Fig. 4

S2Lb-GFP is enriched over highly transcribed genes. a About 96% of the S2Lb-GFP target genes are also occupied by H3K4me3. The Venn diagram displays the overlap between genes marked by H3K4me3 in wild-type and s2lb-2 seedlings and those occupied by S2Lb-GFP in wild-type plants. Gene IDs are listed in Additional files 3 and 4. b Density matrix showing the co-occurrence frequency of H3K4me3 and S2Lb-GFP along S2Lb-occupied gene annotations (N = 4557). c Genome browser view of H3K4me3 and S2Lb-GFP over the TUBULIN8, DOG1, and FT genes. H3K4me3 and GFP signals in different genetic backgrounds are equally scaled. d Wild-type H3K4me3 median enrichment over the genes marked by H3K4me3 (dark green line; N = 17,831) and those occupied by S2Lb-GFP (dashed green line; N = 4557) or not (pale green line; N = 13,455). e Median enrichment of H3K4me3 (upper metagene plot; N = 17,831) or S2Lb-GFP (lower metagene plot; N = 4557) on TAIR10 genes split into six classes ranked by expression level in wild-type seedlings. f Median enrichment of S2Lb and RNA Pol II over the 4557 genes targeted by S2Lb (+S2Lb) versus the genes targeted by RNPII but not by S2Lb (-S2Lb; N = 11,735). RNPII-occupied gene IDs are given in Additional file 6: Table S5. g Both S2Lb and AtCOMPASS-like activities are required for H3K4me3 enrichment and induction dynamics of light-responsive genes during de-etiolation. The histogram shows H3K4me3 enrichment over several light-responsive genes in 3-day-old etiolated seedlings upon transfer from dark to light for 1 or 6 h. ChIP-qPCR analyses were performed with an anti-H3K4me3 antibody and with anti-histone H3 to normalize levels to nucleosome occupancy. H3K4me3/H3 levels are given as percentages of IP/input input relative to the mean signals over two housekeeping genes (At4g23100 and At4g22330) with no change in expression and in H3K4me3 level during the transition [58]. Error bars correspond to standard deviations from two replicates. h RT-qPCR analysis of light-responsive gene expression in samples in f. RNA levels are given relative to the wild-type dark sample (arbitrarily set to 1) normalized to At5g13440 and At2g36060 transcript levels. Error bars correspond to standard deviations from two replicates