Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity

We deep sequence DNA associated with immunoprecipitated chromatin containing histones with specific post-translational modifications (PTMs) to identify transcriptionally active or repressed regions of the genome of the sponge Amphimedon queenslandica. Overall design: We carried out chromatin immunoprecipitation (ChIP) on sexually reproducing Amphimedon adults and larvae using antibodies against specific histone H3 PTMs that have been used to define chromatin states in model bilaterians. The antibodies used target the following histone H3 PTMs: (i) monomethylated lysine 4 (H3K4me1), associated with distal cis-regulatory elements such as enhancers; (ii) trimethylated lysine 4 (H3K4me3), enriched in active promoters; (iii) trimethylated lysine 36 (H3K36me3), found with actively transcribed regions; (iv) trimethylated lysine 27 (H3K27me3), enriched in Polycomb-silenced regions; and (v) acetylated lysine 27 (H3K27ac), which occurs around activated regulatory regions. We also used an antibody against total histone H3. An antibody against unphosphorylated Ser2 residues of RNA polymerase II (RNAPII 8WG16) C-terminal domain also was included.