Fig. 2

CUT&Tag for histone modification profiling and RNAPII. a Representative chromatin landscapes across a 3 Mb segment of the human genome generated by the indicated method. For H3K27me3, we downsampled ChIP-seq and CUT&RUN datasets to the same total mapped read counts as CUT&Tag for direct comparison. The high background in downsampled ChIP-seq is from singleton reads distributed across the genome. b Same as a except for H1 ES cells. c Comparison of profiling methods for the H3K4me1 histone modification in K562 cells. The same antibody was used in all experiments. Peaks were called and ordered for each dataset using MACS2. Each dataset was downsampled to the same read depth for comparison and plotted on their called peaks. Color intensities are scaled to the maximum read count at peaks in each dataset. d Detection of gene activity by RNAPII CUT&Tag. Gene promoters were ordered by associated RNA-seq counts (gray wedge) and read counts from RNAPII S2/5p CUT&Tag were plotted on these sites. e Active RNAPII is enriched at RNAPII CUT&Tag peaks. Peaks were called from RNAPII S2/5p CUT&Tag and ordered using MACS2 (gray wedge). PRO-seq reads were displayed onto these positions for (+) strand reads (yellow) and (–) strand reads (blue). f Comparison of ATAC-seq and H3K4me2 CUT&Tag profiling in K562 cells. Peaks were called on ATAC-seq data and heat maps were produced as in c. The top and bottom 2.5% of peaks were discarded to remove outliers. g Metaplot comparison of H3K4me1 histone modification signal in CUT&RUN, CUT&Tag, and ChIP-seq in K562 cells, averaged at the top 10,000 peaks detected by MACS2 in ChIP-seq data. Profiling with the same antibody was compared at the downsampled read depths of 8 million mapped reads for all three methods (blue, cyan, and green), and for 40 million mapped reads (orange) from ChIP-seq. h Metaplot comparison of ATAC-seq and H3K4me2 CUT&Tag profiling in K562 cells. 53,805 peaks were called on ATAC-seq data using MACS2, and read counts from each method were averaged across the intervals. The top and bottom 2.5% of peaks were discarded to remove outliers. Read counts at 17,000 randomly-chosen intervals for each dataset are displayed as dotted lines. Source data are available in the Source Data file