Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants

Kun Yang,G P Saradhi Varma,Gaurav Sablok,Suresh Mudunuri,Xiaopeng Wen

doi:10.1038/s41598-019-38932-w

Kun Yang, G P Saradhi Varma + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-38932-w

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Abstract

Plants have an amazing ability to cope with wide variety of stresses by regulating the expression of genes and thus by altering the physiological status. In the past few years, canonical microRNA variants (isomiRs) have been shown to play pivotal roles by acting as regulators of the transcriptional machinery. In the present research, we present Diff isomiRs, a web-based exploratory repository of differential isomiRs across 16 sequenced plant species representing a total of 433 datasets across 21 different stresses and 158 experimental states. Diff isomiRs provides the high-throughput detection of differential isomiRs using mapping-based and model-based differential analysis revealing a total of 16,157 and 2,028 differential isomiRs, respectively. Easy-to-use and web-based exploration of differential isomiRs provides several features such as browsing of the differential isomiRs according to stress or species, as well as association of the differential isomiRs to targets and plant endogenous target mimics (PeTMs). Diff isomiRs also provides the relationship between the canonical miRNAs, isomiRs and the miRNA-target interactions. This is the first web-based large-scale repository for browsing differential isomiRs and will facilitate better understanding of the regulatory role of the isomiRs with respect to the canonical microRNAs. Diff isomiRs can be accessed at: www.mcr.org.in/diffisomirs.

Highlights

Functional genomics of abiotic stress tolerance in plants is at the forefront of the 21st century
To the best of the knowledge, this is the first integrated repository that provides the high-throughput detection of the differential isomiRs and features such as target prediction, log2FC across the stress conditions, mapping-based visualization, cross-accessibility of the isomiRs across the species and association of the canonical miRNAs and their templated isomiRs to plant endogenous target mimics (PeTMs) and provides the miRNA-target interactions with respect to the isomiRs originating as a result of the terminal modification from the canonical miRNAs
Post-transcriptional regulation is an important phenomenon controlled by several classes of regulatory RNAs, among which microRNAs play an important role as post-transcriptional regulators and as check points for transcriptional coordination

Summary

Introduction

Functional genomics of abiotic stress tolerance in plants is at the forefront of the 21st century. IsomiRbank lacks the information on miRNA-isomiR target interactions Relative lack of these features prompted the development of the Diff isomiRs, which is the first web-based exploratory repository providing the differential isomiRs across 16 sequenced plant species, covering a total of 433 datasets and representing 21 different stresses and 158 experimental states. To the best of the knowledge, this is the first integrated repository that provides the high-throughput detection of the differential isomiRs and features such as target prediction, log2FC across the stress conditions, mapping-based visualization, cross-accessibility of the isomiRs across the species and association of the canonical miRNAs and their templated isomiRs to PeTMs and provides the miRNA-target interactions with respect to the isomiRs originating as a result of the terminal modification from the canonical miRNAs

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