Expression-based functional investigation of the organ-specific microRNAs in Arabidopsis

PLoS One. 2012;7(11):e50870. doi: 10.1371/journal.pone.0050870. Epub 2012 Nov 30.

Abstract

MicroRNAs (miRNAs) play a pivotal role in plant development. The expression patterns of the miRNA genes significantly influence their regulatory activities. By utilizing small RNA (sRNA) high-throughput sequencing (HTS) data, the miRNA expression patterns were investigated in four organs (flowers, leaves, roots and seedlings) of Arabidopsis. Based on a set of criteria, dozens of organ-specific miRNAs were discovered. A dominant portion of the organ-specific miRNAs identified from the ARGONAUTE 4-enriched sRNA HTS libraries were highly expressed in flowers. Additionally, the expression of the precursors of the organ-specific miRNAs was analyzed. Degradome sequencing data-based approach was employed to identify the targets of the organ-specific miRNAs. The miRNA-target interactions were used for network construction. Subnetwork analysis unraveled some novel regulatory cascades, such as the feedback regulation mediated by miR161, the potential self-regulation of the genes miR172, miR396, miR398 and miR860, and the miR863-guided cleavage of the SERRATE transcript. Our bioinformatics survey expanded the organ-specific miRNA-target list in Arabidopsis, and could deepen the biological view of the miRNA expression and their regulatory roles.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arabidopsis / genetics*
  • Arabidopsis Proteins / genetics
  • Arabidopsis Proteins / metabolism
  • Argonaute Proteins / genetics
  • Argonaute Proteins / metabolism
  • Base Sequence
  • Gene Expression Regulation, Plant*
  • Gene Regulatory Networks / genetics
  • MicroRNAs / genetics*
  • MicroRNAs / metabolism
  • Molecular Sequence Data
  • Organ Specificity / genetics*
  • RNA Stability / genetics
  • Reproducibility of Results
  • Sequence Analysis, RNA

Substances

  • AGO4 protein, Arabidopsis
  • Arabidopsis Proteins
  • Argonaute Proteins
  • MicroRNAs

Grants and funding

This work was funded by the National Natural Sciences Foundation of China [31100937] and [30971743], the Starting Grant funded by Hangzhou Normal University to Yijun Meng [2011QDL60], the Fundamental Research Funds for the Central Universities and the National High Technology Research and Development Program of China (‘863’ Program) (2008AA10Z125). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.