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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.

Author information

1
Molecular Cell Physiology, Bielefeld University.
2
Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany.
3
Max Planck Institute for Developmental Biology, Tuebingen, Germany Department of Animal & Plant Sciences, University of Sheffield, UK.
4
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.
5
Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany German Centre for Integrative Biodiversity Research Halle-Jena-Leipzig, Germany.
6
Max Planck Institute for Developmental Biology, Tuebingen, Germany.
7
Molecular Cell Physiology, Bielefeld University Institute for Genome Research & Systems Biology, CeBiTec, Bielefeld, Germany dorothee.staiger@uni-bielefeld.de.

Abstract

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.

PMID:
25104024
PMCID:
PMC4150807
DOI:
10.1093/nar/gku716
[Indexed for MEDLINE]
Free PMC Article

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