Extended Data Fig. 10: Expanded analysis of ChIP-seq and srHC-seq in siERH. | Nature Cell Biology

Extended Data Fig. 10: Expanded analysis of ChIP-seq and srHC-seq in siERH.

From: Diverse heterochromatin-associated proteins repress distinct classes of genes and repetitive elements

Extended Data Fig. 10

a, DNA size profiles of sonicated fractions from siControl and siERH. b, Combinatorial H3K9me3 and H3K27me3 levels for srHC genes in siControl treated human fibroblasts. c, Heatmap displaying enrichment of H3K9me3, H3K27me3, dual-marked, and unmarked srHC gene subtypes in siControl and siERH from 2kp upstream of TSS to 2kp downstream of TTS. d, Activation of srHC alternative lineage genes in siERH relative to siControl during hiHep reprogramming not activated by siERH without hiHep factors. e, Percent occurrence of top 5 motifs enriched in promoters of non-hepatic genes upregulated in siERH+hiHep conditions and corresponding expression of the putative targeting factors in 4 siControl+hiHep replicates. f, H3K9me3 changes at classes of key hepatic genes, cytochrome p450 (n=50), UGT (n=21), SLC transporter (n=196) and ABC transporter (n=27), in siERH compared to siControl. Boxplot center, bounds and whiskers represent the median, 25–75% range and minimum to maximum values. g,h, Location of srHC genes gaining H3K9me3 (g) and H3K27me3 (h) on t-SNE embedding. i, hiHep motifs from Jaspar database and identified motifs in promoter regions (tss +/− 200) of srHC genes with motif scores >=10. j, Table showing total gene numbers and activation rates in siERH for sets of srHC genes defined by presence of strong hiHep motifs and specific changes in H3K9me3 and H3K27me3 levels.

Back to article page