Exon expression profiling reveals stimulus-mediated exon use in neural cells.
BACKGROUND
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+]i-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 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.


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.
McKee
Adrienne E
AE
Department of Systems Biology, 200 Longwood Avenue, Harvard Medical School, Boston, Massachusetts 02115, USA. adrienne_mckee@student.hms.harvard.edu
Neretti
Nicola
N
Carvalho
Luis E
LE
Meyer
Clifford A
CA
Fox
Edward A
EA
Brodsky
Alexander S
AS
Silver
Pamela A
PA
D017398:Alternative Splicing; D002118:Calcium / Q000378:metabolism* / Q000494:pharmacology; D020013:Calcium Signaling / Q000235:genetics*; D002135:Calcium-Binding Proteins / Q000235:genetics; D045744:Cell Line, Tumor; D002462:Cell Membrane / Q000187:drug effects; D005091:Exons / Q000235:genetics*; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D006801:Humans; D007473:Ion Channels / Q000235:genetics; D008564:Membrane Potentials / Q000187:drug effects; D009419:Nerve Tissue Proteins / Q000235:genetics; D009474:Neurons / Q000187:drug effects / Q000378:metabolism*; D009489:Neurosecretion / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D011189:Potassium Chloride / Q000494:pharmacology; D022821:RNA Splice Sites; D014158:Transcription, Genetic
D002135:Calcium-Binding Proteins; D007473:Ion Channels; D009419:Nerve Tissue Proteins; D022821:RNA Splice Sites; D011189:Potassium Chloride; D002118:Calcium