Automated genotyping for accurate assignment of the (AT)xNz(AT)y motif within the beta-globin locus control region-hypersensitive site 2

Unusual stability exhibited by (AT)XN12(AT)Y motif associated with high fetal hemoglobin levels

Quasi-palindromic sequences (AT)_XN₁₂(AT)_Y present in HS2 (hypersensitive site 2) of the human β-globin locus are known to be significantly associated with increased fetal hemoglobin (HbF) levels. High HbF levels in some adults arise due to pathological conditions such as sickle cell disease and β-thalassemia. However, elevated levels of HbF are also associated with a reducing morbidity and mortality in patients with β-thalassemia and thus ameliorate the severity of the disease. Using gel-electrophoresis, ultraviolet (UV)-thermal denaturation, and circular dichroism (CD) techniques, we demonstrated that it exhibits a hairpin-duplex equilibrium. Intramolecular species (hairpin) were observed in both low and high salt concentrations in gel assay studies displaying the unusual stability of intramolecular species even at the high counter-ion concentration. The unusual stability of hairpin secondary structures was also demonstrated by the monophasic nature of the melting profiles for the oligonucleotides which persisted at low as well as high salt and oligomer concentrations. Change in CD spectra as a function of oligomer concentration indicates that the bimolecular duplex formation is selectively favored over monomolecular hairpin formation at and above 9 µM oligomer concentration. Thus, we hypothesize that imperfect inverted repeat sequence (AT)_XN₁₂(AT)_Y of HS2 of β-globin gene LCR forms the unusually stable hairpins which may result in the formation of a cruciform structure that may be recruited for binding by various nuclear proteins that could result in elevated HbF levels. Communicated by Ramaswamy H. Sarma.

Molecular analysis of β-thalassemia patients: first identification of mutations HBB:c.93-2A>G and HBB:c.114G>A in Brazil

The various clinical phenotypes in β-thalassemias have stimulated the study of genetic factors that could modify the manifestations of these diseases. We examined 21 patients with β-thalassemia (β-thal) in order to identify some genetic modifying factors: β-thalassemia mutations, HBG2:g.-158C>T polymorphism, α-globin gene deletions and (AT)xNz(AT)y motif within the hypersensitive site 2-locus control region (HS2-LCR). In the 42 alleles analyzed, the most frequent mutations observed were HBB:c.92+6T>C (30.9%), HBB:c.118C>T (16.7%), HBB:c.93-21G>A (11.9%) and HBB:c.92+1G>A (4.8%); this finding is in accordance with previous data of the Brazilian population. The other genetic factors analyzed showed no relation with the severity of the disease. For the first time in Brazil, we report HBB:c.93-2A>G and HBB:c.114G>A mutations on the β-globin gene, both in a heterozygous state. This is also the first study to analyze the HS2-LCR in β-thalassemic individuals in the Brazilian population.

Spectrum of beta-thalassemia mutations and their association with allelic sequence polymorphisms at the beta-globin gene cluster in an Eastern Indian population

In this report, the spectrum of beta-thalassemia mutations and genotype-to-phenotype correlations were defined in large number of patients (beta-thalassemia carriers and major) with varying disease severity in an Eastern Indian population mainly from the state of West Bengal. The five most common beta-thalassemia mutations were detected, which included IVS1-5 (G-->C), codon 15 (G-->A), codon 26 (G-->A), codon 30 (G-->C), and codon 41/42 (-TCTT). These accounted for 85% in 80 beta-thalassemic alleles deciphered from 56 patients, including beta-thalassemia major and carriers, and 15% of alleles remained uncharacterized in these patients. Expression of the human beta-globin gene is regulated by an array of cis-acting DNA elements, including five DNase I hypersensitive sites (HSs) in the locus control region (LCR), promoters that incorporate certain silencer elements, and enhancers at 3' of the beta-globin gene. For detailed studies and to understand the molecular basis of beta-thalassemia, we studied two groups of subjects: a group of 12 patients from four families having beta-thalassemia major and carrier phenotype and a control group of 26 healthy individuals. In these two groups, we examined portions of the beta-globin gene locus control region HSs 1, 2, 3, and 4, which included the (CA)(x)(TA)(y) repeat motif, the (AT)(x)N(y)(AT)(z) repeat motif, the inverted repeat sequence TGGGGACCCCA, the promoter region of the (G)gamma-globin gene, an (AT)(x)(T)(y) repeat 5' of the silencer region, and the beta-globin gene and its 3' flanking region. We investigated the allelic sequence polymorphisms in these regions and their association with the beta-thalassemia mutations to know the possible genotype-phenotype relationship in beta-thalassemia patients. An analysis of cis-acting regulatory regions showed varied sequence haplotypes associated with some frequent beta-thalassemia mutations in this Eastern Indian population.