Differential contribution to gene expression prediction of histone modifications at enhancers or promoters
Fig 1
Identification of repressed and active functional regions in ESCs.
(A) State definition of the chromatin segmentation model in ESCs. The values represent the probability (from 0 to 1) of finding each histone modification (vertical) in genomic segments of states 1 to 9 (horizontal). The cells of the matrix are colored according to the value of probability they contain inside. Red: states with histone modifications associated to activation (active, 1–4); dark yellow, H3K4me1-only state (Intermediate, 5); grey, states in which H3K27me3 was present (repressed, 6–8); dark grey, poised states, in which H3K27me3 colocalized with H3K4me3 and/or H3K4me1 (states 6 and 7); light grey, H3K27me3-only regions (state 8); and white, unmarked state (9). (B) Example of a genomic region containing two expressed genes (Skap2 and Halr1), which are covered by active states (in red), and a cluster of repressed genes (HoxA), which are covered by repressed states (in grey). Active chromatin segments integrate the signal of H3K27ac, H3K4me3, and H3K4me1 and lack H3K27me3. Repressed chromatin segments integrate the signal of H3K27me3, H3K4me3, and H3K4me1 and lack H3K27ac. Expression of Skap2 and Halr1, and silencing of HoxA genes, were confirmed by the RNA-seq profiles [23]. Y-axis represents normalized count of reads by total reads. The screenshot was taken from the UCSC Genome Browser [62]. (C) Enrichment of state transitions (e.g., number of observed transitions divided by the number of expected transitions by chance) from the segments of one state (vertical) towards the segments of another state (horizontal) in the linear chromatin. The cells of the matrix are colored according to the value of enrichment they contain inside. (D) Expression of genes associated to active promoters (AP; 10,786 genes) or bivalent promoters (BP; 3,459 genes). The dotted line represents 1 FPKM. (E) Top GO biological process (2018 categories) for each list of genes in D.