Fig. 5

Effects of genetic variations on chromatin topology and transcription. a Rates and numbers of H3K4me3 and H3K9me2binding sites and RNAPII occupancy in the two rice varieties MH63 and ZS97. b Percentages of H3K4me3 and H3K9me2 differential peaks involved and not involved in chromatin interactions. c Pie chart for the proportion of different genetic variation types overlapped with H3K4me3 (upper) and H3K9me2 (bottom) differential peaks involved in interactions. Most (~80%) differential peaks overlapped with single-nucleotide polymorphisms (SNPs), insertion/deletions (InDels), or presence/absence variations (PAVs). d Distributions of H3K4me3 and H3K9me2 differential peak-associated core and distributed genes. Percentages of core and distributed genes in 453 rice accessions serve as control. e Transcription level of loop-connected and not connected genes in MH63 and ZS97 caused by PAV (present in MH63 and absent in ZS97). ***p < 0.001 from Wilcoxon test. f Representative screenshot shows a H3K4me3 loop present in MH63 but absent in ZS97 caused by a PAV. The loop-connected gene MH01g0584200 in MH63 is more active than that in ZS97. g Expression change status of genes around (±10 kb) H3K9me2 differential peaks. From left to right, the bars represent (1) genes surrounding H3K9me2 differential peaks without interactions, (2) H3K9me2 differential peaks associated loop-outer genes, (3) H3K9me2 differential peaks associated loop-inner genes, (4) H3K9me2 differential peaks associated loop-connected loop-inner genes, (5) H3K9me2 differential peaks associated loop-connected loop-outer genes in turn. The red parts refer to the differentially expressed genes (DEGs), which occupy only a very small proportion (<10%). h Effect of H3K4me3 peaks and loops disrupted by H3K9me2 modification on transcription of genes on the indicated locus. Schematic below is a brief model. NS no significant difference. ***p < 0.001 from Wilcoxon test. i An example shows one H3K4me3 anchor was replaced by an H3K9me2 peak, causing the loop changes associated with the H3K4me3-marked region. However, there was no influence on the expression of other looped genes. Boxplots in e, h show the median, and third and first quartiles. Source data of f, i are provided as a source data file