Extended Data Fig. 10 |. Chromatin remodelling and epigenetic changes associated with H1 depletion also occur during normal T cell activation.

a, RNA-seq data¹² from effector CD8⁺ T cells was compared with naive T cells and the 250 most upregulated genes, the 250 most downregulated genes and 250 genes not exhibiting altered expression were selected using the adjusted P value produced by DESeq2. The chromatin state of each gene was determined by identifying the ChromHMM regions from our 15-state map that fell within a window of -200 bp of each TSS through the gene body. The relative abundance of each chromatin type within each gene set is shown as a bar plot and the chromatin types are annotated as Type 1 (black), Type 2 (blue) and Type 3 (red). The set of all genes is shown as a reference. b, ATAC-seq read lengths (bp) were calculated from publicly available ATAC-seq data¹² from naive (black) and effector (green) T cells of wild-type mice for all regions of upregulated gene bodies that fall completely within Type 3 chromatin states. The data are plotted as the number of a given read length normalized to region size in base pairs. The change in accessibility (%) and NRL (bp) are shown as determined by NRLfinder. c, Regions surrounding the TSS of genes identified as in b were identified and stacked to create a “metagene plot.” The average ChIP-seq signal intensity for H3K27me3 in naive and effector T cells is shown (reanalysed from data produced and stored in the Gene Expression Omnibus repository GSE111902). d, Transcripts from WT CD8⁺ T cells were divided into 10 categories based on expression (with “0” representing an additional category of genes with little or no expression). The average NRL of gene bodies within each expression category are plotted against the average CUT&Tag H1 to H3 ratio within the same regions. Type 2 (blue) and Type 3 (red) chromatin designations of each gene expression category (based on Fig. 4c) are shown. A linear regression with 95% confidence interval is shown. e, Top, a linear genome browser view of chr2:11,774,283–13,172,671 in summary of the data presented herein. Shown from top to bottom are the following from WT (black) and H1cTKO;Vav-iCre (red) CD8⁺ T cells: ChIP-seq for H3K27me3 (tracks 1–2), ChIP-seq for H3K36me2 (tracks 3–4), RNA-seq reads (tracks 5–6), defined Chromatin Types 1 (black), 2 (blue) and 3 (red) (track 7), and C-score-defined Hi-C chromatin compartments A and B (tracks 8–9). Bottom, a summary figure of the proposed roles for differences in H1 stoichiometry in regulating local genome architecture, the deposition of core-histone post-translational modifications by modification of the chromatin substrate, and changes in gene expression identified from observed differences in wild-type and H1cTKO;Vav-iCre CD8⁺ T cells.