Prediction of Plant miRNA Targets

  • Priyanka Pandey
  • Prashant K. Srivastava
  • Shree P. PandeyEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1932)


microRNAs (miRNAs) are the central component of an important layer of regulation of gene expression at posttranscriptional level. In plants, miRNAs target the transcripts in a highly complementary sequence-dependent manner. Extensive research is being made to study genome-wide miRNA-mediated regulation of gene expression, which has resulted in the development of many tools for in silico prediction of miRNA targets. Although several tools have been developed for predicting miRNA targets in model plants, genome-wide analysis of miRNA targets is still a challenge for non-model species that lack dedicated tools. Here, we describe an in silico procedure for studying miRNA-mediated interactions in plants, which is based on the fact that canonical miRNA-target sites are highly complementary, the miRNAs negatively regulate the expression of their target genes, and miRNAs may form regulatory networks as one miRNA may target more than one transcript and vice versa to modulate and fine-tune expression of the genome.

Key words

miRNA Target prediction Genome-wide analysis Next-generation sequencing NGS Network analysis 



SPP acknowledges financial support by Max Planck Society and Max Planck India partner group program.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Priyanka Pandey
    • 1
  • Prashant K. Srivastava
    • 2
  • Shree P. Pandey
    • 3
    Email author
  1. 1.National Institute of Biomedical GenomicsKalyaniIndia
  2. 2.Division of Brain Sciences, Department of MedicineImperial CollegeLondonUK
  3. 3.Department of Molecular EcologyMax Planck Institute for Chemical EcologyJenaGermany

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