Housekeeping genes

Housekeeping genes are typically constitutive genes that are required for the maintenance of basal cellular functions that are essential for the existence of a cell, regardless of its specific role in the tissue or organism. Thus, they are expressed in all cells of an organism under normal and patho-physiological conditions, irrespective of tissue type, developmental stage, cell cycle state, or external signal. They gain scientific value in two ways. On the one hand they represent the minimal set of genes required to sustain life. On the other hand Housekeeping genes are widely used as internal controls for experimental studies1. The reliability of any relative RT-PCR experiment can be improved by including an invariant endogenous control (reference gene) in the assay to correct for sample to sample variations in RT-PCR efficiency and errors in sample quantification. A biologically meaningful reporting of target mRNA copy numbers requires accurate and relevant normalization to some standard and is strongly recommended in quantitative RT-PCR.

Characteristics and Issues with Housekeeping Genes

Figure 1: Examples of challenges in housekeeping gene detection. (A) Genes having several splice variants could have different expression levels for different parts of the gene. (B) Duplicative regions, due to pseudogenes and other duplications, complicate unique read alignments, thus biasing expression-level measurement. (C)Lower expression (on average) of the upstream exons due to imperfect reverse transcription resulting in partial cDNA molecules.
The group of housekeeping genes unites unique genomic and evolutionary features. They have for example shorter introns and exons, more simple sequence repeats and lower potential for nucleosome formation in the 5′ region 2. Nevertheless the gathering of new data about possible housekeeping genes struggles with the same reliability problems they are used to compensate. Several splice variants, duplicative regions, and the general lower expression of upstream exons caused by reverse transcriptase errors complicate interpretation of RT-PCR results (fig. 1).

Another issue is the definition of Housekeeping genes itself3. Is it enough to look for genes being expressed in all tissues, or should the genes also be expressed at a constant level across tissues? Early studies generally adopted the first definition and, in fact, GAPDH and other popular Housekeeping genes for experimental controls have been found to vary considerably across tissues. This is why before starting a new experiment it is advisable to review the literature and technical information in your field to determine which gene(s) other researchers commonly use. It is recommended that multiple Housekeeping genes be utilized for each gene expression experiment, to account for any impact that an experimental condition may have on the expression of an individual Housekeeping gene.

Table with important Housekeeping Genes

Below you can find a list of important Housekeeping genes available at genomics-online, if u have further questions concerning your RT-PCR or are unsure which Housekeeping gene is the right choice our team of qualified scientist will gladly assist u, either per chat mail or phone.

Gene Gene symbol Human ABIN Mouse ABIN Rat ABIN
18S ribosomal RNA RRN18S - - Murine RPS18 ABIN3194759 Rattus RPS18 ABIN3196910
Actin, beta ACTB Human ACTB ABIN3188336 - - Rattus ACTB ABIN3197210
Glyceraldehyde-3-phosphate
dehydrogenase		 GAPDH Human GAPDH ABIN3188338 Murine GAPDH ABIN3194093 Rattus GAPDH ABIN3196808
Phosphoglycerate kinase 1 PGK1 Human PGK1 ABIN3188344 Murine PGK1 ABIN3194167 Rattus PGK1 ABIN3196791
Peptidylprolyl isomerase A PPIA Human PPIA ABIN3188345 Murine PPIA ABIN3193637 Rattus PPIA ABIN3196895
Ribosomal protein L13a RPL13A - - Murine RPL13A ABIN3194668 Rattus RPL13 - RPL13A ABIN3196608
Ribosomal protein,
large, P0		 RPLP0 Human RPLP0 ABIN3188347 Murine RPLP0 ABIN3194972 Rattus RPLP0 ABIN3196600
Acidic ribosomal
phosphoprotein PO		 ARBP Human RPLP0 - arbp ABIN3188347 Murine RPLP0 - arbp ABIN3194972 Rattus RPLP0 -
arbp
 ABIN3196600
Beta-2-microglobulin B2M Human B2M ABIN3188337 Murine B2M ABIN3194482 Rattus B2M ABIN3196560
Tyrosine
3-monooxygenase/tryptophan5-monooxygenase activation protein, zeta polypeptide		 YWHAZ Human YWHAZ ABIN3193501 Murine YWHAZ ABIN3193908 Rattus YWHAZ ABIN3197173
Succinate dehydrogenase
complex, subunit A, flavoprotein (Fp)		 SDHA Human SDHA ABIN3188349 Murine SDHA ABIN3195771 Rattus SDHA ABIN3197067
Transferrin receptor TFRC Human TFRC ABIN3188351 Murine TFRC ABIN3194272 Rattus TFRC ABIN3196259
Glucuronidase, beta GUSB Human GUSB ABIN3188339 - - - -
Hydroxymethylbilane
synthase		 HMBS Human HMBS ABIN3191171 - - - -
Hypoxanthine
phosphoribosyltransferase 1		 HPRT1 Human HPRT1 ABIN3188340 Murine HPRT1 ABIN3195457 Rattus HPRT1 ABIN3196970
TATA box binding protein TBP Human TBP ABIN3188350 - - - -

References:

  1. Moein et al: "Identification of Appropriate Housekeeping Genes for Gene Expression Analysis in Long-term Hypoxia-treated Kidney Cells." In: Adv Biomed Res., 2017 Feb, 22;6:15.
  2. Curina et al.: “High constitutive activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins.” In: J Phys D: Appl Phys, 2017 Feb, ;31(4):399-412.
  3. Eisenberg, Levanon: “Human housekeeping genes, revisited.” In: Trends in Gen., 2014 Mar; 30(3):119-20.