We thus examined whether MOF and its interaction partners were enriched on known enhancer regions, using lists of typical and super enhancers defined by binding sites of the pluripotency factors SOX2, NANOG, and OCT4 (Whyte et al., 2013), as well as sets of active and poised enhancers based on histone mark signatures (Creyghton et al., 2010).
While this could seem surprising given that other fragments show a more robust signal for histone modifications associated to regulatory elements (for example AF4, Figure 1B), enhancer prediction based on histone marks is only accurate in a fraction of cases [ 35].
For example, when defining enhancers based on histone marks (either H3K4me1, H3K27ac, or H3K4me1 and H3K27ac jointly) and using completely independent data from human skeletal muscle tissue, we also confirmed that the changing sites were observed predominantly in enhancers (Fig. 2C ).
When prediction was made based on more than one histone mark, a TF with simultaneous "High_Vs" was predicted.
Epigenetic regulation based on histone modification is essential for numerous biological processes in eukaryotic organisms1,2.
As an independent biological validation, we conducted ChIP-seq experiments on one histone mark, dimethylation of lysine 4 at histone H3 (H3K4Me2).
It provides a mechanistic explanation of how, based on epigenetic histone marks, AIRE is guided to its target genes in the thymus.
Based on coexisting histone marks and genome-wide ChIP-seq data available within the ENCODE consortium, principal component analysis has reduced the complexity of the histone code into different chromatin states that are associated with developmental and environmental cues [ 41- 44].
We then clustered the transcripts based on their histone marks in the state where they are more lowly expressed (correlated transcripts: EWS-FLI1-low state after EWS-FLI1 knockdown; anticorrelated transcripts: EWS-FLI1-high state before EWS-FLI1 knockdown).
These were then categorised into lineage-specific promoters and enhancers based on their dominant histone mark enrichment across species within the clade, as described above.
Highly conserved regions were classified as promoters or enhancers based on their consensus histone mark enrichment across all 20 mammals (Experimental Procedures).
