Background: Silencing of transposable elements (TEs) is essential for maintaining genome stability. Plants use small RNAs (sRNAs) to direct DNA methylation to TEs (RNA-directed DNA methylation; RdDM). Similar mechanisms of epigenetic silencing in the fungal kingdom have remained elusive. Results: We use sRNA sequencing and methylation data to gain insight into epigenetics in the dikaryotic fungus Puccinia graminis f. sp. tritici (Pgt), which causes the devastating stem rust disease on wheat. We use Hi-C data to define the Pgt centromeres and show that they are repeat-rich regions (~250 kb) that are highly diverse in sequence between haplotypes and, like in plants, are enriched for young TEs. DNA cytosine methylation is particularly active at centromeres but also associated with genome-wide control of young TE insertions. Strikingly, over 90% of Pgt sRNAs and several RNAi genes are differentially expressed during infection. Pgt induces waves of functionally diversified sRNAs during infection. The early wave sRNAs are predominantly 21 nts with a 5' uracil derived from genes. In contrast, the late wave sRNAs are mainly 22 nt sRNAs with a 5' adenine and are strongly induced from centromeric regions. TEs that overlap with late wave sRNAs are more likely to be methylated, both inside and outside the centromeres, and methylated TEs exhibit a silencing effect on nearby genes. Conclusions: We conclude that rust fungi use an epigenetic silencing pathway that resembles RdDM in plants. The Pgt RNAi machinery and sRNAs are under tight temporal control throughout infection and might ensure genome stability during sporulation.

中文翻译：

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茎锈菌Puccinia graminis f。sp。小麦在后期感染期间诱导着丝粒小RNA，指导全基因组DNA甲基化

背景：转座因子（TEs）的沉默对于维持基因组稳定性至关重要。植物使用小RNA（sRNA）将DNA甲基化引导至TE（RNA定向DNA甲基化； RdDM）。真菌界中类似的表观遗传沉默机制仍然难以捉摸。结果：我们使用sRNA测序和甲基化数据来深入了解双核真菌Puccinia graminis f的表观遗传学。sp。Tritici（Pgt），在小麦上引起毁灭性的茎锈病。我们使用Hi-C数据定义Pgt着丝粒，并显示它们是重复序列丰富的区域（约250 kb），在单倍型之间的序列差异很大，并且像在植物中一样，富含年轻的TE。DNA胞嘧啶甲基化在着丝粒特别活跃，但也与年轻TE插入的全基因组控制有关。惊人地 感染过程中90％以上的Pgt sRNA和几种RNAi基因差异表达。Pgt在感染过程中诱发功能多样化的sRNA波。早期的sRNA主要是21 nt，具有从基因衍生的5'尿嘧啶。相反，晚波sRNA主要是具有5'腺嘌呤的22nt sRNA，并且是从着丝粒区域强烈诱导的。与晚波sRNA重叠的TEs在着丝粒内外都更可能被甲基化，而甲基化的TEs对附近的基因表现出沉默作用。结论：我们得出结论，锈病真菌使用类似于植物中RdDM的表观遗传沉默途径。在整个感染过程中，Pgt RNAi机制和sRNA受到严格的时间控制，并可能确保孢子形成过程中的基因组稳定性。