Multiple forms of RNA processing significantly influence gene expression. Each processing step beyond transcription provides an additional opportunity for gene regulation. While the transcriptional control of gene expression has been a prime research focus for decades, post-transcriptional forms of gene regulation, particularly as they pertain to developmental and signal transduction programs, have been less well studied. My research addresses both the proteins involved in RNA processing as well as the regulation of RNA transcripts through alternative splicing.
With others in the lab, I performed an in situ hybridization screen to investigate the expression of 323 RBPs at two stages of development. We focused on RBP expression in the nervous system: as several neural-specific RBPs have critical functions in neural function, we wondered whether other, uncharacterized RBPs might have specific expression. We found that most of the RBPs profiled demonstrate spatially restricted expression in the brain. In performing our screen we included sections of whole head and upper thoracic tissues. As a result, we obtained information about RBP expression during craniofacial development. Indeed, two of the most specific RBPs we uncovered happen to be expressed in non-neural tissue. These genes exhibit restricted expression in separate and overlapping epithelial cell types. I am investigating these proteins in more detail using a combination of cell biology and protein biochemistry as well as expression studies of homologous genes in zebrafish.
My second project is focused on the phenomenon of stimulus-induced alternative splicing, which can rapidly produce ‘situation-specific’ proteins. This processes has been recognized in neuronal cells for a small number of genes (currently there are 4 reported in the literature), but has not been examined beyond a gene-by-gene approach. These data suggest that, much like transcription, alternative splicing is subject to modulation by signal transduction. I hypothesized that depolarization-induced alternative splicing is actually a widespread mechanism that acts as a dynamic molecular switch to modulate cellular activity in neural cells. To investigate this phenomenon on a genome scale, I am using newly-developed exon microarrays to explore the alternative use of exons in stimulated versus untreated neuroblastoma cells. My preliminary data has identified hundreds of predicted stimulus-regulated exons. I am currently validating candidate exons. Additionally, as the exon microarray provides a platform to assess gene expression, I am collaborating with bioinformaticists to examine changes in transcript levels upon depolarization.