Epigenetic modifications constitute a complicated regulatory network controlling various biological processes from cell development to immune responses. The mechanisms through which CD4+ T cells react to environmental stimuli, including virus intrusion and differentiation signals, represent the fundamental cell biological question of how the external microenvironment influences intrinsic transcriptional networks. This dissertation investigates the epigenetic status changes in CD4+ T cells induced by Marek’s disease virus (MDV) infection in chickens and during differentiation in mice. First, a genome-wide gene expression analysis in the immune organs from resistant line 63 and susceptible line 72 chickens was performed to explore Marek’s disease (MD) resistance mechanisms. MDV infection influences both cytokine-cytokine receptor interaction and cellular development in resistant and susceptible chickens. Second, we examined the epigenetic status of CD4+ T cells induced by MDV infection, including chromatin accessibility and chromosome organization. Our results revealed extensive epigenetic modification changes caused by MDV infection. Only resistant line 63 chickens could initiate robust adaptive immune responses at the transcription level, and the increase in chromatin accessibility and chromosome reorganization represented by A/B compartment flipping were related to up-regulated genes induced by MDV infection at 10 days post-infection in line 63 chickens. Finally, we investigated CD4+ T cells plasticity during Th1 helper cell differentiation. We showed “early” (48 hours) CD4+ T cells were plastic for cellular reprogramming while “late” (72 hours) cells lost reprogram plasticity and became committed to Th1 cell fate. T-bet, the Th1 cell master regulator, was not the direct determinant of Th1 cell plasticity. Our integrative analysis of multiple “omics” datasets revealed dynamic and genome-wide changes of chromatin accessibility associated with the process of cellular differentiation and commitment. We predicted that several candidate regulators could contribute to cellular plasticity, including Mxi1, JunB, BATF, IRF4, and Hif-1α. We observed that substantial alterations of chromatin interactions occurred at the IRF4 locus across differentiation time. Conditional deletion of IRF4 in CD4+ T cells impacted the expression of T cell activation and differentiation genes, including T-bet, and extended Th1 cell plasticity during the differentiation process. Our findings provided deeper understanding of CD4+ T cell commitment and responses toward viral infection.