Cytosine methylation of the FWA promoter promotes direct in vitro shoot regeneration in Arabidopsis thaliana

Regulation of regeneration in Arabidopsis thaliana

We employed several algorithms with high efficacy to analyze the public transcriptomic data, aiming to identify key transcription factors (TFs) that regulate regeneration in Arabidopsis thaliana. Initially, we utilized CollaborativeNet, also known as TF-Cluster, to construct a collaborative network of all TFs, which was subsequently decomposed into many subnetworks using the Triple-Link and Compound Spring Embedder (CoSE) algorithms. Functional analysis of these subnetworks led to the identification of nine subnetworks closely associated with regeneration. We further applied principal component analysis and gene ontology (GO) enrichment analysis to reduce the subnetworks from nine to three, namely subnetworks 1, 12, and 17. Searching for TF-binding sites in the promoters of the co-expressed and co-regulated (CCGs) genes of all TFs in these three subnetworks and Triple-Gene Mutual Interaction analysis of TFs in these three subnetworks with the CCGs involved in regeneration enabled us to rank the TFs in each subnetwork. Finally, six potential candidate TFs-WOX9A, LEC2, PGA37, WIP5, PEI1, and AIL1 from subnetwork 1-were identified, and their roles in somatic embryogenesis (GO:0010262) and regeneration (GO:0031099) were discussed, so were the TFs in Subnetwork 12 and 17 associated with regeneration. The TFs identified were also assessed using the CIS-BP database and Expression Atlas. Our analyses suggest some novel TFs that may have regulatory roles in regeneration and embryogenesis and provide valuable data and insights into the regulatory mechanisms related to regeneration. The tools and the procedures used here are instrumental for analyzing high-throughput transcriptomic data and advancing our understanding of the regulation of various biological processes of interest.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-023-00121-9.

HD-Zip IV transcription factors: Drivers of epidermal cell fate integrate metabolic signals

The leaf epidermis comprises the outermost layer of cells that protect plants against environmental stresses such as drought, ultraviolet radiation, and pathogen attack. Research over the past decades highlights the role of class IV homeodomain leucine-zipper (HD-Zip IV) transcription factors (TFs) in driving differentiation of various epidermal cell types, such as trichomes, guard cells, and pavement cells. Evolutionary origins of this family in the charophycean green algae and HD-Zip-specific gene expression in the maternal genome provide clues to unlocking their secrets which include ties to cell cycle regulation. A distinguishing feature of these TFs is the presence of a lipid binding pocket that integrates metabolic information with gene expression. Identities of metabolic partners are beginning to emerge, uncovering feedback loops to maintain epidermal cell specification. Discoveries of associated molecular mechanisms are revealing fascinating links to phospholipid and sphingolipid metabolism and mechanical signaling.

Analysis of DNA methylation in potato tuber in response to light exposure during storage

Exposure to light induces tuber greening and the accumulation of the toxic alkaloid Solanine in potato (Solanum tuberosum L) during storage greatly reduce tuber value. While the mechanism of this greening process remains unclear, it is well understood that DNA methylation plays an important role in regulating gene expression in response to environmental conditions. In this study, methylation-sensitive amplified polymorphism was used to assess the effect of light exposure on DNA methylation during storage of potato tubers. Light-induced genome-wide DNA demethylation and the rate of DNA methylation decreased with long storage times. Following, the sequencing of 14 differentially amplified fragments and analysis using the Basic Local Alignment Search Tool, eight genomic sequences and six annotated fragment sequences were identified. The latter included ADP glucose pyrophosphorylase 1/2, chlorophyllide a oxygenase 1 (CAO1), receptor-like protein kinase HAIKU2, and repressor of GA4, all of which are involved in starch biosynthesis, chlorophyll synthesis, endosperm development, and gibberellic acid signaling, respectively. Demethylation was observed in the CpG island (-273 to -166 bp) of the CAO1 promoter in response to light, which further confirmed that the variations in genome methylation are dependent upon the light exposure and suggests a direct role for DNA methylation. Our results provide an epigenetic perspective for further exploring the mechanism of light-induced tuber greening.