MiRNA-Seq Related Studies in Rice

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What is microRNA

Figure 1. An overview of canonical miRNA biogenesis, with noncanonical routes.[1]
  • microRNA (abbreviated miRNA) is a kind of small non-coding RNA molecules (containing about 22 nucleotides) that functions in RNA silencing and post-transcriptional regulation of gene expression. In short, MicroRNAs (miRNAs) are a class of small, endogenous, nonoding RNAs with a big impact on virtually all biological processes.[2] Investigations suggest that miRNAs control the gene expression of at least 30% of the protein-coding genes in human beings. Although the diverse fundamental functions of miRNAs have now been well demonstrated in both plants and animals over the past several years, little attention has been paid to this class of small RNAs for about a decade after the first miRNAs were identified in the soil nematode Caenorhabditis elegans in 1993 [1][3]. Currently, it is well known that miRNAs are widely present in plants, animals and some viruses, and miRNAs are involved in regulating almost all biological and metabolic processes, such as stem cell maintenance and differentiation, organ development, signaling pathways, disease, and response to environmental stress[1][3][4] .

Biogenesis of plant miRNAs

  • miRNAs are coded by miRNA genes. Although a majority of miRNAs are 21–23 nucleotides in length [5], miRNA genes are usually very long and it is not certain how long miRNA genes are. The majority of plant miRNA genesare predominantly located at intergenic regions; however, animal miRNA genes can be located anywhere in the genome, including coding sequences. Similar to protein coding genes, miRNA genes are also transcribed by RNA polymerase II (RNA Pol II) ; however, some miRNAs can be transcribed by RNA Pol III . The initial miRNA transcripts are called primary miRNAs (primiRNAs). RNA Pol II generates capped and polyadeny-lated pri-miRNAs in both plants and animals[1].
  • Figure 1 describes An overview of canonical miRNA biogenesis, with noncanonical routes. miRNA biogenesis begins with transcription of MIR loci by RNA polymerase II. 21-nucleotide long canonical miRNAs are mostly processed by Dicer-like 1 (DCL1), while DCL2, DCL3, and DCL4 generate miRNAs of differing lengths. miRNA/miRNA* duplexes are methylated by HEN1 for stabilization, which may also contribute to the export. The export of miRNAs is generally attributed to HASTY, although this is challenged by hst mutants. In contrast to the canonical base-to-loop processing, miRNAs can also be processed from loop to base[1].

Abiotic stresses induce the aberrant expression of miRNAs

  • The role of miRNAs in plant response to abiotic stress was initially suggested after data gathered from miRNA target prediction, miRNA expression profile studies during plant response to abiotic stress, and surveys of NCBI expressed sequence tags (ESTs). In one of the earliest plant miRNA papers, Jones-Rhoades and Bartel [5] predicted and validated that ATP sulphurylase (APS), the enzyme that catalyses the first step of inorganic sulphate assimilation, was one of the targets of miR395, which is responsive to sulphate levels in plants. Based on this initial result, they further analysed the response of miR395 to cellular sulphate levels. Their results showed that in comparison with plants growing under normal sulphate conditions (2 mM SO 42– ), miR395 was induced by >100-fold under low sulphate treatment (0.02 mM SO 42– ), suggesting that miR395 is involved in sulphate uptake and metabolism in plants. At the same time, Sunkar and Zhu (2004) constructed small RNA libraries from Arabidopsis seedling samples treated with cold stress (0 °C for 24 h), salt stress (300 mM NaCl for 5 h), drought stress (dehydration for 10 h), and hormones [100 μM abscisic acid (ABA) for 3 h], as well as from the untreated controls.

Figure 2. The miRNA–target gene network is involved in plant response to environmental abiotic stresses.

  • The Figure2 describes the miRNA–target gene network is involved in plant response to environmental abiotic stresses. Different stresses induced and/or inhibited the expression of individual miRNAs that target transcription factors and/or stress related genes. This network further regulates plant development as well as response to abiotic stress. Plant hormones are also involved in this process through directly/indirectly regulating the expression of miRNAs and their targets.

miRNAs regulate plant leaf development and leaf morphology

  • To date, at least 5 miRNAs (miR156, miR159, miR165, miR166, and miR319) have been dem- onstrated to control the pattern and development of leaves in Arabidopsis, maize, and other plant species (Jung et al. 2009; Kanehira et al. 2010; Kim et al. 2009; Millar and Waterhouse 2005; Pant et al. 2008). These miRNAs regulate leaf development by targeting the homeodomain leucine zipper (HD-ZIP) and the TCP transcription factor genes. miR319, originally reported as miR159, is the first miRNA experimentally shown function during leaf devel- opment (Palatnik et al. 2003, 2007). Overexpression of miR319 resulted in jaw-D phenotypes, including uneven leaf shape and curvature (Palatnik et al. 2003). The reason is that miR319 targets the TCP transcription factor, which regulates leaf development. miR165/166 regulates the developmental polarity of the leaf by targeting the HD-ZIP genes PHAVOLUTA (PHV), PHABULOSA (PHB) and REVOLUTA (REV), whose accumulation alters in adaxial and abaxial regions (Kidner 2010; Rubio-Somoza and Weigel 2011; Williams et al. 2005). In addition to the conserved miRNAs, non-conserved miRNAs may also play roles in leaf development. One example is miR824 that has been reported to play a role in stomatal development (Kutter et al. 2007). Overexpression of one single miRNA, miR156, significantly increases leaf initiation and plant biomass in Arabidopsis (Schwab et al. 2005). This suggests a novel miRNA-based biotechnology for improvement of plant biomass for agriculture purposes and also for biofuel production.

Projects List

Project Title Species Published years Academic Journal RiceWiki Project ID
Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa) Oryza sativa L. ssp. Japnoica 2011 Journal of Experimental Botany IC4R001-miRNA-2011-21362738
Deep sequencing on genome-wide scale reveals the unique composition and expression patterns of microRNAs in developing pollen of Oryza sativa Japnoica Oryza sativa cultivars 2011 Genome Biology IC4R002-miRNA-2011-21679406
Differential expression of the microRNAs in superior and inferior spikelets in rice (Oryza sativa) Oryza sativa L. ssp. Japnoica 2011 Journal of Experimental Botany IC4R003-miRNA-2011-21791435
Identification and Expression Analysis of microRNAs at the Grain Filling Stage in Rice(Oryza sativa L.)via Deep Sequencing Oryza sativa 2013 PLoS One IC4R004-miRNA-2013-23469249
Identification of Novel Oryza sativa miRNAs in Deep Sequencing-Based Small RNA Libraries of Rice Infected with Rice Stripe Virus Oryza sativa L. ssp. Japnoica 2012 PLoS One IC4R005-miRNA-2012-23071571
Differentially expressed microRNA cohorts in seed development may contribute to poor grain filling of inferior spikelets in rice Oryza sativa L. ssp. Japnoica 2014 BMC Plant Biology IC4R006-miRNA-2014-25052585
Identification and characterization of salt responsive miRNA-SSR markers in rice (Oryza sativa) Oryza sativa 2014 Gene IC4R007-miRNA-2014-24315823
Identification and analysis of seven H₂O₂-responsive miRNAs and 32 new miRNAs in the seedlings of rice Oryza sativa L indica 2011 Nucleic Acids Research IC4R008-miRNA-2011-21113019
Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa Oryza Sativa 2010 Journal of Experimental Botany IC4R009-miRNA-2010-20729483
Identification of novel stress-regulated microRNAs from Oryza sativa L. Oryza sativa L 2010 Genomics IC4R010-miRNA-2010-19796675
Highly specific gene silencing by artificial miRNAs in rice Oryza sativa 2008 PLoS One IC4R011-miRNA-2008-18350165
Over-expression of miR172 causes loss of spikelet determinacy and floral organ abnormalities in rice (Oryza sativa) Oryza sativa 2009 BMC Plant Biology IC4R012-miRNA-2009-20017947


  1. 1.0 1.1 1.2 1.3 1.4 Sun, Guiling. "MicroRNAs and their diverse functions in plants." Plant molecular biology 80.1 (2012): 17-36.
  2. https://en.wikipedia.org/wiki/MicroRNA
  3. 3.0 3.1 Lee, Rosalind C., Rhonda L. Feinbaum, and Victor Ambros. "The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14." Cell 75.5 (1993): 843-854.
  4. Lewis, Benjamin P., Christopher B. Burge, and David P. Bartel. "Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets." cell 120.1 (2005): 15-20.
  5. 5.0 5.1 Bartel, David P. "MicroRNAs: genomics, biogenesis, mechanism, and function." cell 116.2 (2004): 281-297.