Transposable elements and the stress response in healthy humans: preliminary characterization to identify a baseline regulation through the MAMELI cohort

Transposable elements (TEs) are often regarded negatively due to their capacity to propagate within the genome. However, growing evidence shows that TEs exert homeostatic effects, contributing to cellular regulatory functions, with adaptive advantages to the host genome. Under stress conditions, TEs can undergo demethylation and activation, influencing the expression of stress-responsive and inflammatory genes to allow plastic adaptation to changing environments. Despite these observations, the relationship between stress, activation of specific TE families, and regulation of gene networks remains poorly understood, particularly in humans. The advent of third-generation sequencing offers new opportunities to elucidate these interactions. This study aims to characterize the baseline methylation status of TEs potentially involved in regulating selected stress- and inflammation-related genes, and to explore how TE methylation relates to the methylation of their target gene promoters. 106 healthy blood donors were enrolled from AVIS (Associazione Volontari Italiani Sangue) as a subset of the MAMELI (MApping the Methylation of repetitive elements to track the Exposome effects on health: the city of Legnano as a LIving lab) cohort. High-molecular-weight DNA was extracted from the buffy coat fraction of blood samples, and sheared using Covaris g-TUBE. Third-generation sequencing was performed via Oxford Nanopore Technology. Reads were aligned to the T2T/CHM13 human genome reference. CpG methylation levels were quantified using modkit. Repetitive genomic elements were annotated with RepeatMasker, excluding satellites, short tandem repeats, and low-complexity elements. We identified multiple CpG sites in the promoter regions of most selected genes, suggesting that these genes are strongly regulated by DNA methylation. Many CpGs were also located within TEs, with distinct subfamily-specific distributions for each gene. Gene-specific analyses revealed that inter-individual methylation variability was pronounced at CpG sites located in TEs within regulatory regions. These findings provide new insights into the functional role of TEs in physiological contexts, suggesting that they may act as mediators of environmental stimuli, possibly promoting adaptive responses in the human genome.