Fig. 3: Gene regulation.

a Hi-C contacts within scaffold (=chromosome) 1 of our assembly, showing contacts in red. Also shown are loops (purple dots) and topologically associating domains (TADs, blue squares) as assessed by HOMER. Note that we do not see mammalian-like corner peaks at the edges of TADs (which would appear as loops at the corner of TADs). b Presence and absence of methylation at CpG sites in 3 species of sponge and 3 previously studied metazoan species. Note that Amphimedon queenslandica and Sycon ciliatum are highly methylated, while Ephydatia muelleri is more modestly methylated, although not quite at the levels seen in Mnemiopsis leidyi, Nematostella vectensis, or Ciona intestinalis. Also shown is the arrangement of possible methylation sites (CpG) relative to transcriptional start sites (TSS) and transcriptional end sites (TES) in sponge genomes. In A. queenslandica these are only slightly enriched at TSS, while in both S. ciliatum and E. muelleri these are highly enriched (CpG/100 bp) near TSS. S. ciliatum maintains these levels across the transcribed region, while they decline in abundance in E. muelleri. In all species TES show a slight depreciation of CpG site abundance relative to other regions of the genome. Source data are provided as a Source Data file.