Eukaryotic genomes are transcribed by at least three RNA polymerases, RNAPI, II, and III. Co-transcriptional R-loops play diverse roles in genome regulation and maintenance. However, little is known about how R-loops regulate transcription interference, the transcriptional event that is caused by different RNA polymerases transcribing the same genomic templates. Here, we established that the intragenic transfer RNA (tRNA) genes can promote sense R-loop enrichment (named intra-tR-loops) in Arabidopsis thaliana, and found that intra-tR-loops are decreased in an RNAPIII mutant, NUCLEAR RNA POLYMERASE C, SUBUNIT 7(nrpc7-1). NRPC7 is co-localized with RNAPIIS2P at intragenic tRNA genes and interferes with RNAPIIS2P elongation. Conversely, the binding of NRPC7 at intragenic tRNA genes is increased following inhibition of RNAPII elongation. The transcription of specific tRNA host genes is inhibited by RNAPIII, and the inhibition of tRNA host genes is intra-tR-loop dependent. Moreover, alleviating the inhibition of tRNAPro-induced intra-tR-loops on its host gene AtNUDX1 promotes oxidative stress tolerance in A. thaliana. Our work suggests intra-tR-loops regulate host gene expression by modulating RNA polymerases interference.

中文翻译：

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基因内 tRNA 促进的 R 环协调植物氧化应激反应的转录干扰

真核基因组由至少三种 RNA 聚合酶 RNAPI、II 和 III 转录。共转录 R 环在基因组调控和维护中发挥着不同的作用。然而，关于 R 环如何调节转录干扰知之甚少，转录干扰是由转录相同基因组模板的不同 RNA 聚合酶引起的。在这里，我们确定基因内转移 RNA (tRNA) 基因可以促进拟南芥中的正义 R 环富集（命名为 tR 环内），并发现 RNAPIII 突变体核 RNA 聚合酶中的 tR 环内减少C，子单元 7（nrpc7-1）。NRPC7 在基因内 tRNA 基因上与 RNAPIIS2P 共定位并干扰 RNAPIIS2P 延伸。相反，在抑制 RNAPII 延伸后，NRPC7 在基因内 tRNA 基因上的结合增加。特定 tRNA 宿主基因的转录受 RNAPIII 抑制，tRNA 宿主基因的抑制依赖于 tR 环内。此外，减轻 tRNAPro 诱导的 tR 内环对其宿主基因 AtNUDX1 的抑制可促进拟南芥的氧化应激耐受。我们的工作表明，tR 环内通过调节 RNA 聚合酶干扰来调节宿主基因的表达。