Functional Genomics PhD Program, University of Maine, Orono, Maine, United States of America.
PLoS One. 2009 Oct 16;4(10):e7479. doi: 10.1371/journal.pone.0007479.
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. 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.
A 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.
The 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.
基因表达微阵列为不同组织类型、发育阶段和疾病状态之间的基因表达模式变化提供了许多深入的了解。这些数据的分析主要集中在测量基因转录本的相对丰度上，而将大多数或所有转录本异构体视为等效。然而，转录本异构体之间选择的差异可能代表蛋白质产物或转录后调控的关键变化。对现有微阵列数据的新分析为整个转录组表达变化提供了新的见解和新的解释。
对现有基因表达阵列的探针水平分析揭示了 mRNA 处理的差异，主要影响 3'非翻译区。以从小鼠卵母细胞转录沉默期获得的微阵列为例，探针水平分析（此处实现为 rmodel）确定了其转录本异构体具有不同稳定性的基因。比较从 oligo-dT 和随机引物生成的 cDNA 测量的微阵列进一步揭示了一些转录物的聚腺苷酸化状态的差异。额外的分析提供了序列靶向切割的证据，包括一些假设的靶向序列，作为成熟卵母细胞中几百个转录物降解的一种机制。
证明了探针水平分析从现有表达微阵列数据中得出新发现的能力。成熟小鼠卵母细胞中转录本异构体稳定性差异的特征提供了降解的一些机制细节。对现有表达微阵列数据档案的类似分析可能会提供类似的发现。
