A Functional Element Necessary for Fetal Hemoglobin Silencing

Background An improved understanding of the regulation of the fetal hemoglobin genes holds promise for the development of targeted therapeutic approaches for fetal hemoglobin induction in the beta-hemoglobinopathies. Although recent studies have uncovered trans-acting factors necessary for this regulation, limited insight has been gained into the cis-regulatory elements involved. Methods We identified three families with unusual patterns of hemoglobin expression, suggestive of deletions in the locus of the beta-globin gene (beta-globin locus). We performed array comparative genomic hybridization to map these deletions and confirmed breakpoints by means of polymerase-chain-reaction assays and DNA sequencing. We compared these deletions, along with previously mapped deletions, and studied the trans-acting factors binding to these sites in the beta-globin locus by using chromatin immunoprecipitation. Results We found a new (delta beta)(0)-thalassemia deletion and a rare hereditary persistence of fetal hemoglobin deletion with identical downstream breakpoints. Comparison of the two deletions resulted in the identification of a small intergenic region required for gamma-globin (fetal hemoglobin) gene silencing. We mapped a Kurdish beta(0)-thalassemia deletion, which retains the required intergenic region, deletes other surrounding sequences, and maintains fetal hemoglobin silencing. By comparing these deletions and other previously mapped deletions, we elucidated a 3.5-kb intergenic region near the 5' end of the delta-globin gene that is necessary for gamma-globin silencing. We found that a critical fetal hemoglobin silencing factor, BCL11A, and its partners bind within this region in the chromatin of adult erythroid cells. Conclusions By studying three families with unusual deletions in the beta-globin locus, we identified an intergenic region near the delta-globin gene that is necessary for fetal hemoglobin silencing. (Funded by the National Institutes of Health and others.)