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Plant miRNA: New Regulators in Functional Genomics

BY: Dhara K Savsani | Category: Agriculture | Submitted: 2017-06-28 08:47:00
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Article Summary: "MicroRNAs (miRNAs) are small RNAs that regulate gene expression by targeting one or more sequences of high complementarity in plants and have been identified as one of the major conserved mechanisms in eukaryotes and represents an attractive modality for trait engineering..."


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Plant miRNA: new regulators in functional genomics
Authors: DHARA SAVSANI1., CHANDNI PATEL2., CHANDANI HIHOR3
1 Ph.D. Scholar, Dept. of Agricultural Biotechnology, B.A.C.A.,
Anand Agricultural University, Anand.
2Junior Research Fellow, Gujarat State Biotechnology Mission, Gandhinagar.
3 Senior Research Fellow, Dept. of Animal Genetics and Breeding, College of Veterinary and Animal Husbandry, Anand Agricultural University, Anand.


Introduction

RNA-based gene regulation has been identified as one of the major conserved mechanisms in eukaryotes and represents an attractive modality for trait engineering in plants. MicroRNAs (miRNAs) are small RNAs that regulate gene expression by targeting one or more sequences of high complementarity in plants. Plant miRNAs occur in gene families, each family contains 1–32 loci within a single genome, each potentially encoding identical or nearly identical mature miRNAs (Mathew et al., 2006).The majority of known plant miRNA targets encode transcription factors or other regulatory proteins, such as components of the ubiquitin and gene knockdown pathways. Many plant miRNAs change their expression during development or in response to environmental challenges, and regulate protein-coding genes involved in development, stress response and nutrient transport.

Biogenesis of miRNA

The miRNAs are expressed from their own genes located in the intergenic (between protein-coding genes) or intragenic region (within protein-coding genes, in an exonic or intronic manner) on the chromosomes. Biogenesis of plant miRNAs requires a multiple biological processes to generate functional mature miRNAs by recruiting several conserved protein families. Plant miRNA genes are principally transcribed into primary miRNA transcripts (pri-miRNA) by RNA polymerase II. The pri-miRNA molecules typically contain a region of imperfect self-complementarity and are processed into stem-loop secondary structures (pre-miRNAs) including mature miRNAs in one arm of the secondary structures (Vahap et al., 2013)

Methods to detect microRNA

  • Microarray profilling
  • Quantitative RT PCR
  • High throughput sequencing
  • Insitu hybridization
Stratergies for engineering microRNA as regulators in functional genomics

  • microRNA serves as positive regulators
  • Constitutive overexpression of microRNA
  • MicroRNA targeted gene knockout
  • microRNA serves as negative regulators
  • Overexpression of microRNA resistant genes
  • Artificial microRNA Bioinformatics approaches have identified targets for nearly all plant miRNAs. Several experimental methods have been used to confirm miRNA-target interactions and explore the biological significance of miRNA-mediated regulation. Case studies Guray et al., (2015) comparatively investigated drought stress-responsive miRNAs in the root and leaf of bread wheat ( Triticum aestivum cv. Sivas 111/33) by miRNA microarray screening. miRNA microarray analysis showed that 285 miRNAs (207 upregulated and 78 downregulated) and 244 miRNAs (115 upregulated and 129 downregulated) were differentially expressed in leaf and root tissues, respectively. Jin et al., (2015) identified the key microRNAs (miRNAs) and miRNA-dependent gene regulation networks of grain filling in maize, through a deep-sequencing technique to research the dynamic expression patterns of miRNAs at four distinct developmental grain filling stages in Zhengdan 958, which is an elite hybrid and cultivated widely in China. The results revealed that the miRNA 156, 393, 396 and 397, with their respective targets, might play key roles in the grain filling rate by regulating maize growth, development and environment stress response. Xiaoming et al., (2015) carried out the computational analyses to identify and characterize miRNAs conserved in barley. They investigated the locations of miRNAs on the barley genome assembly and provide annotation of the functions of their predicted target genes. 116 mature miRNA sequences from 60 miRNA families have been found in the barley genome assembly by the miRNA identification pipeline. The in silico study has provided updated information in characterizing plant miRNAs in barley. The identified miRNA with the precursor sequences and their genomic locations as well as predicted target transcripts will serve as valuable resources for future studies.
Yu Chan et al., (2015) reported the overexpression of the rice microRNA (miRNA) OsmiR397, which is naturally highly expressed in young panicles and grains, enlarges grain size and promotes panicle branching, leading to an increase in overall grain yield of up to 25% in a field trial. OsmiR397 increases grain yield by downregulating its target, OsLAC, whose product is a laccase-like protein that was found to be involved in the sensitivity of plants to brassinosteroids.

Zhang et al., (2015) validated 228 miRNAs with significant changes in expression frequency during embryonic development in Chrysanthemum. Comparative profiling revealed that 69 miRNAs exhibited significant differential expression between normal and abnormal embryos at 18 DAP. A total of 1037 miRNA target genes were predicted, and their annotations were defined by transcriptome data. Target genes associated with metabolic pathways were most highly represented according to the annotation. 52 predicted target genes were identified to be associated with embryonic development, including 31 transcription factors and 21 additional genes.

Li et al., (2014) sequenced four small RNA libraries from two soybean cultivar (Hairbin xiaoheidou, SCN race 3 resistant, Liaodou 10, SCN race 3 susceptible) that were grown under un-inoculated and Soyabean Cyst Nematode (SCN) inoculated soil. Small RNAs were mapped to soybean genome sequence. Comparative analysis of miRNA profiling indicated 101 miRNAs belong to 40 families were SCN-responsive. The findings suggested that miRNA play important role in soybean response to SCN and have important implications for further identification of miRNAs under pathogen stress

Conclusion

  • MicroRNAs are short, endogenously expressed, nontranslated RNAs from stem loop regions of longer RNA precursors.
  • Plant miRNA genes are generally not located within protein-coding genes but comprise their own RNA polymerase II-dependent transcriptional units
  • Overexpression of microRNA OsmiR397 improves rice yield by increasing grain size and promoting panicle branching
  • Plant miRNAs are high-level regulators of gene expression that affect numerous aspects of plant biology, especially developmental patterning. Mutants impaired in miRNA biogenesis exhibit severe, pleiotropic abnormalities, and plants that overexpress particular miRNAs or express miRNA-resistant versions of particular miRNA targets exhibit a wide array of unusual phenotypes
  • Advances in genetic engineering- miRNA based technique, showed the potential to help address food insecurity by breeding crop cultivars with improved agronomic traits contributing to increasing yield and food safety

    Future thrust
  • To develop DNA based molecular markers associated with the desirable alleles of genes encoding individual miRNAs for the marker assisted selection for crop improvement in a time and cost effective manner
  • To design artificial miRNAs that may be used as efficient tools for controlling gene expression at will
  • Artificial microRNA technology, a specific and effective technology need to be developed for stimulating artificial stress conditions



References:
1. Guray A., Ebru D., Serkan U. and Turgay U. (2015). Functional Integral Genomics: 23: 11

2. Jin X., Zhiyuan F., Panqing L., Qian P., Dong D., Weihua L and Jihua T. (2015). Plos One. 10: 5

3. Li X., Xue W., Shaopeng Z., Dawei L., Yuxi D. and Wei D. (2014). Plos One. 7: 6

4. Matthew W., Jones-R., David P. B. and Bonnie B. (2006). Annual Review of Plant Biology. 57: 19-53

5. Vahap E., Sezer O. and Turgay U. (2013). Turkish Journal of Agriculture and Forestry. 37: 1-21

6. Xiaoming W., Csaba., Micha B., David M., Robbie W. and Runxuan Z. (2015). Central European Journal of Biology. 9(9): 841-852

7. Yu-Chan Z., Yang Yu, Cong-Ying W., Ze-Yuan L., Qing L., Jie X., Jian-You L., Xiao-Jing W., Liang-H., Fan C., Peiyong X., Cunyu Y., Jinfang C., Hong-Qing L and Yue-Qin C. (2015). Nature Biotechnology. 13:9

8. Zhang F., Wen D., Lulu H., Aiping S., Haibin W., Weimin F., Fadi Chen and Nianjun T. (2015). Plos One. 10: 4


About Author / Additional Info:
I am doing my Ph. D. in Plant Molecular Biology and Biotechnology from Anand Agricultural University

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