Skip to main content
. 2020 Jan 28;9:e50670. doi: 10.7554/eLife.50670

Figure 6. Hedgehog-responsive GBRs have tissue-specific enhancer activity within HH-specific domains.

Figure 6.

(A) Enhancers with annotated limb activity in VISTA corresponding to representative HH-responsive GBRs (bottom) and Stable GBRs (top) with limbs magnified and outlined in insets. Limb buds containing HH-specific domains of enhancer activity are indicated by an asterisk. (B) Chart indicating total number of VISTA enhancers tested for HH-responsive and Stable GBRs, the numbers of enhancers for each category and their limb enhancer activity. (C) Chart delineating the percentage of HH-responsive and Stable limb enhancers that drive expression in one or more tissues. (D) Venn Diagram of enhancer marks H3K27ac, H3K4me1, H3K4me2 and ATAC, in Stable and HH-responsive GBRs tested in VISTA that drive expression in the limb. GBRs, are by definition are marked by H3K27ac. (E) Enrichment of enhancer markers at a representative HH-responsive GBR tested in VISTA (hs280, Figure 6A). (F) Schematic of NIH3T3 H3K27ac ChIP treated with and without the HH agonist purmorphamine (+HH) and the activity of representative HH-responsive and Stable limb GBRs in response to HH activation in limb and NIH3T3 cells (n = 2). (G) Graph indicating how the acetylation status of HH-responsive and Stable limb GBRs responds to HH signaling in HH-responsive NIH3T3 cells. See Figure 6—source data 1; Figure 6—source data 2.

Figure 6—source data 1. Stable and HH-responsive GLI binding regions with limb enhancer activity in the VISTA dataset.
Tab 1. Columns indicate VISTA enhancer IDs, coordinates, number of tissues with limb enhancer activity as annotated by the VISTA database (Visel et al., 2007) and its corresponding GBR category. Tabs 2–5. Normalized signal and called peaks for H3K27ac, ATAC, H3K4me1 and H3K4me2 in WT, and Shh-/- limbs if applicable, is listed for all HH-responsive GBRs (Tab 2- normalized signal; Tab 3-called peaks) and Stable GBRs (Tab 4- normalized signal, Tab 5-called peaks) that were shown to drive limb activity, as tested in the VISTA database. For called peaks in Tabs 3, 5, ‘NO’ denotes not a significantly called peak, ‘YES’ denotes a called peak.
Figure 6—source data 2. NIH3T3 H3K27ac ChIP-seq analyzed data and called peaks.
H3K27ac called peaks with a FDR < 0.05 from two replicates of purmorphamine (‘pm’) treated or DMSO control NIH3T3 cells. For each peak, the assigned Peak ID, coordinates, peak type, fold change normalized to input for purmorphamine treated and control samples, and fold change of purmorphamine treated over control are listed. Additional tabs include sorted files for each peak type.