Fig. 2: Ly108⁺CX₃CR1⁺ cells possess unique chromatin accessibility and transcriptional features, some of which are shared with effector-like cells.

Day 30 exhausted GP33⁺ CD8⁺ T cell subsets were sorted based on Ly108 and CX₃CR1 expression for ATAC-Seq (A–G) and RNA-Seq (H). A Statistically significant and differentially accessible chromatin regions (DACRs) with > 1.2 log2 fold change from pairwise comparisons were shown. Prog = Progenitor, Eff-like = Effector-like, and Term-Exh = Terminally-exhausted. B Promoter and Enhancer distribution of more and less accessible DACRs in the Ly108⁺CX₃CR1⁺ cells versus progenitors. C Accessibility profiles of DACRS from (B) were visualized in effector-like and Term-Exh cells. D Venn diagram depicting the intersection of DACRs in Ly108⁺CX₃CR1⁺ cells versus progenitors with those in effector-like cells versus progenitors (Left), with the bar graph showing the unique DACRs in effector-like cells (Middle), and heatmap visualization of these regions in progenitors, Ly108⁺CX₃CR1⁺, and effector-like cells (Right). E Bar graph depicting distribution of DACRs in Term-Exh versus Ly108⁺CX₃CR1⁺ cells. F^. Genomic track of accessibility at the Mef2c locus in the 4 exhausted subsets. G De novo HOMER motif analysis of DACRs from Ly108⁺CX₃CR1⁺ versus progenitor cells. H Heatmap visualization of select transcription factors among the 4 exhausted subsets. ATAC- and RNA-seq data were from 2 and 3-4 independent replicates, respectively. Each replicate was a pooled sample of 3-5 mice.