Small RNAs mediate the silencing of transposable elements and other genomic loci, increasing nucleosome density and preventing undesirable gene expression. The unicellular ciliate Paramecium is a model to study dynamic genome organization in eukaryotic cells, given its unique feature of nuclear dimorphism. Here, the formation of the somatic macronucleus during sexual reproduction requires eliminating thousands of transposon remnants (IESs) and transposable elements scattered throughout the germline micronuclear genome. The elimination process is guided by Piwi-associated small RNAs and leads to precise cleavage at IES boundaries. Here we show that IES recognition and precise excision are facilitated by recruiting ISWI1, a Paramecium homolog of the chromatin remodeler ISWI. ISWI1 knockdown substantially inhibits DNA elimination, quantitatively similar to development-specific sRNA gene knockdowns but with much greater aberrant IES excision at alternative boundaries. We also identify key development-specific sRNA biogenesis and transport proteins, Ptiwi01 and Ptiwi09, as ISWI1 cofactors in our co-immunoprecipitation studies. Nucleosome profiling indicates that increased nucleosome density correlates with the requirement for ISWI1 and other proteins necessary for IES excision. We propose that chromatin remodeling together with small RNAs is essential for efficient and precise DNA elimination in Paramecium.

中文翻译：

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草履虫中 sRNA 引导的 DNA 消除需要染色质重塑

小 RNA 介导转座因子和其他基因组位点的沉默，增加核小体密度并防止不良基因表达。单细胞纤毛虫草履虫是研究真核细胞动态基因组组织的模型，因为它具有独特的核二态性特征。在这里，有性生殖过程中体细胞大核的形成需要消除散布在种系微核基因组中的数千个转座子残余物 (IES) 和转座因子。消除过程由 Piwi 相关的小 RNA 指导，并导致在 IES 边界处进行精确切割。在这里，我们表明招募 ISWI1（一种草履虫）有助于 IES 识别和精确切除染色质重塑因子 ISWI 的同系物。ISWI1 敲低显着抑制 DNA 消除，在数量上类似于发育特异性 sRNA 基因敲低，但在替代边界处具有更大的异常 IES 切除。我们还确定了关键的发育特异性 sRNA 生物发生和转运蛋白 Ptiwi01 和 Ptiwi09，作为我们免疫共沉淀研究中的 ISWI1 辅助因子。核小体分析表明，增加的核小体密度与对 ISWI1 和 IES 切除所必需的其他蛋白质的需求相关。我们提出染色质重塑与小 RNA 一起对于草履虫中有效和精确的 DNA 消除至关重要。