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. Author manuscript; available in PMC: 2021 Jun 14.
Published in final edited form as: Cell Rep. 2021 May 18;35(7):109145. doi: 10.1016/j.celrep.2021.109145

Figure 3. Identification of GATA6-dependent chromatin accessibility and histone modifications.

Figure 3.

(A) ATAC-seq fragment depth during definitive endoderm formation at sites bound by GATA6 in definitive endoderm, n = 66, 581 sites; (i) GATA6+/+ pluripotent cells days 0–4; (ii and iii) GATA6+/+ and GATA6Ex4Δ1/Δ2;ind GATA6 cells with and without doxycycline at (ii) mesendoderm and (iii) definitive endoderm.

(B) ATAC-seq profiles aligned with GATA6-bound loci in definitive endoderm at genomic loci neighboring genes with known roles during endoderm formation and specification. GATA6−/− refers to GATA6Ex4Δ1/Δ2;ind GATA6 cells.

(C) Venn diagram of genes that neighbor GATA6-dependent changes in chromatin accessibility, definitive endoderm GATA6-dependent genes (mRNA), and genes with increased mRNA expression during hepatic specification. See also Table S3.

(D) Heatmap of GATA6 (blue) and H3K4me1 (red) at GATA6 binding sites during endoderm formation in GATA6+/+ and GATA6Ex4Δ1/Δ2;ind GATA6 pluripotent cells with and without doxycycline. Signal intensity represents ChIP-seq density. Heatmaps are split based on chromatin accessibility profile during definitive endoderm formation. Related to Figures S3A and S3B. GATA6−/− refers to GATA6Ex4Δ1/Δ2;ind GATA6 cells.

(E) ATAC-seq and H3K4me1 profiles during endoderm formation at the AFP gene loci in GATA6+/+ and GATA6Ex4Δ1/Δ2;ind GATA6 cells with and without doxycycline; GATA6−/− refers to GATA6Ex4Δ1/Δ2;ind GATA6 cells.