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An expression atlas of miRNAs in Arabidopsis thaliana

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Abstract

MicroRNAs (miRNAs) are small non-coding RNAs that regulate a variety of biological processes. MiRNA expression often exhibits spatial and temporal specificity. However, genome-wide miRNA expression patterns in different organs during development of Arabidopsis thaliana have not yet been systemically investigated. In this study, we sequenced small RNA libraries generated from 27 different organ/tissue types, which cover the entire life cycle of Arabidopsis. Analysis of the sequencing data revealed that most miRNAs are ubiquitously expressed, whereas a small set of miRNAs display highly specific expression patterns. In addition, different miRNA members within the same family have distinct spatial and temporal expression patterns. Moreover, we found that some miRNAs are produced from different arms of their hairpin precursors at different developmental stages. This work provides new insights into the regulation of miRNA biogenesis and a rich resource for future investigation of miRNA functions in Arabidopsis.

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Acknowledgements

This work was supported by grants fromNational Key Research and Development Program of China (2016YFA0500800) and National Natural Science Foundation of China (31421001, 31225015) to Yijun Qi. Yijun Qi is a visiting investigator of the CAS Center for Excellence in Molecular Plant Sciences.

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  1. Contributed equally to this work

Authors and Affiliations

  1. Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China

    Le Xu, Jingrui Li, Yan Li & Yijun Qi

  2. Tsinghua-Peking Center for Life Sciences, Beijing, 100084, China

    Jingrui Li, Yan Li & Yijun Qi

  3. College of Biological Sciences, China Agricultural University, Beijing, 100094, China

    Yugang Hu

  4. College of Life Sciences-Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Capital Normal University, Beijing, 100048, China

    Ying Cao & Ligeng Ma

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  1. Le Xu
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  4. Jingrui Li
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  5. Ligeng Ma
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  6. Yan Li
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  7. Yijun Qi
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Corresponding authors

Correspondence to Yan Li or Yijun Qi.

Electronic supplementary material

Figure S1

Correlation between two biological replicates of small RNA sequencing.

Figure S2

Small RNA size distribution and 5′ bias.

Figure S3

S-plots for miRNAs.

Figure S4

Expression pattern and strand bias of conserved versus non-conserved miRNAs.

Figure S5

Expression of representative miRNAs at vegetative stages.

Figure S6

Analysis of miRNA arm switch events.

Table S1

Summary of small RNA libraries used in this study

Table S2

Expression levels of miRNAs in all samples

Table S3

Expression levels of members of highly conserved miRNA families during development

Table S4

The sequences of probes used in small RNA Northern blot

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Xu, L., Hu, Y., Cao, Y. et al. An expression atlas of miRNAs in Arabidopsis thaliana. Sci. China Life Sci. 61, 178–189 (2018). https://doi.org/10.1007/s11427-017-9199-1

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  • DOI: https://doi.org/10.1007/s11427-017-9199-1

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