Fig. 4.

Features of TATA-dependent promoters in O. dioica. a Percentage of all consensus promoters within each expression cluster (left) (profiles shown in Additional file 1: Figure S2A) containing TATA-elements as labelled (TATAW = core TATA motif; TATA-box = consensus TATA-box). Percentage of promoters that contain TATA-elements within each expression cluster is also shown (right): the majority of TATA-dependent promoters are adult-specific. Expression clusters are grouped and coloured according to colours in Fig. 1b. b-c Plots show the mean log₂ ratio of methyl-DNA IP/input (b) or ChIP/input (c) (y-axis) at each probe position (x-axis) in a 1000 bp window centred on the dominant TSS, in ovaries, testes and embryos (tailbud) as labelled. Error bars show 95% confidence intervals for the mean obtained by bootstrapping. Promoters were divided into broad and sharp with sharp subdivided into those with a TATAW-element and those without and, in the testis, those with the position-specific TCTAGA motif. DNA methylation was enriched in the downstream of TATA-dependent promoters (b) and H3K4me2 and H3K4me3 were depleted in the same regions (c)