The genetic pathways underlying shoulder blade development are largely unknown, 
as gene networks controlling limb morphogenesis have limited influence on 
scapula formation. Analysis of mouse mutants for Pbx and Emx2 genes has 
suggested their potential roles in girdle development. In this study, by 
generating compound mutant mice, we examined the genetic control of scapula 
development by Pbx genes and their functional relationship with Emx2. Analyses 
of Pbx and Pbx1;Emx2 compound mutants revealed that Pbx genes share overlapping 
functions in shoulder development and that Pbx1 genetically interacts with Emx2 
in this process. Here, we provide a biochemical basis for Pbx1;Emx2 genetic 
interaction by showing that Pbx1 and Emx2 can bind specific DNA sequences as 
heterodimers. Moreover, the expression of genes crucial for scapula development 
is altered in these mutants, indicating that Pbx genes act upstream of essential 
pathways for scapula formation. In particular, expression of Alx1, an effector 
of scapula blade patterning, is absent in all compound mutants. We demonstrate 
that Pbx1 and Emx2 bind in vivo to a conserved sequence upstream of Alx1 and 
cooperatively activate its transcription via this potential regulatory element. 
Our results establish an essential role for Pbx1 in genetic interactions with 
its family members and with Emx2 and delineate novel regulatory networks in 
shoulder girdle development.