Functional & Integrative Genomics

, Volume 19, Issue 4, pp 597–615 | Cite as

High-throughput sequencing and differential expression analysis of miRNAs in response to Brassinosteroid treatment in Arabidopsis thaliana

  • Gunjan SirohiEmail author
  • Ankitha Khandelwal
  • Meenu KapoorEmail author
Original Article


Brassinosteroids are a class of phytohormones that play crucial roles in improving stress tolerance in plants. Many biochemical and physiological changes in response to abiotic stress are related to regulation of gene expression and accumulation of associated proteins. MicroRNAs (miRNAs) are class of small non-coding RNAs that regulate gene expression post-transcriptionally. Roles of these regulatory RNAs in brassinosteroid (BR) signalling have however remained elusive. In this study using high-throughput small RNA sequencing method, we present a comprehensive compilation of BR-induced differentially expressed microRNAs in root and shoots of Arabidopsis thaliana seedlings. We identified 229 known miRNAs belonging to 102 families and 27 novel miRNAs that express in response to exogenous BR treatment. Out of 102 families, miRNAs belonging to known 48 families and out of 27 novel miRNAs, 23 were observed to be differentially expressed in response to BR treatment. Among the conserved miRNAs, all members of miR169 were observed to be downregulated in both shoot and root samples. While, auxin-responsive factors were predicted to be direct targets of some novel miRNAs that are upregulated in shoots and suppressed in roots. The BR-responsive tissue-specific miRNome characterized in this study can be used as a starting point by investigators for functional validation studies that will shed light on the underlying molecular mechanism of BR-mediated stress tolerance at the level of post-transcriptional gene regulation.


Brassinosteroid MicroRNAs Small RNA sequencing Arabidopsis thaliana GenBank accession no. SRP152755 



We acknowledge Bionivid Pvt. Ltd., Bangalore, India, for small RNA sequencing and preliminary data analysis.

Author contributions

GS conceived, designed and performed the experiments along with AK. MK provided resources and mentored GS. Together, they analysed the data and wrote the manuscript. All authors read and approved the final version of paper.

Funding information

This study was funded by Science and Engineering Research Board (SERB), Government of India, through grant #YSS/2014/000350 to GS.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10142_2019_668_MOESM1_ESM.pdf (25.3 mb)
Supplementary Fig. 1 Fold-back structures of novel miRNAs identified in the study as predicted using MFOLD. The mature miRNAs are highlighted in blue while the miRNA* are shown in red colour. (PDF 25879 kb)
10142_2019_668_MOESM2_ESM.doc (108 kb)
ESM 2 (DOC 108 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  1. 1.University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityNew DelhiIndia

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