Analysis of SAGE data in human platelets: Features of the transcriptome in an anucleate cell
Analysis of SAGE data in human platelets: Features of the transcriptome in an anucleate cell
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DOI：
10.1160/th05-11-0764
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发表时间：
2006-04-01
影响因子：
6.7
通讯作者：
Dandekar, T
中科院分区：
文献类型：
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作者：
Dittrich, M;Birschmann, I;Dandekar, T
建立了一个完整的人血小板基因表达系列分析（SAGE）文库。对25，000个标签进行了测序，去除线粒体标签后，保留了12，609个（51%）非线粒体衍生的标签，对应于2，300个不同的转录本，表达水平高达每百万个30，000个标签。这个新的、高度纯化的血小板SAGE文库富含特异性转录物。标签分布的复杂性类似于仍然能够通过转录补充其mRNA库的细胞。我们表明，我们的SAGE数据与最近发表的微阵列数据一致，但显示了血小板转录组的进一步细节，包括（i）较长的UTR区域和富集的mRNA中更稳定的折叠，（ii）生物学上有趣的新候选mRNA，其显示调控元件，包括RNA稳定或翻译控制元件，和（iii）特异性，与来自其他组织的一组SAGE文库相比，高转录的mRNA。在已知参与mRNA定位和翻译控制的几种调控mRNA元件中，CPE元件特别富集在血小板转录组中。发现先前报道的受抑制调节的mRNA存在于文库中，并通过实时PCR进行验证。此外，特定的分子功能，如信号转导活性被发现显着丰富的血小板转录组。这些发现强调了血小板转录组的丰富性和多样性。
A comprehensive SAGE (serial analysis of gene expression) library of purified human platelets was established. Twenty-five thousand (25,000) tags were sequenced, and after removal of mitochondrial tags, 12,609 (51%) non-mitochondrial-derived tags remained, corresponding to 2,300 different transcripts with expression levels of up to 30,000 tags per million. This new, highly purified SAGE library of platelets is enriched in specific transcripts. The complexity in terms of tag distribution is similar to cells that are still able to replenish their mRNA pool by transcription. We show that our SAGE data are consistent with recently published microarray data but show further details of the platelet transcriptome, including (i) longer UTR regions and more stable folding in the enriched mRNAs, (ii) biologically interesting new candidate mRNAs that show regulatory elements, including elements for RNA stabilization or for translational control, and (iii) significant enrichment of specific, highly transcribed mRNAs compared to a battery of SAGE libraries from other tissues. Among several regulatory mRNA elements known to be involved in mRNA localization and translational control, CPE elements are in particular enriched in the platelet transcriptome. mRNAs previously reported to be translationally regulated were found to be present in the library and were validated by real-time PCR. Furthermore, specific molecular functions such as signal transduction activity were found to be significantly enriched in the platelet transcriptome. These findings emphasize the richness and diversity of the platelet transcriptome.