Genome-wide maps of chromatin state in naïve CD4+ T cells, WT/EZH2-null TFH and TH1 cells

ATAC-Seq experiments were performed to elucidate the chromatin state changes among naïve CD4+ T cells, WT follicular helper T (TFH) cells and WT type 1 helper T (TH1) cells Day2 (D2), Day5 (D5), Day8 (D8) post-LCMV-Armstrong infection, as well as EZH2-null (KO) TFH and TH1 at Day8 post-LCMV-infection. The analysis suggested stringent lineage-specific mode of chromatin accessibility in each group, indicating chromatin remodeling is tightly associated with TFH versus TH1 lineage differentiation in response to acute viral infection. Furthermore, the comparison between wild-type and EZH2-null TFH cells showed that less-opening state of certain chromatin accessible region in TFH-differentiation associated genes in the formers, suggesting EZH2 led to permissive chromatin accessibility primarily at specific regions of TFH-associated genes. H3K27me3-ChIP-seq was performed in WT TFH and TH1 cells to confirm the deposition of the histone marks at those loci. SMARTA TFH and TH1 cells at D2, D5, D8 post-LCMV-Armstrong infection and EZH2-null TFH and TH1 cells at day 8-post LCMV Armstrong infection, and naïve CD4+ T cells were sorted (2 or 3 samples per group, each sample was pooled from at least 5 mice). The ATAC-Seq libraries of the sorted cells were then prepared by using the Nextera DNA Sample Preparation Kit (FC-121-1030, Illumina), followed by next-generation sequencing. H3K27me3-ChIP-seq was also performed on D3 post-LCMV-Armstrong infection SMARTA TFH and TH1 cells, as well as CD4+ Naive T cells.