Fig. 4: H3K4me3 regulates transcriptional elongation.
From: H3K4me3 regulates RNA polymerase II promoter-proximal pause-release
a,b, Metagene profiles for transient transcriptome sequencing (TTchem-seq) in control and auxin-treated (a) or dTAG-13-treated (b) cells in the indicated cell lines. TES, transcription end site. c, Heat maps and profiles showing changes in elongation velocities (TTchem-seq/mNET–seq) after acute loss of H3K4me3. d, H3K36me3 ChIP–seq profiles and heat maps in control and auxin-treated DPY30–mAID cells. e, Outline of the DRB/TTchem-seq experiment to measure RNAPII elongation rates. 4SU, 4-thiouridine. DRB 0 min, no release of DRB. f, DRB/TTchem-seq metagene profiles of protein-coding genes (60–300 kb length) with non-overlapping transcriptional units (n = 3,566) in the depicted cells. Lines are computationally fitted splines. g, Box plot showing decreased RNAPII elongation rates after H3K4me3 loss. P values were calculated using two-sided Wilcoxon tests. n = 855 genes with RPM > 100. The box plots indicate the median (centre line), the third and first quartiles (box limits) and 1.5 × IQR above and below the box (whiskers). h, The upregulated genes response to RA treatment in auxin-treated and DMSO-treated cells (n = 2). Gene expression is shown as relative Z-scores across the samples. i, The changes in H3K4me3 and RNAPII ChIP–seq at TSSs (±2 kb), and RNA-sequencing analysis of RA-response genes (upregulated genes) in the indicated samples. The box plots indicate the median (centre line), the third and first quartiles (box limits) and 1.5 × IQR above and below the box (whiskers). P values were calculated using two-sided Wilcoxon tests. n = 77 genes for each group. j, The correlation of mNET–seq signal around the TSS region (TSS ± 2 kb) at 8 h after RA treatment with or without H3K4me3. Pearson correlation and P values are reported at the top. P values were calculated using two-sided Wilcoxon tests.
