Detection of MicroRNA Processing Intermediates Through RNA Ligation Approaches

  • Belén MoroEmail author
  • Arantxa M. L. Rojas
  • Javier F. PalatnikEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1932)


MicroRNAs (miRNA) are small RNAs of 20–22 nt that regulate diverse biological pathways through the modulation of gene expression. miRNAs recognize target RNAs by base complementarity and guide them to degradation or translational arrest. They are transcribed as longer precursors with extensive secondary structures. In plants, these precursors are processed by a complex harboring DICER-LIKE1 (DCL1), which cuts on the precursor stem region to release the mature miRNA together with the miRNA*. In both plants and animals, the miRNA precursors contain spatial clues that determine the position of the miRNA along their sequences. DCL1 is assisted by several proteins, such as the double-stranded RNA binding protein, HYPONASTIC LEAVES1 (HYL1), and the zinc finger protein SERRATE (SE). The precise biogenesis of miRNAs is of utter importance since it determines the exact nucleotide sequence of the mature small RNAs and therefore the identity of the target genes. miRNA processing itself can be regulated and therefore can determine the final small RNA levels and activity. Here, we describe methods to analyze miRNA processing intermediates in plants. These approaches can be used in wild-type or mutant plants, as well as in plants grown under different conditions, allowing a molecular characterization of the miRNA biogenesis from the RNA precursor perspective.

Key words

MicroRNA Processing Precursor RNA ligation NGS Plants Arabidopsis 



Supported by grants of Argentinean Ministry of Science, PICT-2015-3557 and PICT-2016-0761 to J.P. CONICET fellowships to B.M. and A.M.L.R.


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© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Instituto de Biología Molecular y Celular de Rosario, CONICETUniversidad Nacional de RosarioRosarioArgentina
  2. 2.Facultad de Ciencias Bioquímicas y FarmacéuticasUniversidad Nacional de RosarioRosarioArgentina
  3. 3.Centro de Estudios InterdisciplinariosUniversidad Nacional de RosarioRosarioArgentina

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