Supplementary Material for Dynamics of enhancers in myeloid antigen presenting cells upon LPS stimulation Supporting analysis of “active promoter” and “enhancer” region properties

Supporting analysis of “active promoter” and “enhancer” region properties We compared a number of properties of “promoter” and “enhancer” regions as defined in the main paper. We observed that both clusters contained high levels of PU.1 and C/EBPβ ChIP-seq tags, but Pol2 binding was restricted mainly to the “promoter” cluster (Supplementary Fig. 1B). CpG scores and GC content (not shown) were markedly higher in “promoter” regions (and “repressed 1” regions). The distribution of distances to the most proximal RefSeq TSS showed that “promoter” regions tended to be located proximally to known TSSs (89.8% were located < 5kb from a known Refseq TSS), while “enhancer” regions were typically located more than several kbs away from known TSSs (87.2% were located > 5kb from a known Refseq TSS). Using Refseq gene annotations, we found that 23.3% of “promoter” regions were located around known TSS regions or within 5’UTRs of known genes in contrast to only 0.7% members of the “enhancer” cluster (Supplementary Fig. 1C). The vast majority (94.4%) of “enhancer” members, on the other hand, were located in intergenic regions in contrast to 57.3% for “promoters”. Together, these features support the nomenclature of these regions.