Infection induces extensive changes in the phenotype and function of virus-specific CD8⁺ T cells, ensuring they acquire lineage-specific attributes essential for pathogen clearance and tumour control. Although many of the epigenetic mechanisms driving these changes are increasingly understood, how they integrate to orchestrate CD8⁺ T cell differentiation remains unresolved. To address this, we applied machine learning algorithms to combine multiple genome-wide datasets, including histone post-translational modifications, chromatin interactions (Hi-C), and chromatin accessibility (ATAC-seq). This integrative approach revealed distinct and novel functional chromatin states that are dynamically regulated during virus-specific CD8⁺ T cell differentiation. While this strategy refined our understanding of the histone code, it lacked spatial resolution regarding the organization of these chromatin states within the three-dimensional nuclear architecture. To overcome this limitation, we employed multiplexed single-molecule fluorescence microscopy (dSTORM) to visualize the nuclear positioning of histone PTMs and transcriptional regulators. This analysis uncovered novel subnuclear structures defined by specific chromatin histone PTMs, offering new insights into the interplay between chromatin state and nuclear architecture in regulating gene transcription. Collectively, these findings advance our understanding of the molecular events governing CD8⁺ T cell responses and immunological memory, implying that spatial chromatin organization may represent a previously underappreciated layer of epigenetic regulation critical for adaptive immunity.