Cytosine methylation in genomic DNA and characterization of DNA methylases and demethylases and their expression profiles in viroid-infected hop plants (Humulus lupulus var. ‘Celeia’)

Sečnik, Andrej (author), Štajner, Nataša (author), Radišek, Sebastjan (author), Kunej, Urban (author), Križman, Mitja (author), Jakše, Jernej (author)

Abiotic and biotic stresses can lead to changes in host DNA methylation, which in plants is also mediated by an RNA-directed DNA methylation mechanism. Infections with viroids have been shown to affect DNA methylation dynamics in different plant hosts. The aim of our research was to determine the content of 5-methylcytosine (5-mC) in genomic DNA at the whole genome level of hop plants (Humulus lupulus Var. ‘Celeia’) infected with different viroids and their combinations and to analyse the expression of the selected genes to improve our understanding of DNA methylation dynamics in plant-viroid systems. The adapted HPLC-UV method used proved to be suitable for this purpose, and thus we were able to estimate for the first time that the cytosine methylation level in viroid-free hop plants was 26.7%. Interestingly, the observed 5-mC level was the lowest in hop plants infected simultaneously with CBCVd, HLVd and HSVd (23.7%), whereas the highest level was observed in plants infected with HLVd (31.4%). In addition, we identified three DNA methylases and one DNA demethylase gene in the hop’s draft genome. The RT-qPCR revealed upregulation of all newly identified genes in hop plants infected with all three viroids, while no altered expression was observed in any of the other hop plants tested, except for CBCVd-infected hop plants, in which one DNA methylase was also upregulated.

• Language: English
• Keywords: DNA methylation, viroid, hop plant, HPLC, DNA methylase, DNA demethylase, phylogeny, RT-qPCR
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Year: 2022
• Number of pages: 16 str.
• Numbering: no. 16, art. 2592, vol. 11
• PID: 20.500.12556/RUL-139383
• UDC: 577.2
• ISSN on article: 2073-4409
• COBISS.SI-ID: 119929347
• Publication date in RUL: 01.09.2022

Record is a part of a journal

• Title: Cells
• Shortened title: Cells
• Publisher: MDPI
• ISSN: 2073-4409
• COBISS.SI-ID: 519958809

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 19.08.2022

Secondary language

• Language: Slovenian
• Keywords: metilacija DNA, viroidi, hmelj, DNA demetilaza, filogenija, RNA-usmerjena metilacija DNA

Projects

• Funder: ARRS - Slovenian Research Agency
• Project number: P4-0077
• Name: Kmetijske rastline - genetika in sodobne tehnologije

• Funder: Other - Other funder or multiple funders
• Funding programme: Javni sklad Republike Slovenije za razvoj kadrov in štipendije
• Project number: 200751-53626