What are housekeeping genes?

The concept of housekeeping gene has been used for four decades but remains loosely defined. Housekeeping genes are commonly described as essential for cellular existence regardless of their specific function in the tissue or organism, and stably expressed irrespective of tissue type, developmental stage, cell cycle state, or external signal. However, experimental support for the tenet that gene essentiality is linked to stable expression across cell types, conditions, and organisms has been limited. Here we use genome-scale functional genomic screens together with bulk and single-cell sequencing technologies to test this link and optimize a quantitative and experimentally validated definition of housekeeping gene. Using the optimized definition, we identify, characterize, and provide as resources, housekeeping gene lists extracted from several human datasets, and 10 other animal species that include primates, chicken, and C. elegans. We find that stably expressed genes are not necessarily essential, and that the individual genes that are essential and stably expressed can considerably differ across organisms; yet the pathways enriched among these genes are conserved. Further, the level of conservation of housekeeping genes across the analyzed organisms captures their taxonomic groups, showing evolutionary relevance for our definition. Therefore, we present a quantitative and experimentally supported definition of housekeeping genes that can contribute to better understanding of their unique biological and evolutionary characteristics. Author summaryHousekeeping genes have often been associated with four main biological criteria-stability in expression across samples, essentiality, participation in cellular maintenance, and evolutionarily conserved. However, the relationship between these criteria has not been much discussed. Housekeeping genes are of broad interest for translational and basic science research. Thus, it is important to present experimental bases for these criteria. In this article, using the Gini coefficient, we compare stability of expression with the other three criteria using 15 transcriptomes spanning 11 organisms. We found that: (1) Previously identified housekeeping genes in humans had lower Gini coefficients regardless of whether they were calculated using tissue or cancer transcriptomes. (2) Genes with low Gini coefficients for human tissues and cancer cells were enriched for significantly different cellular functions. (3) Essential genes for humans, CHO cells, and C. elegans were likely to have lower Gini coefficients compared to other genes. (4) Gini coefficients of orthologs conserved across different organisms were able to recapitulate organism-specific information. All these results provide a quantitative view of housekeeping genes across organisms and hint at their evolutionary importance.

Automated summary

The concept of housekeeping gene, which is essential for cellular existence and stably expressed, remains loosely defined. This study presents a quantitative and experimentally supported definition of housekeeping genes by using genome-scale functional genomic screens and sequencing technologies. The authors identify and characterize housekeeping genes in multiple human datasets and other animal species, and find that the essential and stably expressed genes can vary across organisms while the enriched pathways are conserved. This research provides insights into the unique biological and evolutionary characteristics of housekeeping genes.