Krox20 hindbrain regulation incorporates multiple modes of cooperation between cis-acting elements
Fig 4
Chromatin modifications and accessibility within the Krox20 locus.
(A) ChIP-seq was performed for the H3K4me1 mark on wild type E8.5 embryo heads (light blue) using biological duplicates. Only one set of data is shown. ATAC-seq was performed on dissected regions (r3, r5 and a more posterior region (“post”; see text) from wild type embryos at E8.5 (light blue) and E9.5 (dark blue) using biological duplicates. Only one set of data is shown. CTCF ChIP-seq data from E14.5 mouse brain (ENCODE) are indicated below (see Fig 3A). Genes, cis-regulatory elements (orange) and a genomic scale are indicated at the top. (B) ATAC-seq was performed on dissected parts from wild type (light blue), and Krox20ΔC/ΔC (green) and Krox20ΔA/ΔA (red) E8.5 embryos using biological duplicates. Only one set of data is shown. Cis-regulatory elements (orange) and a genomic scale are indicated at the top. Arrowheads indicate the summits (defined by macs2 after peak calling, see Material and methods) used for quantifications in (C). (C) Barplots showing signal intensity of ATAC-seq (normalized fragment counts) at the summit of each element (arrowheads in panel B) for wild type (WT, blue) and Krox20ΔC/ΔC (ΔC, green) embryos at E8.5 for each dissected part. The statistical significance was calculated using a negative binomial Wald Test (R package DESeq2) on the 2 replicates, which are represented by dots. Star indicates p-value < 0.05. ns: non-significant.