Globin gene switching: In vivo protein-DNA interactions of the human β-globin locus in erythroid cells expressing the fetal or the adult globin gene program

To characterize the protein-DNA interactions important for the developmental control of the human β-globin locus, we analyzed by in vivo dimethyl sulfate footprinting erythroid cells expressing either the fetal or the adult globin developmental program. In the locus control region (LCR) of the β-globin locus, in vivo footprints on NF-E2 (or AP-1) and GATA-1 motifs remained the same regardless of whether the fetal or the adult globin genes are expressed. In contrast, in vivo footprints on GT (CACCC) motifs differed between the cells expressing the fetal or the adult globin program. In promoter regions, the actively transcribed genes demonstrated extensive and consistent footprints over the canonical elements, such as CACCC and CCAAT motifs. The adult globin expressing cells displayed more extensive footprints than the fetal globin expressing cells in the 3′ regulatory sequences of both the ^Aγ- and the β-globin genes, suggesting a role of these 3′ elements in β-globin gene expression. Our results suggest that the bulk of protein-DNA interactions that underlies the developmental control of globin genes takes place in the γ- and β-globin gene promoters, and that GT motifs of the β-globin locus LCR may play a role in the developmental regulation of human β-globin gene expression, perhaps by increasing the probability of interaction of the LCR holocomplex with the fetal or the adult globin gene.