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

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Arabidopsis / genetics*
  • Arabidopsis / metabolism
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism*
  • Gene Expression Regulation, Plant*
  • MicroRNAs / metabolism*
  • Molecular Chaperones / metabolism
  • RNA Processing, Post-Transcriptional*
  • RNA, Small Interfering / metabolism
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Superoxide Dismutase / metabolism


  • ATGRP7 protein, Arabidopsis
  • Arabidopsis Proteins
  • GRP8 protein, Arabidopsis
  • MIRN398 microRNA, Arabidopsis
  • MicroRNAs
  • Molecular Chaperones
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • Superoxide Dismutase
  • CSD2 protein, Arabidopsis