Fig. 4

Identification of high-regulatory load genes in human macrophages. a Active enhancer regions were identified via chromatin immunoprecipitation coupled to high throughput sequencing (ChIP-Seq) with an antibody against H3K27ac using chromatin from monocyte-derived day 11 macrophages from 3 anonymous donors. Enhancer regions were considered reproducibly detectable when their genomic coordinates overlapped by at least one nucleotide in all biological replicates. b Selected enriched sequence motifs located within the identified active enhancer regions associated to upregulated genes in macrophages and corresponding to known transcription factor binding sites are shown. See full list in Additional file 1: Figure S4. c Genes associated with at least one active enhancer region were ranked in function of the number of active enhancer regions. A threshold (blue line) corresponding to the top 10 % and at least 7 active enhancer regions was set to segregate between high regulatory load genes and the remaining expressed genes (please see Discussion for details on the threshold selection). 105 kb genomic regions surrounding SPI1 and CD4 loci, mapped reads indicating H3K27ac enrichment from the three donor samples, and called reproducible peaks are shown as examples of high regulatory load and low regulatory load genes, respectively. d The distribution of the expression levels of the high regulatory load genes was compared to genes that have a number of enhancers below the threshold of seven enhancers but that are associated to at least one enhancer (KS-test, p-value = 4.63e-38). e The enhancer load of the metabolic genes present in the consistent version of Recon2 was determined and then manually curated to minimize false peaks-to-gene assignments allowing identification of 74 high-regulatory load genes (≥7 enhancers), 55 of which mapped to the macrophage model. The distribution of expression levels of these metabolic high regulatory load genes was compared to the distribution of expression of the remaining metabolic genes of the macrophage model (KS-test, p-value = 1.8537e-11)