ChIPseq and MNAse of the Paramecium tetraurelia macronuclear chromatin

The unicellular ciliate Paramecium contains a large vegetative macronucleus with a extremely high coding density and high polyploidy. We used ChIP-Seq and MNase-Seq to characterize the epigenomic organisation which is believed to be devoid of heterochromatin. Histone marks (H3K4me3, H3K9ac, H3K27me3) revealed no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicates H3K4me3 levels inside ORFs to be the main factor to associate with gene expression and H3K27me3 appears to occur as a bistable domain with H3K4me3 in plastic genes. Surprisingly, silent and low expressed genes show low nucleosome occupancy suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Due to a high occupancy of Pol II in highly expressed ORFs, transcriptional elongation appears to be quite different to other species. This is supported by missing heptameric repeats of Pol II CTD and a divergent elongation system. Our data implies that unoccupied DNA as a default state with gene activation requiring nucleosome recruitment together with broad domains of H3K4me3. We hypothesize that this could represent a buffer for paused Pol II along ORFs in absence of elongation factors of higher eukaryotes.