This article discusses the specific topic of reference genes. For a more general list of housekeeping genes see housekeeping genes
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]
Gene
Ensembl Transcript no.
Description
Chromosome
AES
ENST00000309311
Amino-terminal enhancer of split
chr19
AP2M1
ENST00000292807
Adaptor related protein complex 2 subunit mu 1
chr3
BSG
ENST00000353555
Basigin (Ok blood group)
chr19
CD59
ENST00000395850
CD59 molecule
chr11
CSNK2B
ENST00000375882
Casein kinase 2 beta
chr6
EDF1
ENST00000224073
Endothelial differentiation related factor 1
chr9
EEF2
ENST00000309311
Eukaryotic translation elongation factor 2
chr19
GABARAP
ENST00000577035
GABA type A receptor-associated protein
chr17
PFDN5
ENST00000334478
Prefoldin subunit 5
chr12
RHOA
ENST00000418115
Ras homolog family member A
chr3
ubiquitin C
ENST00000546120
Ubiquitin C
chr12
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]
^ abcdeHounkpe, 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.
^ abEisenberg 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.
^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.
^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.
^ abcdefgQuiagen. "RT2 Profiler PCR Array (96-Well Format and 384-Well Format". Qiagen Catalog No. 330231 PAHS-00ZA.
^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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