Expanding the concept of housekeeping genes: Examining the influence of retroelements on gene expression stability during cellular differentiation

Housekeeping genes (HKGs), essential for cellular differentiation, are traditionally thought to be uniformly expressed. However, recent analyses show variable expression across tissues, challenging this view. Identifying HKGs based on stable expression necessitates precise, repeated experiments. The limited number of transcription factors during differentiation suggests HKGs stabilise phenotypes via compensatory gene regulation. We examined retroelements, comprising approximately 40% of the human genome, for their influence on gene expression stability near transcriptional start sites (TSSs). By mapping CpG islands and retroelements within 10 kb of TSSs, we analysed 56 RNA sequencing datasets. CpG-island genes near Alu elements exhibited low expression variability, especially when the Alu elements were closer to the TSSs. Conversely, non-CpG island genes near L1 and LTR elements showed high variability, indicating distinct regulatory roles. Despite the constant number of Alu-adjacent CpG-island genes across tissues, their expression was most highly expressed in embryonic stem cells and declined in most differentiated tissues, except for an increase in the ovary and testis. Alu elements near CpG islands help stabilise phenotypes through compensatory downregulation of HKGs. These results expand the HKG concept to include genes maintaining stable phenotypes during differentiation, aiding in differentiation stage identification.