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Characterizing the epigenetic signatures of the human regulatory elements: A pilot study

Background Chromatin modifications have provided promising clues on how cells that share the same copy of the genome can perform distinct functions. It is believed that enhancers and promoters are marked by a single chromatin mark each, H3K4me1 and H3K4me3, respectively. However, other studies have indicated that enhancers and promoters share multiple chromatin marks, including H3K4me1/2/3 and H3K27ac. Therefore, we asked whether the epigenetic signatures of these regulatory elements consist of a single mark or multiple marks. Repetitive regions, repeats, are usually ignored. However, we found, in public data, that repeats include about 25% of active enhancers. Thus, we asked how the epigenetic signatures of repetitive and non-repetitive enhancers differ. We studied the four marks in IRM90 (human lung fibroblast) and H1 (human embryonic stem cell). Results Our results show that enhancers and promoters are enriched significantly with the four marks, which form pyramidal signatures. However, the relative lengths of the marks are different. The promoter signature is directional; H3K4me2/3 and H3K27ac tend to be present downstream of the transcription start site; H3K4me1 tends to be present upstream. H1-specific enhancers have a similar signature to IRM90-specific enhancers; however, it is not the case for active promoters of the two cell types. Interestingly, inactive enhancers show a residual signature that resembles the signature of active enhancers. Finally, the epigenetic signature of enhancers found in repeats is identical to that of enhancers found in non-repetitive regions. Conclusions In this study, we characterized the epigenetic signatures of active and inactive enhancers (pyramidal) as well as active promoters (directional-pyramidal) in two cell types. These signatures consist of four chromatin marks that have been reported to be associated with enhancers and promoters. Interestingly, about one quarter of active enhancers are found in repeats. Active enhancers within repeats and those outside repeats have the same epigenetic signature. These results have great potential to change the way Molecular Biologists think of repeats, and to expand our understanding of gene regulation.