The interplay between small RNA pathways shapes chromatin landscapes in C. elegans

The nematode C. elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both “silencing” siRNAs bound by Worm-specific Argonautes (WAGO) and “activating” siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partial loss-of-function mutant this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements in both drh-3 and csr-1 partial loss-of-function mutants and describe small RNAs matching enhancers. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to increase in silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation. Examination of 3 different histone modifications in 3 nematode strains (2 replicates per each sample).

秀丽隐杆线虫（C. elegans）含有多种由RNA依赖的RNA聚合酶（RdRP）复合物生成的内源性小干扰RNA（endo-siRNAs）。由线虫特异性Argonaute蛋白（WAGO）结合的“沉默型”siRNA，以及被CSR-1 Argonaute结合的“激活型”siRNA，均需要作为RdRP组分的DRH-3解旋酶（DRH-3 helicase）。本研究显示，在RdRP生成的次级内源性siRNA缺陷的drh-3(ne4253)突变体中，沉默型组蛋白修饰H3K9me3（H3K9me3）显著缺失；而在csr-1部分功能丧失突变体中，该修饰会异位沉积于CSR-1靶基因之上。此外，我们在drh-3突变体与csr-1部分功能丧失突变体的增强子元件处均观察到了异位的H3K9me3，并鉴定出匹配增强子的小RNA。最后，我们在drh-3(ne4253)突变体的高表达基因处检测到了H3K27me3（H3K27me3）的富集，这与其转录水平降低呈相关性。本研究表明，当大量RdRP生成的siRNA缺失时，与沉默型染色质修饰增加相关的非编码RNA会出现异位升高。此外，我们的研究结果提示，增强子小RNA可能介导局部的H3K9甲基化。本实验对3株线虫的3种不同组蛋白修饰进行了检测（每个样本设置2次生物学重复）。