Fig. 2

Characterization of ChIA-PET loops. a Global views of intrachromosomal interactions tethered by RNAPII, H3K27me3, and H3K9me2 of chromosome 3 in Arabidopsis. Green peaks above chromosomes indicate binding sites, and curves under chromosomes indicate chromatin interactions. Yellow, blue, and red curves indicate interaction spans smaller than 1 Mb, between 1 to 10 Mb, and larger than 10 Mb, respectively. b Loop span distribution of interactions connected by the indicated factors. c Percentages of promoter-promoter, intergenic-intergenic, and promoter-intergenic interactions mediated by the indicated factors. The regions of 1 kb upstream to 0.5 kb downstream of the transcription start site (TSS) of annotated protein-coding genes were defined as promoters. Intergenic regions referred to the regions excluding 1 kb upstream of the TSS to the transcription termination site. d Boxplot for intensities of the indicated factor-associated anchor peaks and basal peaks. ***p < 0.001 from Wilcoxon test. e Expression levels of the indicated factor-associated anchor genes and basal genes. ***p < 0.001 from Wilcoxon test. f Expression breadth (defined as the number of tissues in which a transcript is detected) of the indicated factor-associated anchor genes and basal genes. Random genes served as control. g Expression levels of the paired active anchor genes. Anchor genes from H3K27me3 and H3K9me2 loops served as control. We sorted the gene expression levels from high to low and divided them into three categories: 80–100%, 20–80%, and 0–20%. More red wavy lines indicate higher expression. ***p < 0.001 from Wilcoxon test. h Co-expression analysis of the active anchor gene pairs. The mean Pearson correlation coefficient (PCC) of anchor gene pairs is much higher than that of both randomly simulated gene pairs A and randomly selected active anchor gene pairs B, which have the same physical distance as anchor gene pairs. ***p < 2.2e-16 from Wilcoxon test