Fig. 6: Characteristics and functional implications of two SSTEs types: stable-SSTEs and dynamic-SSTEs.
From: Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq
a Heatmap showing the enrichment of H3K27ac ChIP-seq, ATAC-seq, KAS-ATAC-seq, GRO-seq, NET-CAGE, mNET-seq, Zcchc8 RIP-seq, and Rbm7 RIP-seq data on intergenic stable-SSTEs (n = 1961) and dynamic-SSTEs (n = 11,013) in mESCs. b Snapshot of UCSC genome browser tracks displaying H3K27ac ChIP-seq, ATAC-seq, KAS-ATAC-seq, GRO-seq, NET-CAGE, mNET-seq, Zcchc8 RIP-seq, Rbm7 RIP-seq, and YY1 ChIP-seq on S-SSTEs, D-SSTEs, and DSEs. YY1 ChIP-seq data from DMSO and Actinomycin D (Act D) treated mESCs are displayed. c Line graph depicting the cumulative frequency of intergenic S-SSTEs (n = 1961) and D-SSTEs (n = 11,013) with detectable nascent RNAs (FPKM ≥ 0.5) detected by nascent RNA-seq assays. d, e Metagene profiles showing the Zcchc8 RIP-seq (d) and Rbm7 RIP-seq (e) read densities across S-SSTEs, D-SSTEs, and DSEs in mESCs. f, g Metagene profiles showing the ATAC-seq (f) and KAS-ATAC-seq (g) read densities across S-SSTEs, D-SSTEs, and DSEs in mESCs. h Stacked bar plot showing the percentages of S-SSTEs, D-SSTEs, and DSEs that overlap with and without super enhancers (SEs). i Snapshot of UCSC genome browser tracks displaying H3K27ac ChIP-seq, ATAC-seq, KAS-ATAC-seq, mNET-seq, and NET-CAGE data in mESCs on a representative SE. j Metagene profile showing STARR-seq signals, with input subtraction, across S-SSTEs, D-SSTEs, and DSEs in mESCs. k Boxplot comparing the transcriptional levels of genes associated with randomly selected 3000 S-SSTEs, D-SSTEs, and DSEs. The two-sided p-values were calculated using the unpaired Student’s t-test. P-values < 0.0001 was shown as ****. The box shows 1st quartile, median and 3rd quartile, respectively. Whiskers show the range from the 10th to the 90th percentile, with data points outside this range not shown. l Table presenting the enriched transcription factors (TFs) motifs identified on S-SSTEs in mESCs. The hypergeometric test was used to calculate p-values. m Metagene profiles showing YY1 ChIP-seq reads density across S-SSTEs, D-SSTEs, and DSEs in mESCs. n, o Scatterplots showing the Pearson correlation between KAS-ATAC-seq (n), NET-CAGE (o), and YY1 binding density reduction caused by Actinomycin D (Act D) treatment on intergenic SSTEs (n = 12,601) in mESCs. The Pearson correlation coefficients and associated two-sided p-values are displayed. Points densities are color-coded in light blue.
