Do Housekeeping Genes Exist?

Abstract

The searching of human housekeeping (HK) genes has been a long quest since the emergence of transcriptomics, and is instrumental for us to understand the structure of genome and the fundamentals of biological processes. The resolved genes are frequently used in evolution studies and as normalization standards in quantitative gene-expression analysis. Within the past 20 years, more than a dozen HK-gene studies have been conducted, yet none of them sampled human tissues completely. We believe an integration of these results will help remove false positive genes owing to the inadequate sampling. Surprisingly, we only find one common gene across 15 examined HK-gene datasets comprising 187 different tissue and cell types. Our subsequent analyses suggest that it might not be appropriate to rigidly define HK genes as expressed in all tissue types that have diverse developmental, physiological, and pathological states. It might be beneficial to use more robustly identified HK functions for filtering criteria, in which the representing genes can be a subset of genome. These genes are not necessarily the same, and perhaps need not to be the same, everywhere in our body.

Verification of suitable and reliable reference genes for quantitative real-time PCR during adipogenic differentiation in porcine intramuscular stromal-vascular cells

“…The ICGs selected can significantly influence the results obtained. However, increasing evidence has shown that all of existing ICGs may vary depending the state of the cell or tissue, age and other experimental conditions (Zhang et al, 2015). Up to now, although numerous qPCR analyses have been conducted to improve IMF content, a through test for the expression stability of Figure 3 Determination of the optimal number of internal control genes for normalization as assessed by geNorm.…”

“…GeNorm and NormFinder are two of the most commonly used method to screen stable ICGs required for qPCR normalization (Zhang et al, 2015). GeNorm identifies the most suitable genes by calculating the gene stability measure (M) values, which indicate the changes in gene expression with respect to other genes.…”

Membrane gene ontology bias in sequencing and microarray obtained by housekeeping-gene analysis

“…We compiled 12,501 HK genes from 15 studies using either MA or sequencing based transcriptomic techniques [12] in which we removed 13 genes annotated to Homo…”

“…ACCEPTED MANUSCRIPT 16 was much more sensitive and identified genes with much less expression levels [12].…”

“…These studies address gene expression at the entire organismal level. Not only that any gene in HK-gene studies was derived from repeated analysis of a broad collection of different A C C E P T E D M A N U S C R I P T ACCEPTED MANUSCRIPT 5 organs, tissues, and cell types [10,11], such that these identifications (often derived from more than a hundred runs) are very reliable; but also that if the studying species is the same, these genes are comparable [12]. Therefore HK genes are ideal candidates for examining the differences in MA and sequencing analyses.…”