Tissue dependent regulation of plant microRNA production

MicroRNAs (miRNAs) are key regulators of plant development. These small molecules are produced by a dynamic but highly coordinated process. The processing of miRNA is carried out by a group of well-characterized proteins. Despite the handful of cofactors regulating this process that have been identified in recent years, it is unclear how the plant fine-tunes the production of miRNA in different tissues. Now, RCF3 was identified as a regulator of the miRNA processing machinery acting preferentially in active dividing and developmental niches in the plant.

HFSP Career Development Award holder Pablo Manavella and colleagues
authored on Tue, 17 November 2015

The miRNAs-mediated silencing of target mRNAs is an essential regulatory process to achieve a correct developmental program in plants. The biogenesis of miRNA is a well-orchestrated process that involves a group of proteins in charge of the precise excision of a mature miRNA from its precursor. In plants, a Dicer-like RNase is the main enzyme processing such miRNA precursors but requires at least two cofactors, SERRATE and HYL1, for accurate activity. In recent years, several proteins modulating the activity of the miRNA-processing complex were identified allowing us to better understand how the miRNA production is achieved. However, our current knowledge is based on evidence obtained from whole plants where the mechanisms of regulation of miRNA production were identified on a global scale. It is still unclear how the production of miRNAs is fine-tuned in those cell niches where miRNA is particularly necessary, such as in dividing cells and developmentally active tissues.

Cartoon by Nicolas Cinquegrani and Pablo Manavella

We created a luciferase-based reporter system to monitor the miRNA production and activity in plants. Using this reporter system, together with a forward genetic screen and a whole genome illumina sequencing-based mapping, we identified RCF3 as a new cofactor modulating miRNA activity. Our results indicated that RCF3 regulates miRNA production preferentially in the vegetative and reproductive meristematic areas of Arabidopsis thaliana plants. Mechanistically, RCF3 acts in these cell niches by modulating the phosphorylation of HYL1, a post-translational modification known to affect this protein activity. RCF3 mutant plants present reduced levels of the active form of HYL1 in the meristems leading to an aberrant processing of miRNA and a deregulation of miRNA-target genes.

Figure: Left: morphological phenotype of miRNA deficient mutants; right: activity of the Luciferase-base miRNA reporter used to identify miRNA deficient mutants.

Together, our results show for the very first time that, as for animals, regulation of miRNA biogenesis is tissue-specific in plants. Our results show that the pathway leading to the production of miRNAs, and especially the regulation of HYL1, is far more complex than originally thought. The identification of a tissue specific regulator of the pathway suggests that experimental procedures aiming to study miRNA related processes will need to narrow the sampling focus to more specific tissues.


KH domain protein RCF3 is a tissue-biased regulator of the plant miRNA biogenesis cofactor HYL1. Karlsson P, Christie MD, Seymour DK, Wang H, Wang X, Hagmann J, Kulcheski F, Manavella PA (2015). Proc Natl Acad Sci U S A. 112(45):14096-14101. doi: 10.1073/pnas.1512865112.

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