Fig. 3

ACT2-seq directly profiles co-occupancy between pairs of epigenetic factors. A Illustration of the types of DNA fragments generated by the ACT2 method. Each fragment type provides enrichment information for either antibody A, antibody B, or both (co-occupancy). B Genome browser snapshot of a representative genomic region enriched for “active” chromatin marks. The top three tracks were obtained from a single sample in which H3K4me3 and H3K27ac were mapped concurrently. Four data tracks are provided: one for total H3K4me3 signal, one for total H3K27ac signal, one for only co-occupancy reads, and one for ENCODE ChIP-Seq of RNA Pol II for comparison. C Genome browser snapshot of a representative genomic region enriched for both H3K9me3 and H3K4me3. The top three tracks were obtained from a single sample in which H3K4me3 and H3K9me3 were mapped concurrently. Four data tracks are provided: one for total H3K4me3 signal, one for total H3K9me3 signal, one for only co-occupancy reads, and one for ENCODE ChIP-seq of RNA Pol II for comparison. Note the region of high H3K9me3 enrichment that roughly correlates to chromosome band p12.1 in black. D Scatter plots examining peak enrichment correlation between two biological replicates of co-enrichment data. Each data point represents the read density of a single enriched region. E Metagene profiles of average read density within annotated genes for co-enrichment of the indicated epigenetic factors. All three co-enrichment data sets were obtained from a single concurrent mapping of H3K4me3, H3K27ac, and H3K9me3. TSS: transcription start site. TTS: transcription termination site. Gene lengths have been scaled to 10 kb to facilitate alignment. Plots are provided for gene sets representing the top and bottom expression quartiles