Degradome sequencing of semi-active DCL1 mutants separates true miRNAs from DCL1-independent small RNAs in Arabidopsis thaliana and illustrates the processing pattern of 147 pri-miRNAs. In parallel, DMS-MaPseq decodes the in vivo secondary structures of pri-miRNAs, enabling a better understanding of cleavage modes and of the impact of DCL1 cofactors on cleavage.
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References
Moro, B. et al. Efficiency and precision of microRNA biogenesis modes in plants. Nucleic Acids Res. 46, 10709–10723 (2018). This paper reports that the processing of many miRNAs follows structural determinants, with alternative processing taking place under certain conditions.
Gonzalo, L. et al. R-loops at microRNA encoding loci promote co-transcriptional processing of pri-miRNAs in plants. Nat. Plants 8, 402–418 (2022). This paper uncovers an unexpected role of R-loops in RNA processing and reports the processing patterns of a few pri-miRNAs.
Wang, Z. et al. SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production. Nature 557, 516–521 (2018). This paper concludes that CHR2 accesses pri-miRNAs through SE, remodelling their secondary structures and preventing downstream processing by DCL1 and HYL1.
Zhu, H. et al. Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nat. Struct. Mol. Biol. 20, 1106–1115 (2013). This paper reports the bi-directional processing patterns of pri-miRNAs with terminal branched loops and provides the theoretical foundation for our current work.
Wang, Z., Wang, M., Wang, T., Zhang, Y. & Zhang, X. Genome-wide probing RNA structure with the modified DMS-MaPseq in Arabidopsis. Methods 155, 30–40 (2019). An article presenting the protocol of a modified DRS method that is a powerful tool for analysing the RNA structurome in plants.
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This is a summary of: Yan, X. et al. Parallel degradome-seq and DMS-MaPseq substantially revise the miRNA biogenesis atlas in Arabidopsis. Nat. Plants https://doi.org/10.1038/s41477-024-01725-9 (2024).
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Exploring the landscape of miRNA production and the structural rules that shape it. Nat. Plants (2024). https://doi.org/10.1038/s41477-024-01728-6
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DOI: https://doi.org/10.1038/s41477-024-01728-6