Details:

Alternative Title:
BMC Genomics
Personal Author:
Whistler, Toni ; Chiang, Cheng-Feng ; Lonergan, William ; Hollier, Mark ; Unger, Elizabeth R
Whistler, Toni ; Chiang, Cheng-Feng ; Lonergan, William ; Hollier, Mark ; Unger, Elizabeth R Less -
Description:
Background

The contribution of alternative splicing and isoform expression to cellular response is emerging as an area of considerable interest, and the newly developed exon arrays allow for systematic study of these processes. We use this pilot study to report on the feasibility of exon array implementation looking to replace the 3' in vitro transcription expression arrays in our laboratory.

Results

Peripheral blood mononuclear cells form healthy donors were activated using phytohemagglutinin, IL2 and ionomycin and harvested at 5 points over a 7 day period. Flow cytometry measured cell cycle events and the Affymetrix exon array platform was used to identify the gene expression and alternate exon usage changes. Gene expression changes were noted in a total of 2105 transcripts, and alternate exon usage identified in 472 transcript clusters. There was an overlap of 263 transcripts which showed both differential expression and alternate exon usage over time. Gene ontology enrichment analysis showed a broader range of biological changes in biological processes for the differentially expressed genes, which include cell cycle, cell division, cell proliferation, chromosome segregation, cell death, component organization and biogenesis and metabolic process ontologies. The alternate exon usage ontological enrichments are in metabolism and component organization and biogenesis. We focus on alternate exon usage changes in the transcripts of the spliceosome complex. The real-time PCR validation rates were 86% for transcript expression and 71% for alternate exon usage.

Conclusions

This study illustrates that the Exon array technology has the potential to provide information on both transcript expression and isoform usage, with very little increase in expense.


Subjects:
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Alternative Splicing Apoptosis Cell Cycle Cell Proliferation Cluster Analysis Exons Female Flow Cytometry Gene Expression Profiling Genome, Human Humans Lymphocyte Activation Lymphocyte Subsets Middle Aged Oligonucleotide Array Sequence Analysis Phytohemagglutinins Polymerase Chain Reaction Quality Control Reproducibility Of Results RNA, Messenger Spliceosomes T-Lymphocytes
Source:
BMC Genomics. 2010; 11:496.
Document Type:
Journal Article
Collection(s):
CDC Public Access
Main Document Checksum:
[+]
urn:sha256:44e78459649a34898a7e8ad42b1d5f0aae7a07a19758175f1488074d66b9bdd0
Download URL:
https://stacks.cdc.gov/view/cdc/3363/cdc_3363_DS1.pdf
File Type:

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