Abstract

BackgroundUsually the microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. However, the higher/lower expression level of miRNAs does not always indicate the higher/lower level of cleavages and such analysis, thus, sometimes ignores the crucial cleavage events. In the present work, the degradome sequencing data were employed to construct the complete miRNA-mediated gene regulatory network in soybean, unlike the traditional approach starting with small RNA sequencing data.ResultsWe constructed the root-, cotyledon-, leaf- and seed-specific miRNA regulatory networks with the degradome sequencing data and the forthcoming verification of miRNA profiling analysis. As a result, we identified 205 conserved miRNA-target interactions (MTIs) involved with 6 conserved gma-miRNA families and 365 tissue-specific MTIs containing 24 root-specific, 45 leaf-specific, 63 cotyledon-specific and 225 seed-specific MTIs. We found a total of 156 miRNAs in tissue-specific MTIs including 18 tissue-specific miRNAs, however, only 3 miRNAs have consistent tissue-specific expression. Our study showed the degradome-dependent miRNA regulatory networks (DDNs) in four soybean tissues and explored their conservations and specificities.ConclusionsThe construction of DDNs may provide the complete miRNA-Target interactions in certain plant tissues, leading to the identification of the conserved and tissue-specific MTIs and sub-networks. Our work provides a basis for further investigation of the roles and mechanisms of miRNA-mediated regulation of tissue-specific growth and development in soybean.

Highlights

  • The microRNA-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions

  • Based on degradome-dependent miRNA regulatory network (DDN) analysis, we found and validated conserved and specific MiRNA-Target Interaction (MTI), using tissue-specific MTIs to construct the root, cotyledon, leave- and seed-specific miRNA regulatory networks based on the degradome sequencing data, annotated with miRNA profiling analysis and discussed some co-interacted miRNA families mediated GRNs

  • Construction and description of global DDNs We took raw tables of degradome-dependent networks as fundamental information to classify the regulatory types of different miRNA mediated subnetworks, and studied further about conserved MTIs and tissue-specific MTIs

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Summary

Introduction

The microRNA (miRNA)-mediated gene regulatory network (GRN) is constructed from the investigation of miRNA expression profiling and target predictions. The scholars started to explore the interactions and regulatory networks medicated by two or more miRNAs with the prosperity of generation sequencing, all kinds of small RNA databases and bioinformatics tools, for instance, miRBase [10], psRNATarget service [11], bowtie [12] and Cytoscape 8 [13]. With such abundant small RNA datasets and tools, it is allowed to apply different patterns of biosynthesis into small RNA quantification and their expression detection.

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