Calcium-induced transcript variation in neuronal cells analyzed with exon microarrays.

Background: Neuronal cells respond to changes in intracellular Ca2+ ([Ca2+]i) by affecting both the abundance and the architecture of specific mRNAs. While Ca2+-induced transcription and transcript variation have both been recognized as important sources of gene regulation, the interplay of these two phenomena has not been evaluated together on a genome scale. Results: Here, we show that exon-centric microarrays can be used to resolve the Ca2+-modulated gene expression response into transcript-level and exon-level regulation. Global assessments of affected transcripts reveal modulation within distinct functional gene categories. We find that transcripts containing Ca2+-modulated exons show enrichment for Ca2+-ion binding, calmodulin-binding, plasma membrane-associated, and metabolic proteins. Additionally, we uncover instances of regulated exon use in potassium channels, neuroendocrine secretory proteins, and in metabolic enzymes, and demonstrate that regulated changes in exon expression give rise to distinct transcript isoforms. Conclusions: Our findings connect extracellular stimuli to specific exon behavior and suggest that changes in transcript and exon abundance are reflective of a coordinated gene expression response to elevated [Ca2+]i. The technology we describe here lends itself readily to the resolution of stimulus-induced gene expression at both the transcript and exon levels. Keywords: Ca2+-modulated exons and transcripts Biological triplicate RNA samples are from untreated (ZERO) Human neuroblastoma IMR-32 cells (ATCC) and IMR-32 cells treated with 50 mM KCl for 0.5, 1.5, 3, 6, 12, or 24 hours, and exposed to 5µM thapsigargin (Tocris) for 24 hours (THAP).