Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
Plant Cell. 2021 Nov 4;33(11):3574-3591. doi: 10.1093/plcell/koab220.
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.
真核生物基因组由至少三种 RNA 聚合酶（RNAPI、II 和 III）转录。共转录性 R 环在基因组调控和维持中发挥着多样化的作用。然而，对于 R 环如何调节转录干扰（即不同 RNA 聚合酶转录同一基因组模板所导致的转录事件），人们知之甚少。在这里，我们发现拟南芥基因内转移 RNA（tRNA）基因可促进 sense R 环富集（命名为 intra-tR-loops），并发现 intra-tR-loops 在 RNA 聚合酶 III 突变体 NUCLEAR RNA POLYMERASE C，SUBUNIT 7(nrpc7-1)中减少。NRPC7 与基因内 tRNA 基因上的 RNAPIIS2P 共定位，并干扰 RNAPIIS2P 的延伸。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 宿主基因的转录被 RNA 聚合酶 III 抑制，而 tRNA 宿主基因的抑制则依赖于 intra-tR-loops。此外，缓解 tRNAPro 诱导的 intra-tR-loops 对其宿主基因 AtNUDX1 的抑制作用，可促进拟南芥的氧化应激耐受性。我们的工作表明，intra-tR-loops 通过调节 RNA 聚合酶干扰来调节宿主基因表达。
