Synnergren Jane, Giesler Theresa L, Adak Sudeshna, Tandon Reeti, Noaksson Karin, Lindahl Anders, Nilsson Patric, Nelson Deirdre, Olsson Björn, Englund Mikael C O, Abbot Stewart, Sartipy Peter
School of Humanities and Informatics, University of Skövde, P.O. Box 408, SE-541 28 Skövde, Sweden.
Stem Cells. 2007 Feb;25(2):473-80. doi: 10.1634/stemcells.2006-0247.
Housekeeping genes (HKGs) are involved in basic functions needed for the sustenance of the cell and are assumed to be constitutively expressed at a constant level. Based on these features, HKGs are frequently used for normalization of gene expression data. In the present study, we used the CodeLink Gene Expression Bioarray system to interrogate changes in gene expression occurring during differentiation of human ESCs (hESCs). Notably, in the three hESC lines used for the study, we observed that the RNA levels of 56 frequently used HKGs varied to a degree that rendered them inappropriate as reference genes. Therefore, we defined a novel set of HKGs specifically for hESCs. Here we present a comprehensive list of 292 genes that are stably expressed (coefficient of variation <20%) in differentiating hESCs. These genes were further grouped into high-, medium-, and low-expressed genes. The expression patterns of these novel HKGs show very little overlap with results obtained from somatic cells and tissues. We further explored the stability of this novel set of HKGs in independent, publicly available gene expression data from hESCs and observed substantial similarities with our results. Gene expression was confirmed by real-time quantitative polymerase chain reaction analysis. Taken together, these results suggest that differentiating hESCs have a unique HKG signature and underscore the necessity to validate the expression profiles of putative HKGs. In addition, this novel set of HKGs can preferentially be used as controls in gene expression analyses of differentiating hESCs.
管家基因（HKGs）参与细胞维持所需的基本功能，并被认为以恒定水平组成性表达。基于这些特性，HKGs经常用于基因表达数据的标准化。在本研究中，我们使用CodeLink基因表达生物芯片系统来研究人类胚胎干细胞（hESCs）分化过程中发生的基因表达变化。值得注意的是，在用于该研究的三个hESC系中，我们观察到56个常用HKGs的RNA水平变化程度使其不适宜作为参考基因。因此，我们专门为hESCs定义了一组新的HKGs。在此，我们列出了在分化的hESCs中稳定表达（变异系数<20%）的292个基因的综合列表。这些基因进一步被分为高表达、中等表达和低表达基因。这些新HKGs的表达模式与从体细胞和组织获得的结果几乎没有重叠。我们进一步在来自hESCs的独立公开可用基因表达数据中探索了这组新HKGs的稳定性，并观察到与我们的结果有很大相似性。通过实时定量聚合酶链反应分析确认了基因表达。综上所述，这些结果表明分化的hESCs具有独特的HKG特征，并强调了验证假定HKGs表达谱的必要性。此外，这组新的HKGs可优先用作分化hESCs基因表达分析的对照。
