Expressed pseudogenes in the transcriptional landscape of human cancers.
Expressed pseudogenes in the transcriptional landscape of human cancers.
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DOI：
10.1016/j.cell.2012.04.041
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发表时间：
2012-06-22
期刊：
影响因子：
64.5
通讯作者：
Chinnaiyan AM
中科院分区：
文献类型：
--
作者：
Kalyana-Sundaram S;Kumar-Sinha C;Shankar S;Robinson DR;Wu YM;Cao X;Asangani IA;Kothari V;Prensner JR;Lonigro RJ;Iyer MK;Barrette T;Shanmugam A;Dhanasekaran SM;Palanisamy N;Chinnaiyan AM
假基因转录物可以通过产生内源性siRNA或miRNA结合位点提供新的基因调控层。然而，假基因表达的表征仍然局限于轶事观察，这是由于与其对应的编码基因的极其接近的序列相似性所带来的分析挑战。在这里，我们描述了对来自293个样本（代表13种癌症和正常组织类型）的RNA-Seq资源的假基因“转录”的系统分析，并观察到假基因的惊人普遍的全基因组表达，这些假基因可以被归类为普遍表达或谱系和/或癌症特异性。此外，我们探索疾病亚型特异性和功能的选择表达的假基因。总之，我们提供的证据表明，转录的假基因是一个显着的贡献者的转录景观的细胞，并定位在细胞分化和癌症进展中发挥重要作用，特别是在最近描述的ceRNA网络。我们的工作提供了一个转录组资源，使高通量分析假基因表达。
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.
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