Figure 6. Identification of candidate TFs.

a, tSNE analysis of ATAC-seq chromatin accessibility.

b, Heatmap plots representing the frequencies of the most enriched TF motifs in regions of increased accessibility (relatively more open in first group than second group, DEseq2 raw P-val < 0.05). Scale, motif frequencies (%).

c, TF footprints derived from ATAC-seq reads over representative TF motifs within accessible ATAC-seq regions.

d, Genome-browser tracks depict ATAC-seq chromatin accessibility and TF occupancy. Peak calls indicated below each track. ** indicates DEseq2 raw p-val ≤ 0.01 in comparison between Bcl6^f/fPrdm1^f/f Cre^CD4 T_FH-like and Prdm1^f/f Cre^CD4 T_FH.

e, Gene expression of Runx1, Runx2, and Runx3 from RNA-seq data of LCMV_Arm infected mice or KLH-gp₆₁ immunized mice. Each data point was collected from three (LCMV_Arm) or four (KLH-gp₆₁) independent experiments.

f, Genome-browser tracks depict BCL-6 ChIP-Seq peaks at RUNX2, RUNX3, and KLF2 loci. Peak calls indicated below each track.

g,i. ChIP-qPCR analysis of Bcl-6 at Runx2 E1, E2 and E3, Runx3 E1, or Klf2 P1 and DE among chromatin prepared from CXCR5^hi T_FH cells as shown in Fig.5e. Three independent experiments were performed. Each data point is from an independent experiment (n=3) and presented as a percent of input. Data are mean ± s.e.m., unpaired two-tailed Student’s t-test.

h, Gene expression of Klf2 from RNA-seq data of LCMV_Arm infected mice or KLH-gp₆₁ immunized mice. Each data point was collected from three (LCMV_Arm) or four (KLH-gp₆₁) independent experiments.