Broad domains of histone marks in the highly compact Paramecium macronuclear genome

Abstract

The unicellular ciliate Paramecium contains a large vegetative macronucleus with several unusual characteristics, including an extremely high coding density and high polyploidy. As macronculear chromatin is devoid of heterochromatin, our study characterizes the functional epigenomic organization necessary for gene regulation and proper Pol II activity. Histone marks (H3K4me3, H3K9ac, H3K27me3) reveal no narrow peaks but broad domains along gene bodies, whereas intergenic regions are devoid of nucleosomes. Our data implicate H3K4me3 levels inside ORFs to be the main factor associated with gene expression, and H3K27me3 appears in association with H3K4me3 in plastic genes. Silent and lowly expressed genes show low nucleosome occupancy, suggesting that gene inactivation does not involve increased nucleosome occupancy and chromatin condensation. Because of a high occupancy of Pol II along highly expressed ORFs, transcriptional elongation appears to be quite different from that of other species. This is supported by missing heptameric repeats in the C-terminal domain of Pol II and a divergent elongation system. Our data imply that unoccupied DNA is the default state, whereas gene activation requires nucleosome recruitment together with broad domains of H3K4me3. In summary, gene activation and silencing in Paramecium run counter to the current understanding of chromatin biology.

Conservation of the ancestral function of GTSF1 in transposon silencing in the unicellular eukaryoteParamecium tetraurelia

“…loss of H3K9me3 and H3K27me3) are downregulated (Wang et al , 2022). Additionally, Drews et al (2022) reported H3K27me3 to be enriched on highly-expressed genes, all of which are consistent with our current observations. In light of multiple lines of evidence, we believe that these histone marks are not repressive in P. tetraurelia .…”

MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma

“…Somatic MACs may generally be unable to repress mobile elements by heterochromatinization like germline MICs and other eukaryotic nuclei. In Tetrahymena , most MAC DNA is not associated with classical heterochromatin marks ( 23 ), while in Paramecium MACs, H3K27me3 is not associated with transcription repression, despite being a classic heterochromatin mark in multicellular eukaryotes ( 59 ). In such a permissive expression environment, selection against mobile elements that are not already excised as IESs may be especially effective, unless they are relatively transcriptionally inactive like the Blepharisma retroelements.…”

A small RNA-guided PRC2 complex eliminates DNA as an extreme form of transposon silencing

“…Although the classical function of PRC2 complexes is gene repression, there have been reports that EZH2 can function as a transcriptional activator in a PRC2-independent manner ( Kim et al., 2015 , 2018 ; Xu et al., 2012 ). A recent report found the vegetative chromatin landscape of Paramecium to be different from most eukaryotes, and that H3K27me3 accumulates on highly expressed genes, questioning its function as a repressive mark in this system ( Drews et al., 2022 ). Whether Paramecium PRC2 is indeed a transcriptional activator, or if it is an indirect effect, remains to be determined.…”