In mouse embryos (Marshall et al. 1994, Studer et al. 1994, Wendling et al. 2001, Huang et al. 2002, Roelen et al. 2002), carcinoma cell lines (Ogura and Evans 1995, Chiba et al. 1997, Langston et al. 1997), and embryonic stem cells (Kashyap et al. 2011, Mazzoni et al. 2013) retinoic acid activates Hoxb1 by binding receptors, Rara or Rarg (in embryos in Wendling et al. 2001, in embryonal carcinoma cells in Chiba et al. 1997), at retinoic acid response elements (RAREs) located 3' to the Hoxb1 gene (Marshall et al. 1994, Ogura and Evans 1995, Langston et al. 1997, Huang et al. 2002) and 5' to the Hoxb1 gene (Ogura et al. 1995), causing dismissal of corepressors, recruitment of coactivators, and alteration of chromatin to an active conformation (inferred from Hoxa1, Gillespie and Gudas 2007, Kashyap and Gudas 2010).
In human cells, KDM6A (UTX) binds the HOXB1 gene upon retinoic acid treatment and may demethylate trimethylated lysine-27 of histone H3 (H3K27me3). Demethylation of H3K27me3 at the Hoxb cluster is similarly observed in mouse embryonic stem cells treated with retinoic acid (Kashyap et al. 2011, Mazzoni et al. 2013). Other factors may also cause demethylation of H3K27me3 (Shpargel et al. 2014). Polycomb repressive complex 2 (PRC2), which binds H3K27me3, is also lost during activation (Mazzoni et al. 2013). In human cells KDM6A associates with the methyltransferases KMT2C,D (MLL2,3) which may participate in methylating histone H3 at lysine-4 (H3K4me3), an activating chromatin modification. Gain of H3K4me3 is also observed in mouse embryonic stem cells (Kashyap et al. 2011). The Mll2 complex methylates H3K4 at Hoxb1 in mouse fibroblasts (Wang et al. 2009). In mouse embryos Hoxa1 synergizes with retinoic acid to activate Hoxb1 (Studer et al. 1998, Gavalas et al. 1998). After activation by retinoic acid, Hoxb1 maintains its own expression by forming a ternary Hoxb1:Pknox1:Pbx1 (Hoxb1:Prep1:Pbx1) complex at elements in its own promoter and activating expression (Ogura and Evans 1995, Di Rocco et al. 1997, Ferretti et al. 2005).
Hoxb1 is expressed in mesoderm and neurectoderm of primitive streak stage embryos and then becomes restricted to rhombomeres of the hindbrain (Murphy et al. 1989, Wilkinson et al. 1989, Bogue et al. 1996). Before rhombomere formation Hoxb1 is initially expressed weakly in the region that will become rhombomere 2 (r2) and strongly in the region that becomes r3-7. After rhombomere formation Hoxb1 becomes restricted to r4 and is also observed in caudal mesoderm (Murphy et al. 1989, Arenkiel et al. 2003). Hoxb1 activates expression of Egr2 (Krox20, Wassef et al. 2008), a transcription factor that subsequently activates Hoxa2, Hoxb2, and Hoxb3 but represses Hoxb1.