With Reference to Reference Genes: A Systematic Review of Endogenous Controls in Gene Expression Studies

• Published in: PloS one Vol. 10; no. 11; p. e0141853
• Main Authors: Chapman, Joanne R, Waldenström, Jonas
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10.11.2015; Public Library of Science (PLoS)
• Subjects: Actin; Animals; Biochemistry; Biokemi; Brain; Gene Expression; Gene Expression Profiling - methods; Genes; Genetic engineering; Genetic research; Genome-wide association studies; Genomics; Glyceraldehyde; Glyceraldehyde 3-phosphate; Glyceraldehyde-3-phosphate dehydrogenase; Humans; Identification; Literature reviews; Mammals - classification; Mammals - genetics; Methods; Phosphates; Polymerase chain reaction; Primers; Real time; Real-Time Polymerase Chain Reaction - methods; Real-Time Polymerase Chain Reaction - standards; Reference Standards; Research Design; RNA, Messenger - biosynthesis; RNA, Messenger - genetics; Specimen Handling; Stability; Statistics, Nonparametric; Studies; Transcription, Genetic
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0141853

The choice of reference genes that are stably expressed amongst treatment groups is a crucial step in real-time quantitative PCR gene expression studies. Recent guidelines have specified that a minimum of two validated reference genes should be used for normalisation. However, a quantitative review of the literature showed that the average number of reference genes used across all studies was 1.2. Thus, the vast majority of studies continue to use a single gene, with β-actin (ACTB) and/or glyceraldehyde 3-phosphate dehydrogenase (GAPDH) being commonly selected in studies of vertebrate gene expression. Few studies (15%) tested a panel of potential reference genes for stability of expression before using them to normalise data. Amongst studies specifically testing reference gene stability, few found ACTB or GAPDH to be optimal, whereby these genes were significantly less likely to be chosen when larger panels of potential reference genes were screened. Fewer reference genes were tested for stability in non-model organisms, presumably owing to a dearth of available primers in less well characterised species. Furthermore, the experimental conditions under which real-time quantitative PCR analyses were conducted had a large influence on the choice of reference genes, whereby different studies of rat brain tissue showed different reference genes to be the most stable. These results highlight the importance of validating the choice of normalising reference genes before conducting gene expression studies.