Exon expression profiling reveals stimulus-mediated exon use in neural cellsReport as inadecuate




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Genome Biology

, 8:R159

First Online: 02 August 2007Received: 15 February 2007Revised: 12 June 2007Accepted: 02 August 2007

Abstract

Background:Neuronal cells respond to changes in intracellular calcium Cai 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 Cai-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.

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 Cai. The technology we describe here lends itself readily to the resolution of stimulus-induced gene expression at both the transcript and exon levels.

AbbreviationsCaiintracellular Ca

ERendoplasmic reticulum

FDRfalse discovery rate

GOgene ontology, NMD, non-sense mediated decay

PTCpremature stop codon

TPGthapsigargin.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2007-8-8-r159 contains supplementary material, which is available to authorized users.

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Author: Adrienne E McKee - Nicola Neretti - Luis E Carvalho - Clifford A Meyer - Edward A Fox - Alexander S Brodsky - Pamela A

Source: https://link.springer.com/







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