Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
Cell. 2012 Jun 22;149(7):1622-34. doi: 10.1016/j.cell.2012.04.041.
Pseudogene transcripts can provide a novel tier of gene regulation through generation of endogenous siRNAs or miRNA-binding sites. Characterization of pseudogene expression, however, has remained confined to anecdotal observations due to analytical challenges posed by the extremely close sequence similarity with their counterpart coding genes. Here, we describe a systematic analysis of pseudogene "transcription" from an RNA-Seq resource of 293 samples, representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific. Further, we explore disease subtype specificity and functions of selected expressed pseudogenes. Taken together, we provide evidence that transcribed pseudogenes are a significant contributor to the transcriptional landscape of cells and are positioned to play significant roles in cellular differentiation and cancer progression, especially in light of the recently described ceRNA networks. Our work provides a transcriptome resource that enables high-throughput analyses of pseudogene expression.
假基因转录本可以通过生成内源性 siRNA 或 miRNA 结合位点提供新的基因调控层次。然而，由于与相应编码基因具有极高的序列相似性，因此分析假基因表达仍然受到限制，仅限于偶然观察。在这里，我们描述了对来自 293 个样本的 RNA-Seq 资源中假基因“转录”的系统分析，这些样本代表 13 种癌症和正常组织类型，观察到假基因在全基因组范围内表达非常普遍，可以归类为普遍表达或谱系和/或癌症特异性。此外，我们还探索了选定表达假基因的疾病亚型特异性和功能。总之，我们提供的证据表明，转录的假基因是细胞转录景观的重要贡献者，并有可能在细胞分化和癌症进展中发挥重要作用，尤其是在最近描述的 ceRNA 网络的背景下。我们的工作提供了一个转录组资源，可实现假基因表达的高通量分析。
