Retinoic acid activates the Hoxd4 gene in rhombomere 7 (r7) of embryos by binding Rarb (Folberg et al. 1999, Serpente et al. 2005), Rara, or Rarg (Wendling et al. 2001) in Rar:Rxr receptor dimers bound to a retinoic acid response element (RARE) in the 5' flanking region of the gene (Popperl and Featherstone 1993, Folberg et al. 1997, Zhang et al. 1997, Zhang et al. 2000, Wendling et al. 2001, Nolte et al. 2003). Ligand binding by retinoic acid receptors causes dismissal of corepressors such as Ncor1 and recruitment of coactivators such as Ncoa3 (Horlein et al. 1995, inferred from Hoxa1 in Gillespie and Gudas 2007, Kashyap and Gudas 2010). Pax6 binds near the RARE and is required for maximal activation (Nolte et al. 2006).
Activation of chromatin at Hoxd4 is accompanied by loss of methylation at lysine-27 (H3K27me3) and gain of H3K4me3 (Rastegar et al. 2012, Williamson et al. 2012, Mazzoni et al. 2013). The Mll2 complex methylates H3K4 at Hoxd4 in fibroblasts (Wang et al. 2009). In human cells the histone demethylase KDM6A (UTX) binds HOXD4 and may participate in demethylating H3K27me3. Other factors may also be involved in histone demethylation. Polycomb repressive complex 2 (PRC2), which binds H3K27me3, and Pcgf2 (Mel18) also dissociate (Kobrossy et al. 2006, Mazzoni et al. 2013). YY1, however, remains associated even after treatment with retinoic acid (Kobrossy et al. 2006). After activation by retinoic acid, Hoxd4 maintains its own expression by binding and activating its own promoter (Kobrossy et al. 2006).