Identification of housekeeping genes suitable for gene expression analysis in the zebrafish

Abstract Housekeeping (HK) genes are constitutively expressed in order to maintain cellular function. They produce the minimal essential transcripts necessary for normal cellular physiology. Wide range expression, stable expression level and high expression level are independent features of a single gene expression and are all desirable for the definition of an “ideal” HK. Recent studies have questioned the possible existence of “ideal” HK mRNAs, mainly because of the wide expression conditions variability. This would imply that for each investigated organism the suitability of a putative HK should be verified. We perform a systematic analysis to identify “optimal” HK genes in Danio rerio (zebrafish), to be used in expression analyses conducted on embryos/larvae at different developmental stages, as well as on differentiated adult tissues from single donors. The expression pattern of candidate genes, selected on the basis of the literature available and of ad hoc bioinformatics analysis, was assessed by quantitative relative RT-PCR in an RNA panel, including six different embryo/larvae developmental stages and six adult tissues. Statistical analysis was performed to identify genes with the lowest expression standard deviation in the studied panel. Our results showed that beta-actin 2 ( bactin2 ) is the mRNA with the lowest variability of expression.