Reference genes

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Reference genes are expressed in all cells of an organism under normal and patho-physiological conditions. [1] [2] [3] [4] Although some housekeeping genes (such as LDHA, [5] NONO, [5] PGK1 [5] and PPIH, [5] ) are expressed at relatively constant levels in most non-pathological situations, other housekeeping genes may vary depending on experimental conditions. [6] Although the terms "housekeeping gene" and "reference gene" are used somewhat interchangeably, caution must be used in selecting genes for reference purposes. Suitable reference genes must be stably expressed in the specific experimental condition or tissue of interest. [1] Recently a web-based database of human and mouse cell specific reference genes/transcripts, named Housekeeping and Reference Transcript Atlas (HRT Atlas), was developed to offer reliable reference genes/transcripts for RT-qPCR data normalization. [1]

This is a list of housekeeping genes and transcripts stably expressed across 52 human tissues and cell types that may be used for reference purposes after empirical validation: [1]

GeneEnsembl Transcript no.DescriptionChromosome
AES ENST00000309311Amino-terminal enhancer of splitchr19
AP2M1 ENST00000292807Adaptor related protein complex 2 subunit mu 1chr3
BSG ENST00000353555Basigin (Ok blood group)chr19
CD59 ENST00000395850CD59 moleculechr11
CSNK2B ENST00000375882Casein kinase 2 betachr6
EDF1 ENST00000224073Endothelial differentiation related factor 1chr9
EEF2 ENST00000309311Eukaryotic translation elongation factor 2chr19
GABARAP ENST00000577035GABA type A receptor-associated proteinchr17
PFDN5 ENST00000334478Prefoldin subunit 5chr12
RHOA ENST00000418115Ras homolog family member Achr3
ubiquitin C ENST00000546120Ubiquitin Cchr12

HRT Atlas allows searching of a complete list of reliable candidate reference genes and transcripts for RT-qPCR normalization in more than 120 human and mouse tissues or cell types. The database also offers some empirically validated primers and predicted modifiers (disease and small molecules) of the expression of these reference genes.

The following represent genes that should probably not be used for reference purposes: GUSB, [5] RPLP0, [5] TFRC, [5] GAPDH, HSP90, and β-actin. Although they were once considered as "housekeeping genes," recent data suggests that they are not as reliable as once thought. [1] [2]

See also

References

  1. 1 2 3 4 5 Hounkpe, Bidossessi Wilfried; Chenou, Francine; de-Lima, Franciele; De-Paula, Erich Vinicius (2020-07-14). "HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets". Nucleic Acids Research. 49 (D1): D947 –D955. doi: 10.1093/nar/gkaa609 . ISSN   0305-1048. PMC   7778946 . PMID   32663312.
  2. 1 2 Eisenberg E, Levanon EY (October 2013). "Human housekeeping genes, revisited". Trends in Genetics. 29 (10): 569–574. doi:10.1016/j.tig.2013.05.010. PMID   23810203.
  3. ↑ kon Butte, AJ.; et al. (2001). "Further defining housekeeping, or "maintenance," genes focus on 'a compendium of gene expression in normal human tissues'". Physiol. Genomics. 7 (2): 95–96. doi:10.1152/physiolgenomics.2001.7.2.95. PMID   11773595.
  4. ↑ Zhu, J.; et al. (2008). "On the nature of human housekeeping genes". Trends in Genetics. 24 (10): 481–484. doi:10.1016/j.tig.2008.08.004. PMID   18786740.
  5. 1 2 3 4 5 6 7 Quiagen. "RT2 Profiler PCR Array (96-Well Format and 384-Well Format". Qiagen Catalog No. 330231 PAHS-00ZA.
  6. ↑ Greer S, Honeywell R, Geletu M, Arulanandam R, Raptis L (Feb 19, 2010). "Housekeeping genes; expression levels may change with density of cultured cells". J Immunol Methods. 355 (1–2): 76–9. doi:10.1016/j.jim.2010.02.006. PMID   20171969.
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