Sequence analysis and expression mapping of the rat clustered protocadherin gene repertoires

Three closely-linked clusters of protocadherin (Pcdh) genes (alpha, beta, and gamma) encoding more than 50 distinct mRNAs have been identified in humans and mice, and proposed to play important roles in neuronal connectivity in the CNS. The human and mouse Pcdh alpha and gamma clusters each span a region of about 300 kb genomic DNA, and are each organized into a tandem array of more than a dozen highly-similar "variable" exons, and three downstream "constant" exons. Little is known about the expression patterns of the alpha and gamma repertoires in the CNS. Here, we comprehensively analyzed the one megabase rat Pcdh genomic DNA sequences at the nucleotide level using various computational methods. We found that the clustered rat Pcdh genes display strict orthologous relationships with those of mice but not humans. Moreover, each rat Pcdh variable exon is preceded by a distinct promoter. We designed two complete sets of isoform-specific probes and extensively mapped the expression patterns for each member of the alpha and gamma repertoires in the adult rat CNS by non-isotopic in situ hybridization experiments. We found that most alpha and gamma mRNA isoforms are broadly expressed in similar patterns in subsets of cells (with some displaying interesting cortical layer-specific expression) throughout various CNS regions, including the olfactory bulb, cerebral cortex, hippocampus, cerebellum, and spinal cord. The broad expression of most alpha or gamma mRNAs throughout various regions of the CNS is consistent with the hypothesis that these genes may be used for neurons to establish their individuality and also provide the adhesive diversity required for complex synaptic connectivity in the mammalian CNS.