Systems analysis of RNA-binding proteins and regulatedmRNA processing

RNA-binding proteins (RBPs) impact the abundance, architecture, and cellular localization of mRNA transcripts. These gene regulators account for many distinctive features of RNA processing in cells of the vertebrate brain. Furthermore, the mRNA processing events that render diversity in transcript architecture are paramount to generating the protein complement of neural cells. Currently, numerous studies have examined neural RBPs or mRNAs in singular contexts. Despite the importance of mRNA regulation however, few studies have examined neural mRNA diversity or mRNA regulators on a whole-genome level. Here, we employed two genome-scale approaches to investigate either RBPs or mRNA regulation in neural systems. We utilized gene and protein repositories to first identify nearly 400 RBPs. To then gain a systems perspective of neural RBP expression, we characterized this functional class of proteins in the developing nervous system through in situ hybridization analysis. The evaluation of RBPs for their expression in discrete neural structures revealed that the majority are not uniformly expressed, but show regional distribution, with many RBP genes exhibiting a similar pattern of neural expression. These data are consistent with a consensus that the expression levels of RBPs are differentially regulated, perhaps in a cell type manner, and support the idea that multiple RBPs function concurrently. In addition to assessing the global properties that emerge from this system, we extended our studies to resolve the behavior of an individual RBP. Separately, we used exon-centric microarrays to examine global changes in transcript abundance and architecture that arise during changing intracellular conditions in a model of neural excitation. The evaluation of exon behavior for thousands of transcripts across a 24 hour time course revealed that both individual exons and whole transcripts are subject to stimulus-induced regulation. Assessments of affected transcripts revealed modulation within distinct functional gene categories, including Ca 2+ -ion binding, calmodulin-binding, plasma membrane-associated, and metabolic proteins. These data suggest that changes in transcript and exon abundance are reflective of a coordinated gene expression response to changing cellular conditions. In sum, our data provide a systems-level perspective of mRNA regulation and RBP expression in the context of mammalian neural cells.