As inferred from mouse embryos and cell lines, retinoic acid binds the RARA or RARG receptor in a RAR:RXR dimer bound to the 3' region of HOXA1. Ligand binding by retinoic acid receptors causes dismissal of corepressors such as NCOR1 (Klein et al. 2000), recruitment of coactivators such as NCOA3, and alteration of chromatin at the HOXA1 gene to an active conformation. Similar activation of HOXA1 is also observed in vitro in human breast cancer cells (Chariot et al. 1995). In mouse and Xenopus Hoxa1 acts in a feedback loop to maintain retinoic acid synthesis by directly binding and activating the promoter of the Raldh2 gene.
In addition to recruiting transcription coactivators, retinoic acid also appears to affect histone modifications and DNA methylation. In human embryonal carcinoma cells, KDM6A (UTX) binds the HOXA1 gene upon retinoic acid treatment and demethylates trimethylated lysine-27 of histone H3 (H3K27me3) (Lee et al. 2007). Reduced H3K27me3 is also observed at HOXA1 in lung fibroblasts (Lan et al. 2007). Experiments with mouse embryos lacking Kdm6a and Kdm6b indicate other factors also participate in demethylation of H3K27me3 (Shpargel et al. 2014). Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation by retinoic acid (inferred from mouse cells and also observed in human embryonal carcinoma cells, Lee et al. 2007, Sessa et al. 2007). KDM6A forms complexes with the histone methyltransferases KMT2C,D (MLL2,3) (Lee et al. 2007) which may participate in methylating histone H3 at lysine-4 (H3K4me3), an activating chromatin modification. At the 3' end of the HOXA cluster 5-methylcytosine in CG-rich regions is converted to 5-hydroxymethylcytosine by TET2 during retinoic acid induced differentiation of embryonal carcinoma cells (Bocker et al. 2012). During retinoic acid activation of HOXA genes in human monocytic leukemia cells the HOXA cluster is unfolded and its chromosomal domain is repositioned within the nucleus (Rousseau et al. 2014). Similar large-scale rearrangements may occur during embryogenesis.
In mouse embryos, expression of Hoxa1 occurs in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from rhombomere 4 to the caudal-most region of the embryo. (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)