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.

中文翻译：

---

高度紧凑的草履虫大核基因组中广泛的组蛋白标记域

单细胞纤毛虫草履虫含有一个大的营养大核，具有几个不寻常的特征，包括极高的编码密度和高多倍体。由于大核染色质没有异染色质，我们的研究表征了基因调控和适当的 Pol II 活性所必需的功能性表观基因组组织。组蛋白标记（H3K4me3、H3K9ac、H3K27me3）沿基因体显示没有窄峰但有宽域，而基因间区域没有核小体。我们的数据表明 ORF 内的 H3K4me3 水平是与基因表达相关的主要因素，并且 H3K27me3 与塑料基因中的 H3K4me3 相关。沉默和低表达的基因显示低核小体占有率，表明基因失活不涉及增加的核小体占有率和染色质凝聚。由于 Pol II 在高表达的 ORF 上的占有率很高，转录延伸似乎与其他物种完全不同。Pol II 的 C 端结构域中缺失的七聚体重复和发散延伸系统支持这一点。我们的数据表明未占用的 DNA 是默认状态，而基因激活需要核小体募集以及 H3K4me3 的广泛结构域。总之，基因激活和沉默在草履虫与目前对染色质生物学的理解背道而驰。