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Early-life stress (ELS) can influence physiology, behaviour, and health well into adulthood, yet its lasting molecular effects remain poorly understood. Using stressors typical of commercial chickens, this thesis investigates the long-term effect of ELS on the epigenome and transcriptome of chickens, integrating red blood cells (RBCs) and multiple brain regions. We identify DNA methylation and miRNA trajectories and markers of long-term exposure using GBS-MeDIP and miRNA sequencing across three studies.

Study I examined the long-term effects of early social isolation stress (SIS) and environmental enrichment (EE) on RBC DNA methylation at two life stages (3.5 weeks and six months). While both treatments initially induced predominantly hypermethylated DMRs, SIS led to an age-dependent accumulation of hypermethylation, whereas EE produced fewer DMRs and a shift toward hypomethylation, indicating that early environments leave persistent and distinct epigenetic signatures in RBC.

Study II mapped methylation dynamics across 11 stages and five brain regions in transported (TPS) and hatched on-farm (OFH) chickens, both undergoing a second transport at ~100 days. Unsupervised analysis identified six latent factors capturing distinct region-specific methylation patterns. Supervised analyses revealed that the hypothalamus showed the most extensive methylation reorganization, especially during the production peak. The hippocampus exhibited a rapid hypermethylation after early transport in TPS birds, and a diminished response to a later transport, indicating epigenetic resilience; in contrast, OFH birds displayed rapid hypermethylation after relocation at ~100 days, revealing vulnerability to stress. The nidopallium showed delayed TPS effects, whereas the amygdala remained largely stable.

Study III profiled miRNA regulation in RBCs and three brain regions at four stages in the cohort used in Study II. RBCs showed a rapid, transient response dominated by the miR-130 and miR-15/16 families, whereas brain responses were delayed and region-specific, with late alterations in caudal hippocampal miRNAs linked to neuronal plasticity. Target analyses highlighted BCL11A as a cross-tissue integrator.

Together, these studies demonstrate that ELS leaves a tissue- and age-specific molecular footprint. This work advances our understanding of stress biology in birds and how early experiences shape molecular trajectories across the lifespan.