The clustered protocadherin (Pcdh) genes appear to be the primary source of single cell diversity in the mammalian nervous system. The complex genetic organization of this gene cluster suggested that single cell diversity might arise through somatic recombination, akin to that found in Immunoglobulin and T-Cell receptors or through an alternative splicing mechanism similar to that found in Dscam in Drosophila Melanogaster. Surprisingly, Pcdh isoform diversity appears to be generated through a combination of stochastic promoter choice and alternative pre-mRNA splicing. This model for Pcdh diversity is based primarily on a limited amount of data from one neuronal sub-type. The primary objective of the current proposal is to develop and apply innovative single cell expression profiling and single molecule in situ detection methods to examine the validity and/or generality of this model, to study the complexity of Pcdh gene expression in multiple neuronal cell types and developmental stages, and to determine the time during neurogenesis that Pcdh promoter choice occurs.
The protocadherin gene cluster has been implicated in neural circuit assembly, and with mood disorders and autism, making a detailed study of its regulation during neural development of paramount importance. In this study, we propose to develop and apply single cell RNA-seq methods to the problem of Pcdh promoter choice.