Abstract
BackgroundGene expression microarrays have provided many insights into changes in gene expression patterns between different tissue types, developmental stages, and disease states. Analyses of these data focused primarily measuring the relative abundance of transcripts of a gene, while treating most or all transcript isoforms as equivalent. Differences in the selection between transcript isoforms can, however, represent critical changes to either the protein product or the posttranscriptional regulation of the transcript. Novel analyses on existing microarray data provide fresh insights and new interpretations into transcriptome-wide changes in expression.MethodologyA probe-level analysis of existing gene expression arrays revealed differences in mRNA processing, primarily affecting the 3′-untranslated region. Working with the example of microarrays drawn from a transcriptionally silent period of mouse oocyte development, probe-level analysis (implemented here as rmodel) identified genes whose transcript isoforms have differing stabilities. Comparison of micorarrays measuring cDNA generated from oligo-dT and random primers revealed further differences in the polyadenylation status of some transcripts. Additional analysis provided evidence for sequence-targeted cleavage, including putative targeting sequences, as one mechanism of degradation for several hundred transcripts in the maturing oocyte.ConclusionsThe capability of probe-level analysis to elicit novel findings from existing expression microarray data was demonstrated. The characterization of differences in stability between transcript isoforms in maturing mouse oocytes provided some mechanistic details of degradation. Similar analysis of existing archives of expression microarray data will likely provide similar discoveries.
Highlights
Gene expression microarrays and isoforms The presence of alternative transcript isoforms can complicate the interpretation of gene expression microarray data [1,2]
The characterization of differences in stability between transcript isoforms in maturing mouse oocytes provided some mechanistic details of degradation
Probeset re-mapping efforts in recent years have focused on identifying the unique probes that map to gene regions that are constitutively expressed across tissues and developmental stages [4]
Summary
Gene expression microarrays and isoforms The presence of alternative transcript isoforms can complicate the interpretation of gene expression microarray data [1,2]. Probeset re-mapping efforts in recent years have focused on identifying the unique probes that map to gene regions that are constitutively expressed across tissues and developmental stages [4] These updated probesets have led to improved gene expression interpretation [4,5,6], they can mask potentially critical changes in expression that are manifested as changes in isoform rather than total transcript abundance. Gene expression microarrays have provided many insights into changes in gene expression patterns between different tissue types, developmental stages, and disease states Analyses of these data focused primarily measuring the relative abundance of transcripts of a gene, while treating most or all transcript isoforms as equivalent. Novel analyses on existing microarray data provide fresh insights and new interpretations into transcriptome-wide changes in expression
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