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Gene regulation is tightly regulated to produce individual phenotypes appropriate to a animal’s placement in time and space. How specific genetic and environmental factors shape gene regulation has been extensively studied in laboratory model species. However, far less is known about sources of variance in gene regulation in the wild, in populations where natural selection operates. My dissertation research aimed to identify factors that influence individual variation in gene regulation by evaluating transcriptome-wide gene expression levels within and across populations. In my first chapter, I evaluated gene expression changes in captive Swainson’s thrushes (Catharus ustulatus) originating from two populations as they transitioned from the non-migratory to migratory condition. Birds exhibited significant seasonal differences in the expression of genes involved in cellular development in the brain, providing support for seasonal neural plasticity in migratory birds. In my second chapter, I focused on a single population, the North American gray wolves (Canis lupus) of Yellowstone National Park, to evaluate the relative impacts of intrinsic (age and sex) and environmental variables (social status and presence of sarcoptic mange) on gene expression variation in blood. I found that, unexpectedly, animal age, but not sex, social status, or sarcoptic mange infestation, impacted gene expression, suggesting that age may have pervasive, evolutionarily conserved effects on gene expression variation in natural populations of mammals. Finally, in my third chapter, I adopted an in vitro experimental approach to study how gene regulation is impacted by genotype at the CBD103 gene, which encodes a protein with antimicrobial properties, exists in two forms (alleles) in North American gray wolves, and is associated with lifetime reproductive success. I established keratinocyte lines from 24 gray wolves and utilized CRISPR/Cas9 to generate one heterozygous and homozygous line. To test whether the fitness effects of CBD103 genotype are explained by their roles in immune defense, I challenged the cells with synthetic antigens and live canine distemper virus. No effect of CBD103 genotype was detected, but immune challenge altered expression of thousands of genes. This work demonstrated the ability to establish a population panel of cell lines from a wild mammal, a potentially powerful method for studying gene regulation in natural populations.