To determine whether the expression of a common set of genes is altered in the two phenotypically indistinguishable mutants, we carried out deep sequencing (RNA-Seq) studies using embryonic spinal cords at E13.5, a developmental stage when neurogenesis is near completion (Nornes and Carry, 1978), but elevated apoptosis is not yet detected in the mutants (Prasad et al., 2008). Surprisingly, we observed no striking changes in global gene expression in either of the two mutants other than those in the Pcdh gene clusters themselves (Figures S4A-B and Table S1). In the case of Pcdhgdel/del mutants, the majority of Pcdhb genes are significantly upregulated, likely the consequence of the closer proximity of a Pcdhb cluster enhancer (HS16-20) located downstream of the Pcdhg cluster (Yokota et al., 2011), which is now repositioned ~300 kb closer to the Pcdhb cluster (Figures 4F–G). The largest increase in expression is observed with an EST gene (AK149307), which is located immediately upstream of the Pcdhg cluster (Figures 4F–G and Table S1). Sequence analyses revealed that this gene is a relic of the B-type Pcdhg isoforms, and its
