Genes related to neurodevelopment and HPA axis regulation are commonly altered in both developmental stress and alcohol models. Clustered protocadherin genes are important for establishing neuronal identity in the developing brain and can be epigenetically regulated by prenatal alcohol exposure or adverse maternal care (Chater-Diehl et al., 2016; Laufer et al., 2015; Laufer et al., 2013; McGowan et al., 2011). Protocadherin expression has been implicated in neurodevelopmental disorders, including schizophrenia, due to changes in axonal guidance and cortical folding (Gregório et al., 2009; Hirabayashi and Yagi, 2014). Protocadherin genes are also regulated by CCCTC-binding factor (CTCF), a transcription factor downregulated in somatic DNA of offspring following paternal drinking (Knezovich and Ramsay, 2012).