During development, gene loci must acquire an active chromatin conformation before they are transcribed, a process called chromatin priming. We previously showed that chromatin priming is essential for the rapid recall response by memory T-cells. After T-cell receptor (TCR) activation by antigens (Ags), naïve T-cells activate hundreds of gene loci and stably acquire thousands of open chromatin regions which are bound by RUNX1, ETS1, TCF1 and JUND and maintain H3K9ac and H3K4me2. These active chromatin regions remain during homeostasis in the absence of transcription and they function to maintain a memory of previous Ag encounters to keep gene loci competent for rapid transcriptional re-activation.
Here we used DNase-Seq, RNA-Seq and ChIP-SEq to globally investigate the molecular mechanisms by which the gene regulatory program that keeps inducible genes primed but silent is replaced by the TCR signalling-induced reactivation program. We employed an in vivo murine model that allows for purification Ag-specific memory T-cells. We revealed two mutually exclusive pathways controlling the fate of inducible genes. We show that the maintenance of memory T-cells during homeostasis in vivo requires low level IL-7 signalling to immunosuppressive JUND. After re-stimulation, the ETS/TCF homeostatic gene regulatory program was transcriptionally shut down before inducible genes were reactivated. Within 3 hours of peptide Ag injection the ETS1 and TCF/LEF genes were silenced and replaced by the ETS-repressor ETV6. In parallel, the IL-7-inducible AP-1 family member JUND was replaced by TCR-inducible JUN and FOS, together with NFAT and EGR1, which directly activate transcription. Our data suggest that the maintenance of memory T-cells relies on a regulatory program that must be turned off before inducible genes can be turned on. We believe that mechanisms mediating the switch from a self-renewing to a rapidly proliferating state lies at the heart of signalling-induced changes in cell function.