Extended Data Fig. 10: SDG25 and SDG26 have overlapped regulating sites for H3K36me3 modification, but their functions are not consistent.
From: H3K36 methylation stamps transcription resistive to preserve development in plants
a, Metaplot illustrates the averaged H3K36me3 changes of C3 genes in the multiple double mutants including sdg8 sdg25 and sdg8 sdg26 compared to sdg8. b, Proportions of H3K36me3 up-regulated genes in the double mutant compared to sdg8 (shown in red), H3K36me3 downregulated genes in the double mutant compared to sdg8 (shown in blue) and H3K36me3 unchanged genes in the double mutant compared to sdg8 (shown in grey) in C1-C4 genes. H3K36me3 downregulated genes in the double mutant compared to sdg8 are highly enriched in the C3 genes. c, Metaplot of the H3K36me3 in sdg8 sdg25 and sdg8 sdg26 compared to sdg8 on G1-G4 genes. d, Venn diagram shows the overlap of the top 3000 genes with the most reduced H3K36me3 in the double mutants compared to sdg8. e, Boxplots of the mRNA length, exon number and exon ratio of top 3000 genes with the most decreased H3K36me3 in the double mutants compared to sdg8. The statistical significance was determined by the unpaired t test with a two-tailed p-value. ****, p < 0.0001. From left to right panel, the p values are 4.5E-210, 1.3E-258, 3.9E-263, 5.9E-298, 1.8E-191 and 8.1E-197, respectively. PCGs are abbreviated for protein-coding genes. Sample numbers: n25 = 2896, n26 = 2901, nG1 = 1929, nPCGs = 26853. Boxplots show the median, 25th-75th percentiles, and minima and maxima (whiskers). f, Metaplots illustrate the averaged H3K36me3 changes of genes that decreased in sdg8 sdg25 sdg26 compared to sdg8 sdg25 (Top) or sdg8 sdg26(Bottom) which belonged to C3. g, The comparison of H3K36me3 ChIP-seq and RNA-seq between double mutants (x-axis) and sdg8 (y-axis) is shown. Each gene is represented by a dot. Pink dots represent H3K36me3 fold change (FC) (double mutant_H3K36me3/sdg8_H3K36me3) ≥ 1.2, p < 0.05; blue dots represent H3K36me3 FC (sdg8_H3K36me3/double mutant_H3K36me3) ≥ 1.2, p < 0.05; yellow dots represent the top 3000 genes with the most significant reduction in H3K36me3 in the sdg8 sdg25 mutant compared to sdg8 (referred to as SDG25-regulated); green dots represent the top 3000 genes with the most significant reduction in H3K36me3 in the sdg8 sdg26 mutant compared to sdg8 (referred to as SDG26-regulated). The genes with the most loss of H3K36me3 in sdg8 sdg25 compared to sdg8 (referred to as sdg25 overlap), and sdg8 sdg26 compared to sdg8 are colored in orange, and green, respectively. DEseq2 was used to evaluate the significance of each gene. P-values were adjusted for multiple comparisons with Benjamini and Hochberg correction. h, Metagene profile of NET-seq (Ser2P) signal over genes that decreased in sdg8 sdg25 sdg26 compared to sdg8 sdg25 (Top) or sdg8 sdg26 (Bottom) which also belonged to C3.
