Abstract
Housekeeping (HK) genes fulfill the basic needs for a cell to survive and function properly. Their ubiquitous expression, originally thought to be constant, can vary from tissue to tissue, but this variation remains largely uncharacterized and it could not be explained by previously identified properties of HK genes such as short gene length and high GC content. By analyzing microarray expression data for human genes, we uncovered a previously unnoted characteristic of HK gene expression, namely that the ranking order of their expression levels tends to be preserved from one tissue to another. Further analysis by tensor product decomposition and pathway stratification identified three main factors of the observed ranking preservation, namely that, compared to those of non-HK (NHK) genes, the expression levels of HK genes show a greater degree of dispersion (less overlap), stableness (a smaller variation in expression between tissues), and correlation of expression. Our results shed light on regulatory mechanisms of HK gene expression that are probably different for different HK genes or pathways, but are consistent and coordinated in different tissues.
Highlights
Housekeeping (HK) genes are defined as genes that are permanently activated throughout the life cycle of the cell [1]
Activation or modulation of regulatory events triggered by different stimuli, such as hormones, transcription factors, or other environmental changes, results in different levels of expression of the same gene in different cells or tissues and, one would not necessarily expect tissue-wide gene expression profiles to exhibit a preserved ranking order
In this study, we showed that the ranking order for the expression levels of the HK genes was significantly more preserved than that of the NHK genes in human tissues (Figure 1; Table 1)
Summary
Housekeeping (HK) genes are defined as genes that are permanently activated throughout the life cycle of the cell [1]. As they constitute the basic transcriptome for maintaining cellular functions for cell survival, HK genes are called maintenance genes [2]. Genes that participate in essential cellular processes can be considered to have HK functions. These include genes involved in transcription [3], translation [4,5], energy production and transmission [6,7], and maintaining cell organization, shape, and motility [8]. In disease states, such as liver and breast tumors, HK genes can exhibit very different expression patterns from those observed in normal tissues [15]
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