ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Metabolism and Chemodiversity
Volume 16 - 2025 | doi: 10.3389/fpls.2025.1647622
DNA methylation valley as a distinguishing feature occurs in root-specific expressed nicotine-related genes in Nicotiana attenuata
Provisionally accepted
- 1Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
- 2Yunnan Academy of Tobacco Science, Kunming, China
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Nicotine, the main defense alkaloid of Nicotiana species, is synthesized exclusively in the roots. Several studies have shown that changes in DNA methylation patterns are associated with altered expression of genes involved in the biosynthesis of some secondary metabolites. It remains unknown whether DNA methylation pattern of nicotine-related genes differs in root and leaf tissues.By combining RNA sequencing, quantitative real time PCR and whole-genome bisulfite sequencing of Nicotiana attenuata root and leaf samples, we found that most of the nicotine-related genes were exclusively and highly expressed in the root, while their DNA methylation patterns were very similar in both tissues. Interestingly, these genes with root-specific expression share a prominent DNA methylation valley (DMV) as a distinguishing feature. Further analysis revealed that 37.4% of the root-preferentially expressed genes were DMV genes, suggesting that root-specific expressed genes, including these nicotine-related genes, were strongly associated with DMV.Our results revealed that having a DMV is a common feature of most nicotine-related genes that are expressed only in the root. Thus, our results provide new insights into the regulation of alkaloid biosynthesis by epigenetic modification.
Keywords: Nicotine, DNA Methylation, DNA methylation valley, Nicotiana, Root-specific expression
Received: 16 Jun 2025; Accepted: 14 Jul 2025.
Copyright: © 2025 Tong, Wang and Wu. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence:
Bingwu Wang, Yunnan Academy of Tobacco Science, Kunming, China
Jinsong Wu, Kunming Institute of Botany, Chinese Academy of Sciences (CAS), Kunming, China
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