Hypermethylation of Auxin-Responsive Motifs in the Promoters of the Transcription Factor Genes Accompanies the Somatic Embryogenesis Induction in Arabidopsis.

Daria Grzybkowska,Małgorzata D Gaj,Katarzyna Nowak

doi:10.3390/ijms21186849

Daria Grzybkowska, Małgorzata D Gaj + Show 1 more

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https://doi.org/10.3390/ijms21186849

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Abstract

The auxin-induced embryogenic reprogramming of plant somatic cells is associated with extensive modulation of the gene expression in which epigenetic modifications, including DNA methylation, seem to play a crucial role. However, the function of DNA methylation, including the role of auxin in epigenetic regulation of the SE-controlling genes, remains poorly understood. Hence, in the present study, we analysed the expression and methylation of the TF genes that play a critical regulatory role during SE induction (LEC1, LEC2, BBM, WUS and AGL15) in auxin-treated explants of Arabidopsis. The results showed that auxin treatment substantially affected both the expression and methylation patterns of the SE-involved TF genes in a concentration-dependent manner. The auxin treatment differentially modulated the methylation of the promoter (P) and gene body (GB) sequences of the SE-involved genes. Relevantly, the SE-effective auxin treatment (5.0 µM of 2,4-D) was associated with the stable hypermethylation of the P regions of the SE-involved genes and a significantly higher methylation of the P than the GB fragments was a characteristic feature of the embryogenic culture. The presence of auxin-responsive (AuxRE) motifs in the hypermethylated P regions suggests that auxin might substantially contribute to the DNA methylation-mediated control of the SE-involved genes.

Highlights

Plants have a unique capacity for switching on of embryogenic development in in vitro cultured somatic cells
We found that the promoters (P) and coding (GB) sequences of the somatic embryogenesis (SE)-involved transcription factors (TFs) genes, including LEC1, LEC2, BABY BOOM (BBM), WUS and AGL15, showed significantly different methylation patterns in response to 2,4-D, which implies the that there are different roles for P versus gene body (GB) methylation in the auxin-mediated mechanism that controls SE induction
We found that auxin treatment modulated the level of the methylation of the ethylene-responsive element that is present in the AGL15 promoter, and this implies a contribution of ethylene to the methylation-mediated control of AGL15 during auxin-induced SE

Summary

Introduction

Plants have a unique capacity for switching on of embryogenic development in in vitro cultured somatic cells. The genes that control the induction of SE have been intensively studied in order to understand the molecular determinants of cellular toti-/pluripotency in plants [1]. The impact of auxin treatment on the global methylome of in vitro cultured plant explants, including those undergoing SE induction, has been reported [5,6,7]. Auxin-modulated changes in the global transcriptomes have been reported in embryogenic cultures of plants including Arabidopsis [8,9,10]. The analysis of global methylome implies that auxin treatment might control the embryogenic reprogramming of explant cells via the DNA methylation-mediated regulation of gene expression [11]

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Conclusion