At HMEC specific enhancer loci (HSEL), H3K4me1 marks were highly enriched in HMEC, compared to MDAMB231 with more than 60 fold higher mean density of H3K4me1 ChIP-seq tags.
The measured signals for specific marks were highly reproducible in separate biological replicates, and Hairy-induced changes in histone marks were consistently observed at specific loci, such as the widespread loss of the H4Ac signal on the ftz locus, with little change to the overall global chromatin landscape.
Methylation changes may or may not persist over time in the human genome, as epigenetic marks are highly plastic.
Understanding the functional/mechanistic role of epigenetic marks is highly desirable, but that in many cases it may be difficult to directly obtain such insight.
Although the presence of a distinct nucleosome signature can have predictive value, the function of a given histone mark is highly context dependent.
As previously shown (Smagulova et al. 2011), H3K4me3 marks are highly overrepresented in DSB hotspots in testis, but not in liver (fig. 4 D).
For instance, the activating mark H3K4me2 mark was highly enriched in nucleosome ChIPed with H3.3 or H2A.Z (11.5-fold in H3.3 and 19.8-fold in H2A.Z as compared with the genomic chromatin levels).
Interestingly, the positive genes that are enriched in both the histone marks are highly enriched in the categories of tissue specific cellular functions, such as endocrine system disorders, gastrointestinal disease.
Since PR-SET7 is the sole enzyme capable of generating H4K20Me1, this suggests that the H4K20Me1 mark is highly stable in non-dividing cells, as it can persist for at least 100 days in the complete absence of the enzyme.
Genome-wide profiling of H3K9ac and H3K27ac reveals that both marks are highly induced on the PPARγ gene locus during 3T3-L1 differentiandon and correlate with PPARγ gene expression [ 76, 77].
