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. Author manuscript; available in PMC: 2024 Jan 19.
Published in final edited form as: Cell. 2023 Jan 12;186(2):305–326.e27. doi: 10.1016/j.cell.2022.12.027

Figure 5. Erosion of the epigenetic landscape in ICE cells.

Figure 5.

(A) Quantitative mass spectrometry of histone H3 and H4 modifications in 96-hour post-treated ICE cells. %, relative abundance; unmod, unmodified; me, methylation; ac, acetylation.

(B) Genome-wide changes of H3K27ac in 96-hr post-treated cells. Heatmap of ICE/Cre.

(C) Gene Ontology analysis of H3K27ac-increased, H3K56ac-increased, or H3K27me3-decreased peaks ordered by top 20 processes enriched in H3K27ac-increased regions (padj < 0.01). ↑, Cre < ICE peaks, padj < 0.01; ↓, Cre > ICE peaks, padj < 0.01.

(D) TreeFam analysis of gene families with overlapping regions with histone modification changes (padj < 0.01) in ICE cells.

(E) Volcano plot of H3K27ac peaks. All peaks and peaks in Hox genes shown white to yellow and blue to purple, respectively.

(F) ChIP-seq track of histone modifications and mRNA levels across the 120 kb Hoxa locus of post-treated ICE cells. Difference = ICE – Cre

(G) Hi-C contact matrices and HiChIP contact loops in Hoxa. Red, chromatin contacts between Hoxa promoters and other regions. Lower panels, regions with ChIP-seq or RNA-seq peaks. Peak regions, red (Cre<ICE), blue (Cre>ICE) or grey (unchanged).