Experiments in mouse embryos (Frasch et al. 1995, Dupe et al. 1997, Paschaki et al. 2013), embryonal carcinoma cell lines (Langston and Gudas 1992, Langston et al. 1997, Gillespie and Gudas 2007, Kashyap and Gudas 2010), and embryonic stem cells (Lee et al. 2007, Chen and Reese 2011, Kashyap et al. 2011, Mazzoni et al. 2013) indicate retinoic acid binds the Rara or Rarg receptor in a RAR:RXR dimer bound to the 3' region of Hoxa1 and causes activation of Hoxa1 expression. Hoxa1 in turn binds and activates the promoter of the Raldh2 gene to create a feedback loop that maintains retinoic acid synthesis (Vitobella et al. 2011).
Observations in embryonic carcinoma cells indicate the mechanism of activation of retinoic acid receptors proceeds through ligand-dependent release (dismissal) of corepressors such as Ncor1, Ajuba, and Hdac3 followed by recruitment of coactivators such as Ncoa3 and Ep300 (p300) (Horlein et al. 1995, Perissi et al. 2004, Gillespie and Gudas 2007, Hou et al. 2010, Kashyap and Gudas 2010, Bajpe et al. 2013). During activation by retinoic acid chromatin in the region of the Hoxa1 gene is modified from a bivalent state to an active conformation by losing methylation at lysine-27 of histone H3 and associated polycomb repressive proteins (Gillespie and Gudas 2007, Lee et al. 2007, Kashyap and Gudas 2010, Kashyap et al. 2011, Mazzoni et al. 2013). Though experiments with cultured human cells show KDM6A (UTX) and KDM6B (JMJD3) actively demethylate H3K27me3, mouse embryos that lack both Kdm6a and Kdm6b still show loss of H3K27me3 during activation of Hox genes in embryos (Shpargel et al. 2014), therefore other factors may also participate in loss of H3K27me3. A loss of histone deacetylases (HDAC1,2,3) and a gain of histone acetylation (Lee et al. 2007, Urvalek and Gudas 2014) and H3K4me3 (Kashyap et al. 2011) is also associated with activation of Hoxa1 in embryonic stem cells. The Mll2 complex acetylates H3K4 at Hoxa1 in fibroblasts (Wang et al. 2009).
Expression of Hoxa1 occurs in the neural tube, adjacent mesenchyme, paraxial mesoderm, somites, and gut epithelium from the the border between rhombomeres 3 and 4 (r3/r4) to the caudal-most region of the embryo (Baron et al. 1987, Sundin et al, 1990, Murphy and Hill 1991, Godwin et al. 1998, reviewed in Alexander et al. 2009). Prior to formation of rhombomeres, Hoxa1 is expressed weakly in the region of the embryo that will become rhombomere 2 (r2) and strongly in the region that will become r3-7. Expression is transient and ceases by the time rhombomeres form. (Rhombomeres are transiently formed segments in the neural tube that will eventually form the hindbrain.)