The day before transfection, we seeded HSF cell lines in a 6-cm dish to obtain 40–50% confluency at the time of transfection. Cells were transfected with a 10-nM concentration of HERV_00001917-target siRNA (5′-GAUGUAAUGAUCAAUGUCCUAUGUC-3′) or non-targeting control siRNA that had been formulated with INTERFERin® transfection reagent (Polyplus) for three biological replicates. As both HERV_00001917 and target siRNA are unique sequence when aligning to the human genome and transcriptome by BLAST [70], we considered the siRNA as specific to the target hervRNA.

Background: Human endogenous retroviruses (HERVs), the remnants of ancient retroviruses, account for 8% of the human genome, but most have lost their transcriptional abilities under physiological conditions. However, mounting evidence shows that several expressed HERVs do exert biological functions. Here, we systematically characterize physiologically expressed HERVs and examine whether they may give insight into the molecular fundamentals of human development and disease. Results: We systematically identify 13,889 expressed HERVs across normal body sites and demonstrate that they are expressed in body site-specific patterns and also by sex, ethnicity, and age. Analyzing cis-ERV-related quantitative trait loci, we find that 5435 hervRNAs are regulated by genetic variants. Combining this with a genome-wide association study, we elucidate that the dysregulation of expressed HERVs might be associated with various complex diseases, particularly neurodegenerative and psychiatric diseases. We further find that physiologically activated hervRNAs are associated with histone modifications rather than DNA demethylation. Conclusions: Our results present a locus-specific landscape of physiologically expressed hervRNAs, which represent a hidden layer of genetic architecture in development and disease.