Identification of candidate genes for controlling development of the basilar pons by differential display PCR

The basilar pons, a major hindbrain nucleus involved in sensory-motor integ ration, has become a model system for studying long-distance neuronal migra tion, axon-target recognition by collateral branching, and the formation of patterned axonal projections. To identify genes potentially involved in th ese developmental events, we have performed a differential display PCR scre en comparing RNA isolated from the developing basilar pons with RNA obtaine d from developing cerebellum and olfactory bulb, as well as the mature basi lar pons. Using 400 different combinations of primers, we screened more tha n 11,000 labeled DNA fragments and identified 201 that exhibited higher exp ression in the basilar pons than in the control tissues. From these, 138 di stinct gene fragments were cloned. The differential expression of a large s ubset of these fragments was confirmed using RNase protection assays. In si tu hybridization analysis revealed that the expression of many of these gen es is limited to the basilar pons and only a few other brain regions, sugge sting that they may play specific roles in pontine development.