Chromatin supplement (draft v4; results/182/182_FigS_chromatin_v4; Fig. S8). Groups (RP genes excluded): Alu-near (classes 1 + 5), Alu-mid (2 + 3 + 6), Alu-far (4 + 7), L1/LTR CGI (8 + 9). Even-numbered autosomes in A and B; all autosomes in C.
(A) As Fig. 6A for HPC, T cells and B cells: H3K4me3 and H3K27me3 signal and CpG methylation around the TSS (separate y scales for the histone rows in each cell type; common scale for methylation). CpGs overlapping RepeatMasker elements excluded; bands, gene-level bootstrap 95% intervals; ticks, median TSS-to-edge distance; grey line, 50%.
(B) Mean histone signal within TSS +/- 2.5 kb by expression tertile (Corces TPM within the cell type) in HPC, T and B cells; open symbol, fewer than 30 genes; bars, gene-level 95% intervals (Data S2, Table 1b).
(C) Methylation boundary by expression for L1/LTR CGI in HPC, as Fig. 6B: Kaplan-Meier fraction of sides risen by distance from the TSS (rise = first 100-bp bin from the TSS with >= 2 non-repeat CpGs at >= 50% followed by an informative bin >= 50%; sides censored where informative CpGs end); expression tertiles bottom (light), middle, top; ticks, tertile KM medians; grey line, 0.5.
