The 3′ breakpoint of the Yunnanese (Aγδβ)0-thalassemia deletion lies in an L1 family sequence: implications for the mechanism of deletion and the reactivation of the Gγ-globin gene

We have cloned the junction region of the previously characterized Yunnanese (Aγδβ)0-thalassemia deletion and the normal DNA region surrounding its 3′ breakpoint. The sequence of 1138 bp of the 3′-flanking region and 555 bp of the normal region surrounding the 3′ breakpoint was determined. The 5′ breakpoint of the deletion is positioned between 116 and 117 bp upstream of the Aγ-globin gene, and the 3′ breakpoint at 34 bp downstream of the BglII site that lies ∼12.7 kb upstream of the 3′ deletion breakpoint of Chinese (Aγδβ)0-thalassemia. There is no significant homology between the normal DNAs flanking the 5′ and 3′ breakpoints, except 2-bp (TG) identity and two pairs of short direct repeats at the deletion junction. The 3′ breakpoint is within an L1 family sequence that normally occurs about 66 kb downstream of the β-globin gene in 11p15. This L1 element is partially in reversed orientation at the 5′ side and is therefore, presumably, an inactive element. This type of junction indicates illegitimate DNA breakage and end-joining involving the L1 sequence. Similar to many other deletions in the β-globin locus, the Yunnanese (Aγδβ)0-thalassemia deletion lacks a sequence characteristic of defined recombination factors near the deletion junction, suggesting that chromatin configuration and other locus-specific features are important. Computer-aided analysis revealed that several transcriptional factors could bind to putative motifs present in the 3′-flanking sequence. It is possible that binding features of the distal L1 element are required to generate a suitable chromatin configuration for the recombination event in Yunnanese (Aγδβ)0-thalassemia. This may also be related to the reactivation of the Gγ-globin gene in adults with the Yunnanese (Aγδβ)0-thalassemia mutation.