Secondly, the ENCODE analyses are built on deep layers of previous functional genomics work, and are in essence a series of correlations: the following epigenetic marks correlate with such and such other features of the genome.
We have demonstrated in senescent and Polycomb mutant cells that the "bivalent" domain at the INK4a/ARF locus (H3K27me3 and H3K4me3) is resolved and the locus remains only enriched in H3K4me3 positive marks correlating with the recruitment of MLL1 protein.
ATAC-seq is highly correlated with permissive marks, while Ring1b shows a high degree of correlation with H3K27me3, the mark of Polycomb Repressive Complex 2. (e) Enrichment of enhancers, transcription start sites (TSSs), transcription termination sites (TTSs), and intergenic regions in ATAC-seq datasets by class.
In other words, enrichment of H3K4me1 and H3K27Ac correlated with active and engaged enhancers [ 38, 39], whereas poised enhancers (H3K4me1 without H3K27Ac marks) correlated with relatively lower expression levels of the target genes [ 36].
Total scores for AW and AECOPD questionnaires were modestly positively correlated with students' marks on the end-of-rotation final written exam (Pearson correlation of 0.22, p < 0.0001 for CIWA, 0.28, p < 0.0001 for AECOPD).
MYST1 is negatively correlated with the aforementioned marks yet positively correlated with H3K27acK36un and H3K9acK14un.
Overall, the presence of H3K4me3 marks correlated tightly with the expression of both miRNAs and mRNAs, while H3K27me3 modifications negatively correlated with their expression.
It doesn't affect time spent studying, either, and while there's a small correlation between its use and poorer grades, intense messaging actually correlated with better marks.
Finally, students' academic literacy results were correlated with their marks in other subjects.
All 4 collective marks correlated with each other significantly (P < 0.001).
a. Venn diagram of overlap between BAF activity-dependent peaks and two histone marks correlated with transcriptional repression, H3K27me3 and H3K9me3.
