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R 环在 microRNA 编码基因座处促进植物前体 miRNA 的共转录加工。

R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants.

机构信息

Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas, Universidad Nacional del Litoral, Santa Fe, Argentina.

Department of Gene Expression, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznan, Poland.

出版信息

Nat Plants. 2022 Apr;8(4):402-418. doi: 10.1038/s41477-022-01125-x. Epub 2022 Apr 21.

DOI:10.1038/s41477-022-01125-x
PMID:35449404
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9023350/
Abstract

In most organisms, the maturation of nascent RNAs is coupled to transcription. Unlike in animals, the RNA polymerase II (RNAPII) transcribes microRNA genes (MIRNAs) as long and structurally variable pri-miRNAs in plants. Current evidence suggests that the miRNA biogenesis complex assembly initiates early during the transcription of pri-miRNAs in plants. However, it is unknown whether miRNA processing occurs co-transcriptionally. Here, we used native elongating transcript sequencing data and imaging techniques to demonstrate that plant miRNA biogenesis occurs coupled to transcription. We found that the entire biogenesis occurs co-transcriptionally for pri-miRNAs processed from the loop of the hairpin but requires a second nucleoplasmic step for those processed from the base. Furthermore, we found that co- and post-transcriptional miRNA processing mechanisms co-exist for most miRNAs in a dynamic balance. Notably, we discovered that R-loops, formed near the transcription start site region of MIRNAs, promote co-transcriptional pri-miRNA processing. Furthermore, our results suggest the neofunctionalization of co-transcriptionally processed miRNAs, boosting countless regulatory scenarios.

摘要

在大多数生物体中，新生 RNA 的成熟与转录过程相偶联。与动物不同的是，RNA 聚合酶 II（RNAPII）在植物中作为长且结构可变的前体 miRNA 转录 miRNA 基因（MIRNAs）。目前的证据表明，miRNA 生物发生复合物的组装在植物前体 miRNA 的转录早期就开始了。然而，miRNA 加工是否发生在共转录过程中尚不清楚。在这里，我们使用天然延伸转录测序数据和成像技术证明了植物 miRNA 的生物发生与转录过程相偶联。我们发现，整个生物发生过程对于从发夹环加工的前体 miRNA 来说是共转录的，但对于从碱基加工的前体 miRNA 来说需要第二个核质步骤。此外，我们发现，对于大多数 miRNA 来说，共转录和转录后 miRNA 加工机制在动态平衡中共存。值得注意的是，我们发现，R 环在 MIRNAs 的转录起始位点区域附近形成，促进了共转录的前体 miRNA 加工。此外，我们的结果表明，共转录加工的 miRNA 发生了新功能化，从而促进了无数调控场景的发生。

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