UC San Diego

CD8+ T cells play an indispensable role in the host protection from infections and malignancies. As such, many current immunotherapies target molecules that alter CD8+ T cell function and differentiation. Although genome organization is known to be important for regulating cell development and function, the changes in spatial chromatin organization accompanying effector and memory CD8+ T cell differentiation remain unknown. Here, we studied how genome organization is integrated with other molecular mechanisms regulating CD8+ T cell differentiation and targeted CTCF, a key factor that regulates genome organization through blocking or facilitating chromatin interactions, to determine how altering interactions affect the CD8+ T cell response. We observed T cell subset-specific changes in intra-TAD interactions at sites related to transcriptional rewiring, such as genes encoding for transcription factors that regulate CD8+ T cell differentiation. Further, terminally-differentiated effector cell differentiation was accompanied by enrichment of interactions among subset-specific enhancers and promoters, reflecting their terminally differentiated state. We next characterized the binding profile of CTCF, a known regulator of chromatin interactions. CTCF binding changed with CD8+ T cell differentiation, and weak-affinity CTCF binding is needed to promote terminal differentiation in both an infection and tumor setting. Strikingly, disruption of a single CTCF binding site upregulated expression of corresponding memory-associated molecules, providing clear evidence that CD8+ T cell differentiation is regulated through chromatin interactions. Thus, this study not only provides key insights into the remodeling of chromatin architecture during the CD8+ T cell response to infection, but also provides high quality sequencing data to act as a resource to further identify novel regulators of the CD8+ T cell response.