Examples of histone modification patterns in promoters and enhancers. (A) Promoter prediction using chromatin signature. TSS near chr1:148185131 shows a typical histone modification pattern for promoter while H3K4me3 has a relatively weak signal for the TSS near chr1:148158254. The predictions made by the profile based method of Heintzman et al. are labeled in green and the predictions made by the HMM developed in this study are in red. (B) Enhancer prediction using chromatin signature. A p300 binding site is shown at chr6:132486009 and overlaps with a DHS site, which is a strong evidence to support an enhancer site. (C) Enhancer prediction using chromatin signature. A DHS site near chr8:119170000 overlaps with a weak H3K4me3 signal but is not found as an enhancer by the profile-based method.
Won et al. BMC Bioinformatics 2008 9:547 doi:10.1186/1471-2105-9-547