An expression atlas of miRNAs in Arabidopsis thaliana

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.

MicroRNA Dynamics and Functions DuringArabidopsisEmbryogenesis

“…Twelve miRNA families had relatively high levels during early embryogenesis and decreased thereafter. Based on further analysis of internally generated and publicly available sRNA-seq data from 26 tissue-types (Xu et al, 2018) , five miRNA families were highly enriched during the initial stages of embryogenesis including miR156b-3p, miR831, miR845, miR866-3p and miR3440b-3p ( Figures 3B and S2). To examine whether miRNA levels vary between early embryonic cell-types, we adapted a sRNA in situ protocol (Ghosh Dastidar et al, 2016) to detect four selected miRNAs in early embryos.…”

“…Five miRNA families were selected based on their enrichment in embryos compared to internally generated leaf and floral bud sRNA-seq libraries. sRNA-seq libraries generated internally are marked in bold and published sRNA-seq data from 26 tissue types (Xu et al, 2018) are also shown. (C) Representative images of miRNA in situ hybridizations on sections of embryos.…”

“…Despite the individual examples of embryonic miRNA functions described above and miRNA profiling studies on late-staged plant embryos (Huang et al, 2013;Oh et al, 2008;Xu et al, 2018) , a comprehensive understanding of embryonic miRNA populations and their individual contributions to embryogenesis is incomplete. Arabidopsis thaliana ( Arabidopsis ) embryos are ideal model systems to investigate the roles of miRNAs during plant embryogenesis.…”

Recent progress in microRNA-based delivery systems for the treatment of human disease

“…Recently, miRNA expression profiling studies of multiple tumor types have revealed that aberrantly expressed miRNAs are beneficial for the classification, diagnosis, staging, and prognosis of disease [15]. The analysis of sequencing data from 27 different organs/tissues of Arabidopsis also proved that most miRNAs are widely expressed, whereas a fraction of miRNAs exhibit tissue-specific expression patterns [16].…”

AP2/ERF Transcription Factors Integrate Age and Wound Signals for Root Regeneration

“…Juvenile plants exhibit a high cytokinin response and regenerative capacity. As a plant ages, miR156 levels decline, alleviating the repression of its SPL targets (Wang et al, 2009;Yamaguchi et al, 2009;Xu et al, 2018). SPL directly inhibits the transcriptional activity of B-type ARABIDOPSIS RESPONSE REGULATORs and thereby impairs shoot regenerative capacity (Zhang et al, 2015).…”