Exon expression profiling reveals stimulus-mediated exon use in neural cells
McKee, Adrienne E
Carvalho, Luis E
Brodsky, Alexander S
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CitationMcKee, Adrienne E., Nicola Neretti, Luis E. Carvalho, Clifford A. Meyer, Edward A. Fox, Alexander S. Brodsky, and Pamela A. Silver. 2007. Exon expression profiling reveals stimulus-mediated exon use in neural cells. Genome Biology 8(8): R159.
AbstractBackground: Neuronal cells respond to changes in intracellular calcium ([Ca2+]i) by affecting both
the abundance and architecture of specific mRNAs. Although calcium-induced transcription and
transcript variation have both been recognized as important sources of gene regulation, the
interplay between these two phenomena has not been evaluated on a genome-wide scale.
Results: Here, we show that exon-centric microarrays can be used to resolve the [Ca2+]imodulated
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 calcium-modulated exons exhibit enrichment for calcium 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 metabolic enzymes, and demonstrate that regulated changes in exon expression give rise to
distinct transcript variants.
Conclusion: 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.
Citable link to this pagehttp://nrs.harvard.edu/urn-3:HUL.InstRepos:4889588