downstream of the pre-Gγ framework. This study suggests that variability in HbF level associated with polymorphisn of the HS2 enhancer depend on downstream determinant (s) in tight linkage disequilibrium with HS2. The pre-Gγ framework is the only known polymorphiccis-active determinant in this region.