CTCF translates IL-2- and aKG-sensitive metabolic changes in T cells into context-dependent differentiation gene programs [RNA-Seq]

We found that aspects of the IL-2-sensitive effector gene program in CD4+ Th1 and CD8+ Tc1 cells are regulated by glutamine and alpha-ketoglutarate (aKG)-induced events, in part through changes in DNA and histone methylation states. We further identified a novel mechanism by which IL-2- and aKG-sensitive metabolic changes regulate the association of CTCF with select genomic sites. aKG-sensitive CTCF sites were often associated with loci containing IL-2- and aKG-sensitive genome organization patterns and gene expression in T cells. Surprisingly, IL-2- and aKG-sensitive CTCF sites in T cells were also associated with genes from developmental pathways that had aKG-sensitive expression in ES cells. The data collectively support a novel mechanism wherein CTCF serves to translate aKG-sensitive metabolic changes into context-dependent differentiation gene programs. Overall design: We conducted an RNA-seq analysis on CD4+ Th1 or CD8+ Tc1 cells maintained in high IL-2, low IL-2, or low IL-2 with aKG to define the composition of the IL-2-sensitive gene program that is impacted by metabolic changes related to aKG. We also performed an RNA-seq analysis on CD4+ T cells polarized in Th1 conditions to define the role for glutamine in the IL-2- and aKG-sensitive program. For these experiments, primary CD4+ T cells were isolated and were stimulated with aCD3 and aCD28 in Th1 polarizing conditions either in the presence or absence of glutamine. After 3 days, the cells were split and maintained in Th1 polarizing conditions in either the presence or absence of glutamine in either high or low environmental IL-2 conditions. In addition, an RNA-seq analysis was performed in the mouse ES cell line E14Tg2a, with cells cultured in glutamine free-conditions either left untreated or exposed to aKG for 2 days. This study was performed to address whether a subset of genes associated with aKG-sensitive CTCF peaks in Th1 cells might be induced by aKG in the context of a cell type where they are naturally expressed.