Structure of SALL4 zinc-finger domain reveals link between AT-rich DNA binding and Okihiro syndrome

Spalt-like 4 (SALL4) maintains vertebrate embryonic stem cell identity and is required for thedevelopment of multiple organs, including limbs. Mutations in SALL4 are associated with Okihirosyndrome and SALL4 is also a known target of thalidomide. SALL4 protein has a distinct preference forAT-rich sequences, recognised by a pair of zinc fingers at the C-terminus. However, unlike manycharacterised zinc finger proteins, SALL4 shows flexible recognition with many different combinationsof AT-rich sequences being targeted. SALL4 interacts with the NuRD corepressor complex whichpotentially mediates repression of AT-rich genes. We present a crystal structure of SALL4 C-terminalzinc fingers with an AT-rich DNA sequence, which shows that SALL4 uses small hydrophobic and polarside chains to provide flexible recognition in the major groove. Missense mutations reported inpatients that lie within the C-terminal zinc fingers reduced overall binding to DNA but not thepreference for AT-rich sequences. Furthermore, these mutations altered association of SALL4 with ATrichgenomic sites, providing evidence that these mutations are likely pathogenic.