Mll1 pioneers histone H3K4me3 deposition and promotes formation of CD8⁺T stem cell memory

Abstract

Memory Cd8+ T cells with stem cell-like properties (TSCM) sustain long-lived adaptive immunity to intracellular pathogens and tumors. However, the chromatin regulatory factors (CRFs) and transcriptional dynamics that program their differentiation are unclear. Using an RNA interference screen of all CRFs we discovered that Mll1 was essential during initial T cell receptor (TCR) stimulation of naive Cd8+ T cells to establish long-lived memory and progenitor TSCM-like cells during acute and during chronic viral infections and tumors. We demonstrate that primary TCR stimulation drives de novo histone H3 lysine 4 trimethylation (H3K4me3) deposition and RNA polymerase II pausing at genes whose RNA velocities explain single-cell trajectories that diversify nascent effector and memory cell states early during viral infection. Mll1 was essential for induced H3K4me3 at half of all TCR-activated transcription start sites (> 7,000 regions), especially those specific to memory cells. Our results suggest that Mll1-dependent H3K4me3 and regulation of RNA Pol II pausing govern dynamic transcriptional states that patterns TMEM cell diversity.