CHANGES IN DNA ACCESSIBILITY OCCUR IN PUTATIVE ENHANCER REGIONS OF A SUBSET OF T CELL MEMORY RESPONSIVE GENES

Naive T cells exist in a resting state until activated by the antigen they are specific for. Upon activation, T cells produce cytokines and other proteins necessary to fight infections and proliferate to produce more T cells specific for that antigen. Some of these descendants will be long-lived memory T cells, which will return to a resting state but are primed for a more rapid and robust immune response upon re-exposure to the same antigen. The molecular mechanisms responsible for this enhanced response are still unclear. Using a Jurkat cell culture model of transcriptional memory we have investigated the possibility that previously stimulated cells have differences in DNA accessibility compared to non-stimulated cells. We used Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) in conjunction with high throughput sequencing to identify changes in DNA accessibility in response to stimulation, resting and re-stimulation. We found that although many of the changes in accessibility that were induced upon stimulation, were reversed upon stimulus withdrawal and resting of the cells, a large proportion remain accessible and a subset of these are near genes that have enhanced induction upon re-stimulation. Interestingly the accessibility associated with these ‘memory-responsive’ genes was not always at the transcription start site but sometimes occurred in putative enhancers of these genes. The role of Protein Kinase C in mediating these changes in accessibility was also examined using the inhibitor rottlerin. Overall design: 8 different biological samples were analysed. FAIRE samples and a Total Input sample were obtained.