Conservation and innovation in the DUX4-family gene network [MMH6 ChIP-Seq]

Facioscapulohumeral dystrophy (FSHD; OMIM #158900, #158901) is caused by mis-expression of the DUX4 transcription factor in skeletal muscle1. Animal models of FSHD are hampered by incomplete knowledge of the conservation of the DUX4 transcriptional program in other species. Despite divergence of their binding motifs, both mouse Dux and human DUX4 activate genes associated with cleavage-stage embryos, including MERV-L and ERVL-MaLR retrotransposons, in mouse and human muscle cells respectively. When expressed in mouse cells, human DUX4 maintained modest activation of cleavage-stage genes driven by conventional promoters, but did not activate MERV-L-promoted genes. These findings indicate that the ancestral DUX4-factor regulated genes characteristic of cleavage-stage embryos driven by conventional promoters, whereas divergence of the DUX4/Dux homeodomains correlates with retrotransposon specificity. These results provide insight into how species balance conservation of a core transcriptional program with innovation at retrotransposon promoters and provide a basis for animal models that recreate the FSHD transcriptome. Overall design: We generated one new ChIP-seq dataset in mouse myoblasts and compared it to a published ChIP-seq dataset for human DUX4 expressed in human myoblasts (GSE33838; 10.1016/j.devcel.2011.11.013). This new dataset was generated from a monoclonal cell line using a doxycycline-inducible system and a MMH transgene. MMH is a chimeric gene whose N-terminus is codon-altered mouse Dux through the mouse Dux homeodomains and its C-terminus is codon-altered human DUX4 starting just after human DUX4''s homeodomains. The MMH-chimera maintained the DNA binding domain of Dux and the carboxy-terminal epitopes of DUX4, permitting us to use the same DUX4 antisera to immunoprecipitate the MMH-chimera and DUX4. For MMH peaks, we compared MMH-expresssing cells at 18-hours of induction immunoprecipitated with a 50:50 mixture of the DUX4 antibodies MO488 and MO489 to MMH-expressing cells immunoprecipitated with an antibody to GFP, which was not present in these cells.