ChIA-PET from naïve and in vitro-induced antigen-specific effector and memory CD8+ T cells

The scATAC-seq approach identifies cell type-specific cis- and trans-regulatory elements in a genome-wide manner. However, which genes targeted by the identified cis-regulatory elements (CREs) remain unresolved, regarding CREs usually putatively assigned to their nearest genes in bioinformatic analysis. Additionally, it is important to characterize CREs that play essential roles in gene regulation from non-functional “parking spots”. To this end, we applied ChIA-PET approach to mapping RNAPII-mediated enhancer-promoter chromatin interactions between enhancers and their target genes genome-wide. We performed ChIA-PET on antigen specific naïve CD8+ T cells and in vitro-induced antigen specific effector and memory CD8+ T cells.