Fig. 3

Features of maternal, zygotic and ubiquitous promoters in O. dioica. a Ordered nucleosome positioning at broad promoters in the ovary. Data are shown for H3, H3K4me1, H3K4me2, H3K4me3 and E2F1 ChIP-chip experiments. Each plot shows the mean log₂ ratio of ChIP/input at each probe position in a 1000 bp window centred on the dominant TSS. Promoters were categorized into sharp (blue) and broad (pink) using lower and upper quartiles of widths across all stages. Error bars show 95% confidence intervals for the mean obtained by bootstrapping. b Percentage of all consensus promoters (left) within each expression cluster (x-axis) (profiles shown in Additional file 1: Figure S2A) containing sequence elements as labelled (O. dioica TFAP4-like motif, ACCATAA motif). Percentage of promoters that contain each motif falling within each expression cluster is also shown (right). Expression clusters are grouped and coloured as coded in Fig. 1b. c Sequence logo for an over-represented motif (E-value and number of sites as indicated) in zygotic promoters (tailbud sequences from TCs with dominant CTSS in cluster 0_0) in O. dioica (top), and its alignment to a significant match (E-value and p as indicated) for the binding site motif of human TFAP4. d Heatmap shows the density of the zygotic promoter motif matching TFAP4 at each position (x-axis) in a -500 to +500 bp region centred on the tailbud dominant TSS for zygotic promoter sequences (rows) ordered by promoter width (top to bottom = broad to sharp). Darker blue indicates higher enrichment. e Distance relative to the dominant TSS in day 2 animals for the ACCATAA motif found in sharp promoters that have ubiquitous and day 2-specific expression profiles