Fig. 3: RT&Tag captures transcripts within polycomb domains.
From: Profiling RNA at chromatin targets in situ by antibody-targeted tagmentation
a, Illustration showing RT&Tag being used to capture transcripts within H3K27me3 demarcated polycomb domains. b, Volcano plot showing transcripts that are differentially enriched for H3K27me3 RT&Tag over IgG (FC >2, FDR < 0.05, n = 5). Genes enriched for H3K27me3 are highlighted in red, nonenriched are in black and depleted are in blue. The two most highly significant transcripts are labeled. c, Genome browser track showing the distribution of H3K27me3 and IgG RT&Tag signal over the gene bodies of CR43334 and CR42862. Combined reads from five replicates are shown. d, Bar graph showing the number of H3K27me3-enriched transcripts that are protein coding or noncoding. e, Boxplot showing the RNA-seq expression levels (CPM) of H3K27me3-enriched or nonenriched transcripts. *P = 4.32 × 10−10, Welch two sample t-test (two-sided), n = 1,343 for H3K27me3-enriched, n = 14,403 for nonenriched, n = 2 independent RNA-seq experiments. For the boxplots, the interquartile range (IQR) is shown within the limits of the box, the center line represents the median, the whiskers show data that is within 1.5 times the IQR and outliers are omitted. f, Profile plots showing the H3K27me3 (left), H3K36me3 (middle) and H3K4me3 (right) CUT&Tag signal around the gene bodies or TSS of genes that were categorized as being enriched for H3K27me3 RT&Tag or nonenriched. Combined reads from two replicates for H3K27me3 and from one replicate for H3K36me3 and H3K4me3 are shown. Error bands indicate standard error. g, Graph showing the IgG and H3K27me3 RT&Tag signal (CPM) for the HOX cluster genes. *FDR < 0.05, n = 5 independent RT&Tag experiments. h, Profile plots and heatmaps showing the H3K27me3 (left), H3K36me3 (center) and H3K4me3 (right) signal over the gene bodies or TSS of H3K27me3 RT&Tag-enriched transcripts that have high or low levels of H3K27me3 CUT&Tag signal over their gene bodies. Heatmaps are plotted in order of decreasing CUT&Tag signal. Error bands indicate standard error.
