Housekeeping genes
Julian PampelHousekeeping 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
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.
Figure 1: Problems occuring in Housekeeping Gene detection. (I) Genes having several splice variants could have different expression levels for different parts of the gene. (II) Duplicative regions, may bias expression-level measurement. (III) Lower expression (on average) of the upstream exons due to imperfect reverse transcription resulting in partial cDNA molecules.
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.
