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Nucleic Acids Res. 2018 Nov 16;46(20):10709-10723. doi: 10.1093/nar/gky853.

Efficiency and precision of microRNA biogenesis modes in plants.

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IBR (Instituto de Biología Molecular y Celular de Rosario), CONICET and Universidad Nacional de Rosario, Rosario 2000, Argentina.
Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario 2000, Argentina.
Department of Agronomy, Kamphaeng Saen and Rice Science Center, Kasetsart University, Nakhon Pathom 73140, Thailand.
Institut für Organische Chemie, Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.
Donald Danforth Plant Science Center, St. Louis, MO 63132, USA.
Department of Plant Science, University of Missouri - Columbia, MO 65211, USA.
Centro de Estudios Interdisciplinarios, Universidad Nacional de Rosario, Rosario 2000, Argentina.


Many evolutionarily conserved microRNAs (miRNAs) in plants regulate transcription factors with key functions in development. Hence, mutations in the core components of the miRNA biogenesis machinery cause strong growth defects. An essential aspect of miRNA biogenesis is the precise excision of the small RNA from its precursor. In plants, miRNA precursors are largely variable in size and shape and can be processed by different modes. Here, we optimized an approach to detect processing intermediates during miRNA biogenesis. We characterized a miRNA whose processing is triggered by a terminal branched loop. Plant miRNA processing can be initiated by internal bubbles, small terminal loops or branched loops followed by dsRNA segments of 15-17 bp. Interestingly, precision and efficiency vary with the processing modes. Despite the various potential structural determinants present in a single a miRNA precursor, DCL1 is mostly guided by a predominant structural region in each precursor in wild-type plants. However, our studies in fiery1, hyl1 and se mutants revealed the existence of cleavage signatures consistent with the recognition of alternative processing determinants. The results provide a general view of the mechanisms underlying the specificity of miRNA biogenesis in plants.

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