Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation.
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation.
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DOI：
10.1371/journal.pone.0007479
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发表时间：
2009-10-16
期刊：
影响因子：
3.7
通讯作者：
Graber JH
中科院分区：
文献类型：
--
作者：
Salisbury J;Hutchison KW;Wigglesworth K;Eppig JJ;Graber JH
基因表达微阵列提供了许多见解，在不同组织类型，发育阶段和疾病状态之间的基因表达模式的变化。对这些数据的分析主要集中在测量基因转录物的相对丰度，同时将大多数或所有转录物同种型视为等同物。然而，转录异构体之间的选择差异可以代表蛋白质产物或转录后转录调控的关键变化。对现有微阵列数据的新分析为全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加工的差异，主要影响3′-非翻译区。以取自小鼠卵母细胞发育转录沉默期的微阵列为例，探针水平分析（此处作为rmodel实现）识别了转录亚型具有不同稳定性的基因。微阵列测量寡聚脱氧胸苷和随机引物产生的cDNA的比较揭示了进一步的差异，在多聚腺苷酸化状态的一些成绩单。额外的分析提供了序列靶向切割的证据，包括推定的靶向序列，作为成熟卵母细胞中数百个转录物的降解机制之一。证明了探针水平分析从现有表达微阵列数据中引出新发现的能力。成熟小鼠卵母细胞中转录异构体之间稳定性差异的表征提供了一些降解的机制细节。对表达微阵列数据的现有档案进行类似分析可能会提供类似的发现。
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.
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影响因子：
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影响因子：
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