(A) Numbers of experimentally identified promoters (H3K4me3&H3K27ac, purple; H3K4me3, blue) and enhancers (H3K27ac, orange) per species are represented as stacked barplots in the upper plot, ordered by decreasing number of biological replicates used for each species (lower plot). Except for Bbor (Balaenoptera borealis), where a single replicate was used, the number of biological replicates has little influence on the number of active regulatory regions identified per species.

(B) As in (A), but numbers of promoters/enhancers in each species are now ordered by decreasing scaffold or contig N50 values, both indicative of genome assembly quality. Species highlighted in blue correspond to genomes in the EPO multiple alignment, considered to be the highest-quality reference genomes. Assembly qualities do not appear to influence experimental variation in the number of promoters or enhancers identified in each species.

Kim et al., 2010 Kim T.K.

Hemberg M.

Gray J.M.

Costa A.M.

Bear D.M.

Wu J.

Harmin D.A.

Laptewicz M.

Barbara-Haley K.

Kuersten S.

et al. Widespread transcription at neuronal activity-regulated enhancers. (C) The distribution of distances to the nearest transcriptional start site (TSS) was calculated for all experimentally identified regions in each species’ data (thin lines). Bolded lines represent the average distance distribution across all species for H3K4me3 (blue), H3K4me3&H3K27ac (purple) and H3K27ac (orange) elements. In agreement with their categorisation as enhancer elements, in all species most H3K27ac locations are distal to coding regions. Both H3K4me3 and H3K4me3&H3K27ac elements are largely located close to annotated TSSs consistent with being proximal promoters. The minority of distal elements marked by H3K4me3 or H3K4me3&H3K27ac may correspond to unannotated transcripts; further, the latter may also act as enhancers ().

Kheradpour et al., 2013 Kheradpour P.

Ernst J.

Melnikov A.

Rogov P.

Wang L.

Zhang X.

Alston J.

Mikkelsen T.S.

Kellis M. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. (D) H3K27ac-defined enhancers enrich for regulatory activity: Human liver enhancers identified in this study through H3K27ac ChIP-seq (bottom inset) were overlapped with 145 bp sequence elements assayed for reporter activity in human liver carcinoma (HepG2) and human erythroleukemia cells (K562) (top inset;). These correspond to enhancer candidates identified in HepG2 cells and containing motifs for liver-specific transcription factors.