Crystal Structure of the Double Homeodomain of DUX4 in Complex with DNA

• Published in: Cell reports (Cambridge) 2018-12, Vol.25 (11), p.2955-2962.e3
• Main Authors: Lee, John K., Bosnakovski, Darko, Toso, Erik A., Dinh, Tracy, Banerjee, Surajit, Bohl, Thomas E., Shi, Ke, Orellana, Kayo, Kyba, Michael, Aihara, Hideki
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; B cell leukemia; Cell Line; cleavage stage development; crystal structure; Crystallography, X-Ray; DNA - chemistry; DNA - metabolism; DNA sequence readout; double homeobox; DUX; facioscapulohumeral muscular dystrophy; FSHD; Homeodomain Proteins - chemistry; Homeodomain Proteins - metabolism; Mice; Models, Molecular; Protein Domains; Protein Multimerization; retrovirus-like elements; tandem homeodomains
• ISSN: 2211-1247; 2211-1247
• DOI: 10.1016/j.celrep.2018.11.060

Double homeobox (DUX) transcription factors are unique to eutherian mammals. DUX4 regulates expression of repetitive elements during early embryogenesis, but misexpression of DUX4 causes facioscapulohumeral muscular dystrophy (FSHD) and translocations overexpressing the DUX4 double homeodomain cause B cell leukemia. Here, we report the crystal structure of the tandem homeodomains of DUX4 bound to DNA. The homeodomains bind DNA in a head-to-head fashion, with the linker making anchoring DNA minor-groove interactions and unique protein contacts. Remarkably, despite being tandem duplicates, the DUX4 homeodomains recognize different core sequences. This results from an arginine-to-glutamate mutation, unique to primates, causing alternative positioning of a key arginine side chain in the recognition helix. Mutational studies demonstrate that this primate-specific change is responsible for the divergence in sequence recognition that likely drove coevolution of embryonically regulated repeats in primates. Our work provides a framework for understanding the endogenous function of DUX4 and its role in FSHD and cancer. [Display omitted] •DUX4 binds DNA with its tandem homeodomains (HDs) arranged head to head•DUX4 HD1 and HD2 bind different core sequences: TAAT and TGAT, respectively•A Glu70-Arg73 salt bridge in HD1 explains differential core sequence specificity•HD1-altered target specificity appears unique to primates Lee et al. determine the crystal structure of the facioscapulohumeral muscular dystrophy and cancer-associated transcription factor DUX4, bound to DNA. The structure gives insight into how the double homeodomain of DUX4, which is related by duplication of an ancestral homeodomain, has evolved different sequence specificities, uniquely in the primate lineage.