Figure 2.

H3K4me3 peaks are found at promoters, where peak heights parallel gene expression levels. (a) 330 kb section of the gene-dense major histocompatibility complex (MHC) visualised in the Integrative Genomics Viewer [25]. Tracks display read depth for benchmark (gray) and new (black) ChIP methods at decreasing input cell numbers. Maximum read depth over the displayed area is indicated on the right of each track. Only uniquely mapping, non-duplicate reads are displayed. (b) 8 kb region showing H3K4me3 signal over the promoter of the RPL30 gene. (c) Sequence coverage over transcription start sites (TSS). Coverage is displayed as a function of gene expression, with genes divided into quartiles based on expression level.