Analyzing histone ChIP-seq data with a bin-based probability of being signal
Fig 3
Using PBS to detect changes in H3K27me3 levels during cell differentiation.
(A) Summary of genome-wide PBS across H3K27me3 datasets of iPSCs, myeloid progenitors, or neutrophils. The number of bins with high PBS (> 0.8) increases with increased cell differentiation. Additionally, moderate levels of PBS (between 0.2 and 0.8) corresponding to low, broad H3K27me3 signal, appear exclusively in more differentiated cell types (myeloid progenitor cells and neutrophils). (B) Comparing iPSC, myeloid progenitor cells and neutrophils, including signal tracks (top), MACS2 peaks (middle), and PBS (bottom). Highlighted are regions with no signal in all three datasets (i); no signal in iPSC but moderate signal in myeloid progenitors and moderate-high signal in neutrophils (ii); and high signal in all three cell types (iii). While both peak calling and PBS identify the consistent sharper peak in (iii), only PBS meaningfully detects the spreading enrichment in (ii) (14 peaks, spanning 3.8% of the region vs. 74% of the region with PBS equal to 0.8 or higher).