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Nucleic Acids Res. 2014 Sep;42(15):9925-36. doi: 10.1093/nar/gku716. Epub 2014 Aug 7.

Regulation of pri-miRNA processing by the hnRNP-like protein AtGRP7 in Arabidopsis.

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Molecular Cell Physiology, Bielefeld University.
Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany.
Max Planck Institute for Developmental Biology, Tuebingen, Germany Department of Animal & Plant Sciences, University of Sheffield, UK.
Max Planck Institute for Developmental Biology, Tuebingen, Germany Center for Plant Molecular Biology, University of Tuebingen Chemical Genomics Centre of the Max Planck Society, Dortmund, Germany.
Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Germany.
Max Planck Institute for Developmental Biology, Tuebingen, Germany.
Molecular Cell Physiology, Bielefeld University Institute for Genome Research & Systems Biology, CeBiTec, Bielefeld, Germany


The hnRNP-like glycine-rich RNA-binding protein AtGRP7 regulates pre-mRNA splicing in Arabidopsis. Here we used small RNA-seq to show that AtGRP7 also affects the miRNA inventory. AtGRP7 overexpression caused a significant reduction in the level of 30 miRNAs and an increase for 14 miRNAs with a minimum log2 fold change of ± 0.5. Overaccumulation of several pri-miRNAs including pri-miR398b, pri-miR398c, pri-miR172b, pri-miR159a and pri-miR390 at the expense of the mature miRNAs suggested that AtGRP7 affects pri-miRNA processing. Indeed, RNA immunoprecipitation revealed that AtGRP7 interacts with these pri-miRNAs in vivo. Mutation of an arginine in the RNA recognition motif abrogated in vivo binding and the effect on miRNA and pri-miRNA levels, indicating that AtGRP7 inhibits processing of these pri-miRNAs by direct binding. In contrast, pri-miRNAs of selected miRNAs that were elevated or not changed in response to high AtGRP7 levels were not bound in vivo. Reduced accumulation of miR390, an initiator of trans-acting small interfering RNA (ta-siRNA) formation, also led to lower TAS3 ta-siRNA levels and increased mRNA expression of the target AUXIN RESPONSE FACTOR4. Furthermore, AtGRP7 affected splicing of pri-miR172b and pri-miR162a. Thus, AtGRP7 is an hnRNP-like protein with a role in processing of pri-miRNAs in addition to its role in pre-mRNA splicing.

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