Fig. 7: Gas41 KD perturbs the balance of bivalent domains.

a Heatmap profiles of H3K4me3, H3K27me3, Flag-GAS41, H2A.Z, H3K27ac and H3K14ac occupancies at TSSs (±5 kb) of the active (H3K4me3 only, n = 8618) or bivalent genes (n = 2389) in mESCs. b Box plots representing the log₂ fold change in expression (FPKM, reads per kilobase per million) of Gas41 KD (shGas41-1) relative to control (shNT) mESCs at all (n = 19,548), active and bivalent genes. The center line represents the median and box limits indicate the 25th and 75th percentiles. c Pie chart showing the proportion of bivalent genes that are upregulated (Up Bivalent, log₂FC ≥ 1, FDR ≤ 0.05), downregulated (Down, log₂FC ≤ −1, FDR ≤ 0.05), or genes with no change upon Gas41 KD. The “Down” and “No Change” groups were combined as “Other Bivalent”. The numbers of genes in each group are indicate in brackets. d Box plots showing the basal expression levels of the Up Bivalent and the Other Bivalent genes in mESCs. Center lines represent median values, and box limits indicate the 25th and 75th percentiles. Two-tailed unpaired Student’s t-test was used for statistical analyses. e Box plots of H2A.Z, H3K27me3, H3K4me3, H3K27ac, and H3K14ac occupancies at promoters of the Up Bivalent genes or Other Bivalent genes in mESCs. Boxes are defined as in b. Two-tailed unpaired Student’s t-test was used for statistical analyses. f Heatmap profiles of H2A.Z, H3K27me3 and H3K4me3 occupancies at the TSSs (±5 kb) of the Up Bivalent genes in control (shNT), Gas41 KD (shGas41) mESCs, and the difference between them (Δ, shGas41-shNT). Gray indicates a reduction and yellow indicates an increase in the Gas41 KD cells compared to the control cells. g Average profiles of H2A.Z (left panel), H3K27me3 (middle panel) and H3K4me3 (right panel) occupancies at the TSS (±5 kb) of the Up Bivalent genes in control (shNT, black line) and Gas41 KD (shGas41, red line) mESCs. Significance is determined by two-tailed unpaired Wilcoxon test. h Working model. Gas41 binds to acetylation on H3K27 and H3K14 through its YEATS domain and facilitates the recruitment of the SRCAP complex to bivalent gene promoters to exchange the canonical H2A for H2A.Z, which, in turn, maintains a poised state of the chromatin by facilitating the recruitment of PRC2 complex