Extended Data Fig. 9: Characterization of primed enhancers in undifferentiated naive CD4 T cells.

a, Heat maps show H3K27ac in naive T cells and p300 in T_H1 and T_H2 cells around naive T cell-specific, T_H1-specific and T_H2-specific enhancers. b, Profile of nucleosome occupancy from pooled naive T cell scMNase-seq around T cell-specific, T_H1-specific and T_H2-specific enhancers. c, Normalized nucleosome occupancy within ± 200 bp of the centre of de novo T_H1 enhancers (left) or de novo T_H2 enhancers (right) for subgroups of T cells primed for T_H1 cells (green), T_H2 cells (blue) or none (black). d, e, Plots of fragment-size ratio of subnucleosome-sized particles-to-nucleosomes versus nucleosome occupancy score at de novo T_H1 (d) and T_H2 (e) enhancers for 237 naive CD4 T cells reveal that nucleosome occupancy score is not correlated with fragment-size ratio. Pearson correlation coefficient and P value are indicated. P value is the probability that one would have found the current result if the correlation coefficient were zero (null hypothesis), and was calculated using R. f, Subgroups of naive CD4 T cells primed for T_H1 and T_H2 do not have much overlap. g, Plots of de novo T_H1 enhancers ranked on the basis of differences in nucleosome occupancy between pooled primed cells and the non-primed cells (y axis, see Supplementary Methods). Enhancers associated with key genes for T_H1 were labelled by genes along with ranks. h, Nucleosome positions in pooled or single primed (red) and non-primed (blue) cells at de novo T_H1-specific enhancers for Ifng gene. i, Plots of de novo T_H2 enhancers ranked on the basis of differences in nucleosome occupancy between pooled primed cells and the non-primed cells (y axis, see Supplementary Methods). Enhancers associated with key genes for T_H2 were labelled by genes along with ranks. j, Nucleosome positions in pooled or single primed (red) and non-primed (blue) cells at de novo T_H2-specific enhancers for Il4 gene. k, Motifs enriched in the top 1,000 T_H1/T_H2-primed enhancers are shown. l, m, Gene Ontology analysis for top 1000 T_H1-primed (l) and T_H2-primed (m) enhancers. Significant Gene Ontology terms with P values are reported using GREAT v.3.0.0.