An important issue in developmental biology is the identification of homeop
rotein target genes. We have developed a strategy based on the internalizat
ion and nuclear addressing of exogenous homeodomains, using an engrailed ho
meodomain (EnHD) to screen an embryonic stem (ES) cell gene trap library. E
ight integrated gene trap loci responded to EnHD. One is within the bullous
pemphigoid antigen 1 (BPAG1) locus, in a region that interrupts two neural
isoforms. By combining in vivo electroporation with organotypic cultures,
we show that an already identified BPAG1 enhancer/promoter is differentiall
y regulated by homeoproteins Hoxc-8 and Engrailed in the embryonic spinal c
ord and mesencephalon. This strategy can therefore be used for identifying
and mutating homeoprotein targets. Because homeodomain third helices can in
ternalize proteins, peptides, phosphopeptides, and antisense oligonucleotid
es, this strategy should be applicable to other intracellular targets for c
haracterizing genetic networks involved in a large number of physiopatholog
ical states.