Fig. 6

Subgenome-specific recruitment of p300 is associated with TEs. Subgenome-specific p300 peaks are enriched for TEs carrying transcription factor (TF) motifs active in early development. a Differential regulation of the slc2a2 homeologs at stage 10.5. Shown are the genomic profiles of H3K4me3 (green), RNA Polymerase II (RNAPII; purple), H3K36me3 (blue), and p300 (yellow) ChIP-seq tracks, as well as DNA methylation levels determined by WGBS (gray). The top panel shows slc2a2.L, which is highly expressed, as evidenced by RNAPII and H3K36me3, and has a number of active enhancers (a–g), while slc2a2.S, shown in the bottom panel, is expressed at a lower rate. The conservation between the L and S genomic sequence is shown in gray between the panels. Differential enhancers between L and S are highlighted in yellow, which illustrates lost enhancer function (a, b), conserved enhancer function (c–e), and deleted enhancers (f, g). b Subgenome-specific p300 peaks are associated with DNA transposon repeats (threshold p ≤ 10e-4, twofold enrichment compared to all X. laevis peaks and present at least in 15% of the peaks). The barplots show the frequency of occurrence of each of the three repeat types per megabase in the three (sub)genomes. Over the bars is represented the percentage of subgenome-specific peaks overlapping with the corresponding repeat. c TF found to be enriched in the subgenome-specific p300 peaks (threshold p ≤ 10e-4, threefold enrichment compared to all X. laevis peaks and present at least in 20% of the peaks)