XB-IMG-175979
Xenbase Image ID: 175979
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Figure 6. Otx1, Vegt, and Foxh1 Establish SEs near Key Endodermal Genes
(A) Categorization of H3K4me1 enhancer regions as regular enhancers (REs) and super-enhancers (SEs) using the rank order of super-enhancers (ROSE) algorithm based on H3K4me1 signal.
(B) Length of RE and SE in kilobases.
(C) Number of constituent enhancers (H3K4me1 peaks) within REs and SEs.
(D) Genome browser view of SEs in the pnhd, admp, foxa4, and sox17 locus, which are populated with Otx1, Vegt, and Foxh1 ChIP-seq peaks.
(E) Comparison of epigenetic marks in REs and SEs focusing on heterochromatin, enhancer, and polycomb marks. Plotted is the fold change of the median ChIP read density in SE over RE.
(F) Maternal TF ChIP read density in REs and SEs.
(G) Overlap of 1-TF, 2-TF, or 3-TF CRMs (OVF-CRMs) peaks with the H3K4me1-identified REs or SEs.
(H) GO analysis of genes associated with SEs.
(I) Temporal expression of genes associated with REs and SEs, along with randomly selected genes, normalized to the gene expression at 0 hpf.
(J) Gastrula stage spatial expression of genes associated with REs and SEs, along with randomly selected genes in log2(TPM).
(K) Log2-fold change of gene expression in Vegt + Otx1 MO and Foxh1 MO over uninjected control of genes associated with REs and SEs, along with randomly selected genes.
Significance for (E) and (F) was determined using the Wilcoxon rank-sum test by comparing the signals in the set of SEs (N = 441) to the set of REs (N = 7,468). The significance for (K) was determined using the Wilcoxon rank-sum test whereby the number of random genes was sampled to the number of SE genes (N = 490) from the set of genes not associated with REs or SEs. The number of RE genes was sampled down to the number of SE genes. Image published in: Paraiso KD et al. (2019) Image reproduced on Xenbase with permission of the publisher and the copyright holder. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial-NoDerivatives license Larger Image Printer Friendly View |