MicroRNAs Are Intensively Regulated during Induction of Somatic Embryogenesis in Arabidopsis

Abstract

Several genes encoding transcription factors (TFs) were indicated to have a key role in the induction of somatic embryogenesis (SE), which is triggered in the somatic cells of plants. In order to further explore the genetic regulatory network that is involved in the embryogenic transition induced in plant somatic cells, micro-RNA (miRNAs) molecules, the products of MIRNA (MIR) genes and the common regulators of TF transcripts, were analyzed in an embryogenic culture of Arabidopsis thaliana. In total, the expression of 190 genes of the 114 MIRNA families was monitored during SE induction and the levels of the primary (pri-miRNAs) transcripts vs. the mature miRNAs were investigated. The results revealed that the majority (98%) of the MIR genes were active and that most of them (64%) were differentially expressed during SE. A distinct attribute of the MIR expression in SE was the strong repression of MIR transcripts at the early stage of SE followed by their significant up-regulation in the advanced stage of SE. Comparison of the mature miRNAs vs. pri-miRNAs suggested that the extensive post-transcriptional regulation of miRNA is associated with SE induction. Candidate miRNA molecules of the assumed function in the embryogenic response were identified among the mature miRNAs that had a differential expression in SE, including miR156, miR157, miR159, miR160, miR164, miR166, miR169, miR319, miR390, miR393, miR396, and miR398. Consistent with the central role of phytohormones and stress factors in SE induction, the functions of the candidate miRNAs were annotated to phytohormone and stress responses. To confirm the functions of the candidate miRNAs in SE, the expression patterns of the mature miRNAs and their presumed targets were compared and regulatory relation during SE was indicated for most of the analyzed miRNA-target pairs. The results of the study contribute to the refinement of the miRNA-controlled regulatory pathways that operate during embryogenic induction in plants and provide a valuable platform for the identification of the genes that are targeted by the candidate miRNAs in SE induction.

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

“…Extensive modulation of the TF genes in an embryogenic culture of Arabidopsis is accompanied by differential expression of numerous miRNAs, suggesting the function of miRNA-regulation in the embryogenic transition of plant somatic cells [54,55]. In support, the dcl1 mutant, a defect in the DICERLIKE1 (DCL1) gene with a key role in miRNA biogenesis, was shown to be unable for SE induction [56].…”

“…Numerous MIRNA genes, including members of the same gene family of SE-modulated expression, have been reported in transcriptomic analyses of different plant cultures [55,58,66,68,73,79]. The expression of different MIRNA gene family members is strictly regulated during plant development in an organ-and tissue-specific manner [80,81], and thus reporter line analyses could be important in identifying the specific MIRNA genes that contribute to SE induction.…”

“…The auxin-related miRNAs frequently target the fundamental components of the auxin signaling pathway, including the ARFs, which are involved in SE induction [27,93]. Accordingly, insights into embryogenic cultures of Arabidopsis and other plants indicated that miR160 could directly regulate the expression of ARF10, ARF16, and ARF17; miR167 seems to the control expression of ARF6 and ARF8, while miR390 possibly downregulates the ARF2, ARF3, ARF4 transcripts [55,63,64,68,81,85,86].…”

Azacitidine (5-AzaC)-treatment and mutations in DNA methylase genes affect embryogenic response and expression of the genes that are involved in somatic embryogenesis in Arabidopsis

“…Thus, to fully understand the function of DNA methylation in the embryogenic transition the functional outcome of DNA methylation in the context of other epigenetic changes remains to be uncovered. Moreover, it is of importance to reveal the relation of DNA methylation with the recently identified miRNA that plays a regulatory role in the SE of Arabidopsis (Wójcik and Gaj 2016;Szyrajew et al 2017;Wójcik et al 2017). …”

Impact of small RNAs in retrograde signalling pathways inArabidopsis thaliana

“…We did not predict any target for miR169g-3p according to our parameters. Generally, miR169 has already been shown to act in stress-responses including heat and salt stress (Szyrajew et al, 2017, Pegler et al, 2019 and regulates targets such as the NUCLEAR FACTOR Y, SUBUNIT A5 that was shown to be important in the heat stress response. In tomato leaves miR169g-3p was reported to be downregulated under Pi deficiency, but a target for this particular miRNA could not be predicted (Gu et al, 2010).…”