Extended Data Fig. 6: Knock-down of SDG8 ortholog in rice causes up-regulated of H3K36me3 in some loci.
From: H3K36 methylation stamps transcription resistive to preserve development in plants
a, The Neighbor-Joining phylogenetic tree of SDG8 and its orthologs in different species (Oryza sativa, Zea mays, Sorghum bicolor, Brachypodium distachyon, Hordeum vulgare, Triticum aestivum, Glycine max, Mimulus guttatus, Vitis vinifera VIT, Nicotiana attenuata, Brassica rapa). b, Box and whisker plot showing H3K36me3 enrichment on H3K36me3 up- and down-protein coding genes in WT and SDG725 RNAi line. Boxplots show the median, 25th-75th percentiles, and minima and maxima (whiskers). Average values from two biological replicates are shown. c, Box and whisker plot showing nascent RNA abundance on H3K36me3 up- and down-genes (SDG725Ri vs WT) in WT. Boxplots show the median, 25th-75th percentiles, and minima and maxima (whiskers). p = 3.54E-81 by two-tailed Student’s t test. Average values from two biological replicates are shown. d, Box and whisker plot showing FAIRE-seq signals on H3K36me3 up- and down-genes (SDG725Ri vs WT) in WT. The H3K9me2 marked genes were used as a negative control of the dense chromatin state. Average values from two biological replicates are shown. Boxplots show the median, 25th-75th percentiles, and minima and maxima (whiskers). e, Gene Ontology (GO) analysis of 1738 H3K36me3-up genes in rice. f, Snapshots from Integrative Genomics Viewer showing H3K36me3 (in WT and SDG725 RNAi line), FAIRE-seq (in WT), and NET-seq (in WT). g. Gene Ontology (GO) analysis shows the biological process of H3K36me3-up genes in Arabidopsis, transcription resistive genes in Arabidopsis and H3K36me3-up genes in rice respectively. The x-axis displayed the level of enrichment for each GO term. The p-value for each GO term was shown by the color gradient. P values were adjusted for multiple comparisons with Benjamini and Hochberg correction.
