Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome

Yakovlev, Igor A.; Gackowski, Daniel; Abakir, Abdulkadir; Viejo, Marcos; Ruzov, Alexey; Olinski, Ryszard; Starczak, Marta; Fossdal, Carl Gunnar; Krutovsky, Konstantin V.

Abstract

5-Methylcytosine (5mC) is an epigenetic modification involved in regulation of gene expression in metazoans and plants. Iron-(II)/α-ketoglutarate-dependent dioxygenases can oxidize 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Although these oxidized forms of 5mC may serve as demethylation intermediates or contribute to transcriptional regulation in animals and fungi, experimental evidence for their presence in plant genomes is ambiguous. Here, employing reversed-phase HPLC coupled with sensitive mass spectrometry, we demonstrated that, unlike 5caC, both 5hmC and 5fC are detectable in non-negligible quantities in the DNA of a conifer, Norway spruce. Remarkably, whereas 5hmC content of spruce DNA is approximately 100-fold lower relative to human colorectal carcinoma cells, the levels of both - 5fC and a thymine base modification, 5-hydroxymethyluracil, are comparable in these systems. We confirmed the presence of modified DNA bases by immunohistochemistry in Norway spruce buds based on peroxidase-conjugated antibodies and tyramide signal amplification. Our results reveal the presence of specific range of noncanonical DNA bases in conifer genomes implying potential roles for these modifications in plant development and homeostasis.

Citation

Yakovlev, I. A., Gackowski, D., Abakir, A., Viejo, M., Ruzov, A., Olinski, R., …Krutovsky, K. V. (2019). Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome. Scientific Reports, 9, Article 19314. https://doi.org/10.1038/s41598-019-55826-z

• Journal Article Type: Article
• Acceptance Date: Nov 29, 2019
• Online Publication Date: Dec 17, 2019
• Publication Date: 2019-12
• Deposit Date: Jan 29, 2020
• Publicly Available Date: Jan 29, 2020
• Journal: Scientific Reports
• Electronic ISSN: 2045-2322
• Publisher: Nature Publishing Group
• Peer Reviewed: Peer Reviewed
• Volume: 9
• Article Number: 19314
• DOI: https://doi.org/10.1038/s41598-019-55826-z
• Keywords: Multidisciplinary
• Public URL: https://nottingham-repository.worktribe.com/output/3611659
• Publisher URL: https://www.nature.com/articles/s41598-019-55826-z
• Additional Information: Received: 27 December 2018; Accepted: 29 November 2019; First Online: 17 December 2019; : The authors declare no competing interests.