Endogenous target mimics, microRNA167, and its targets ARF6 and ARF8 during somatic embryo development in Dimocarpus longan Lour.

Lin, Yuling; Zhang, Lai; Lin, Lixia; Lai, Renchun; Tian, Qifeng; Ye, Wei; Zhang, Dongmin; Yang, Manman; Chen, Yukun; Zhang, Zihao

doi:10.1007/s11032-015-0420-4

Cited by 21 publications

(13 citation statements)

References 60 publications

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“…The importance of miR167-ARF6/ARF8 in the acquisition of embryogenic competence during SE has also been indicated in cotton by a decrease in the miR167 activity, which led to enhanced callogenesis and an increased production of somatic embryos [ 154 ], while an overexpression of MIR167 genes inhibited the formation of somatic embryos in Arabidopsis, which showed that miR167 negatively regulates SE induction [ 112 ]. Moreover, Lin et al identified the expression of two endogenous TM transcripts that modulate the miR167 activity during SE in D. longan , which resulted in increased expression of ARF6 and ARF8 , thus indicating the important role of miR167-ARF6/ARF8 in the development of somatic embryos [ 155 ], which is in line with previous analyses that were carried out using other available functional genomics tools ([ 75 , 156 , 157 ] reviewed in [ 94 ]). Moreover, the TM approach has been successfully used for the functional analysis of miR156, miR160, miR166, miR393, miR396, miR398, and miR1432, thereby indicating their importance in regulating sexual and asexual embryogenesis in barley [ 102 ], tomato [ 158 , 159 ], rice [ 160 , 161 ], and Arabidopsis [ 115 , 126 , 162 , 163 ].…”

Section: Available Plant Mirna-dedicated Research Toolssupporting

confidence: 71%

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Wójcik

2020

IJMS

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During early plant embryogenesis, some of the most fundamental decisions on fate and identity are taken making it a fascinating process to study. It is no surprise that higher plant embryogenesis was intensively analysed during the last century, while somatic embryogenesis is probably the most studied regeneration model. Encoded by the MIRNA, short, single-stranded, non-coding miRNAs, are commonly present in all Eukaryotic genomes and are involved in the regulation of the gene expression during the essential developmental processes such as plant morphogenesis, hormone signaling, and developmental phase transition. During the last few years dedicated to miRNAs, analytical methods and tools have been developed, which have afforded new opportunities in functional analyses of plant miRNAs, including (i) databases for in silico analysis; (ii) miRNAs detection and expression approaches; (iii) reporter and sensor lines for a spatio-temporal analysis of the miRNA-target interactions; (iv) in situ hybridisation protocols; (v) artificial miRNAs; (vi) MIM and STTM lines to inhibit miRNA activity, and (vii) the target genes resistant to miRNA. Here, we attempted to summarise the toolbox for functional analysis of miRNAs during plant embryogenesis. In addition to characterising the described tools/methods, examples of the applications have been presented.

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Section: Available Plant Mirna-dedicated Research Toolssupporting

confidence: 71%

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Wójcik

2020

IJMS

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“…it regulates embryonic development by regulating ARF -mediated transcription [ 36 , 37 ], and Aux/IAAs also participate in the regulation of auxin by inhibiting ARF -mediated transcription [ 52 ]. Our laboratory has studied related genes including TIF1 [ 53 ], DlARF8 [ 17 ], ARF3/4 [ 18 ] and ARF10 , − 16 , and − 17 [ 19 ] that regulate the auxin response. In the KEGG enrichment results, it seemed that longan had begun to establish disease resistance mechanisms and other metabolic components based on hormones in the GE stage.…”

Section: Discussionmentioning

confidence: 99%

“…In addition, miR160a* largely interacted with its predicted eTMs during the GE and EC stages [ 19 ], and the interaction between miR172 and eTMs could delay flowering and eliminate top-of-the-range benefits [ 58 , 59 ]. MiRNAs and their predicted eTMs have also been reported during longan SE: miR167 cleaved the DlARF8 mRNA during longan SE [ 17 ], and an eTM down-regulated miR167, and the regulation of miR160 and its predicted eTM were involved in hormone signaling in longan [ 19 ].…”

Section: Discussionmentioning

confidence: 99%

“…A total of 643 conserved and 29 novel miRNAs (including star strands) of 169 miRNA families were identified during longan SE [ 16 ]. The molecular mechanisms of miR167 [ 17 ], miR390 [ 18 ] and miR160 [ 19 ] in the regulation of the auxin response factors were demonstrated in longan SE. In addition, miR159 family members [ 20 ] and miR171 [ 21 ], which are involved in flower organ formation, were found to have the most stable expression among miRNAs at different developmental stages of longan SE [ 22 ].…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour

Chen

Xue

et al. 2018

BMC Genomics

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BackgroundLong non-coding RNAs (lncRNAs) are involved in variable cleavage, transcriptional interference, regulation of DNA methylation and protein modification. However, the regulation of lncRNAs in plant somatic embryos remains unclear. The longan (Dimocarpus longan) somatic embryogenesis (SE) system is a good system for research on longan embryo development.ResultsIn this study, 7643 lncRNAs obtained during early SE in D. longan were identified by high-throughput sequencing, among which 6005 lncRNAs were expressed. Of the expressed lncRNAs, 4790 were found in all samples and 160 were specifically expressed in embryogenic callus (EC), 154 in incomplete embryogenic compact structures (ICpECs), and 376 in globular embryos (GEs). We annotated the 6005 expressed lncRNAs, and 1404 lncRNAs belonged to 506 noncoding RNA (ncRNA) families and 4682 lncRNAs were predicted to target protein-coding genes. The target genes included 5051 cis-regulated target genes (5712 pairs) and 1605 trans-regulated target genes (3618 pairs). KEGG analysis revealed that most of the differentially expressed target genes (mRNAs) of the lncRNAs were enriched in the “plant-pathogen interaction” and “plant hormone signaling” pathways during early longan SE. Real-time quantitative PCR confirmed that 20 selected lncRNAs showed significant differences in expression and that five lncRNAs were related to auxin response factors. Compared with the FPKM expression trends, 16 lncRNA expression trends were the same in qPCR. In lncRNA-miRNA-mRNA relationship prediction, 40 lncRNAs were predicted to function as eTMs for 15 miRNAs and 7 lncRNAs were identified as potential miRNA precursors. In addition, we verified the lncRNA-miRNA-mRNA regulatory relationships by transient expression of miRNAs (miR172a, miR159a.1 and miR398a).ConclusionAnalyses of lncRNAs during early longan SE showed that differentially expressed lncRNAs were involved in expression regulation at each SE stage, and may form a regulatory network with miRNAs and mRNAs. These findings provide new insights into lncRNAs and lay a foundation for future functional analysis of lncRNAs during early longan SE.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5158-z) contains supplementary material, which is available to authorized users.

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“…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].…”

Section: Auxin-related Mirnas Fine-tune the Genetic Network That Contmentioning

confidence: 99%

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

Wójcikowska

Wójcik

Gaj

2020

IJMS

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Somatic embryogenesis (SE) that is induced in plant explants in response to auxin treatment is closely associated with an extensive genetic reprogramming of the cell transcriptome. The significant modulation of the gene transcription profiles during SE induction results from the epigenetic factors that fine-tune the gene expression towards embryogenic development. Among these factors, microRNA molecules (miRNAs) contribute to the post-transcriptional regulation of gene expression. In the past few years, several miRNAs that regulate the SE-involved transcription factors (TFs) have been identified, and most of them were involved in the auxin-related processes, including auxin metabolism and signaling. In addition to miRNAs, chemical modifications of DNA and chromatin, in particular the methylation of DNA and histones and histone acetylation, have been shown to shape the SE transcriptomes. In response to auxin, these epigenetic modifications regulate the chromatin structure, and hence essentially contribute to the control of gene expression during SE induction. In this paper, we describe the current state of knowledge with regard to the SE epigenome. The complex interactions within and between the epigenetic factors, the key SE TFs that have been revealed, and the relationships between the SE epigenome and auxin-related processes such as auxin perception, metabolism, and signaling are highlighted.

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Endogenous target mimics, microRNA167, and its targets ARF6 and ARF8 during somatic embryo development in Dimocarpus longan Lour.

Cited by 21 publications

References 60 publications

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Research Tools for the Functional Genomics of Plant miRNAs During Zygotic and Somatic Embryogenesis

Genome-wide identification and characterization of long non-coding RNAs involved in the early somatic embryogenesis in Dimocarpus longan Lour

Epigenetic Regulation of Auxin-Induced Somatic Embryogenesis in Plants

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