The SNP site is enriched with active enhancer epigenetic marks, H3K4me1/2 and H3K27ac (Fig. 4a).
Angiosperm DRMs are a part of the RNA directed DNA methylation (RdDM) pathway that utilizes small RNA to establish de novo methylation within euchromatic transposons, that is enriched with active histone marks such as H3K4me3 and depleted of repressive marks as H3K9me222,23,24,25.
We find that most TSSs are repressed in the cell lines studied here, however, a substantial number of the repressed TSSs are enriched with active chromatin marks.
Finding both that families of TEs are enriched with active histone modifications, and old families more so than younger, they conclude, "'With a few exceptions', most of our findings support the exaptation hypothesis" (Huda et al. 2010).
Bioinformatic analyses of genome-wide data sets from worms and humans revealed that exons are enriched with active histone modifications while introns are generally depleted of these same marks [ 5, 7, 9].
The rs4795397 region is enriched with the active histone mark H3K9Ac, but not the repressive chromatin mark H3K27me3, an observation which is consistent with the histone acetyltransferase activity of EP300 (Ogryzko et al. 1996).
As expected, the pluripotency module is enriched with genes active in transcriptional regulation, e.g. Oct4, Sox2, Klf2, Nanog, Jarid1b, Jarid2, Nodal, Tgif1, and Esrrb, and contains other genes expected to play a role in ES cell function, such as Dppa4 and Dppa5.
We conclude that HCC is enriched with candidate MSCs, suggesting active sequestration of these cells by the tumor and a possible role of MSCs in HCC tumorigenesis.
The fifth cluster (8% of all genes) is enriched with both elongation (H3K36me3) and active marks (H3k9me1) but depleted of the canonical activating marks (H3k4me, H3k9ac, and H3k27ac).
