The oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), known as oxi-mCs, garners significant interest in plants as potential epigenetic marks. While research in mammals has established a role in cell reprogramming, carcinogenesis, and gene regulation, their functions in plants remain unclear. In rice, 5hmC has been associated with transposable elements (TEs) and heterochromatin. This study utilizes Silene latifolia, a dioecious plant with heteromorphic sex chromosomes and a genome with a large proportion of TEs, which provides a favourable environment for the study of oxi-mCs in individual sexes. Notably, we detected surprisingly high levels of oxi-mCs in S. latifolia comparable with mammals. Nuclei showed enrichment in heterochromatic regions, except for 5hmC whose signal was homogeneously distributed. Intriguingly, the same X chromosome in females displayed overall enrichment of 5hmC and 5fC compared with its counterpart. This fact is shared with 5mC, resembling dosage compensation. Co-localization showed higher correlation between 5mC and 5fC than with 5hmC, indicating no potential relationship between 5hmC and 5fC. Additionally, the promoter of several sex-linked genes and sex-biased TEs clustered in a clear sex-dependent way. Together, these findings unveil a hypothetical role for oxi-mCs in S. latifolia sex chromosome development, warranting further exploration.

Department of Clinical Biochemistry Faculty of Pharmacy Ludwik Rydygier Collegium Medicum in Bydgoszcz Nicolaus Copernicus University in Toruń ul Karlowicza 24 PO 85 092 Bydgoszcz Poland

Department of Plant Developmental Genetics Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 612 65 Brno Czech Republic

National Centre for Biomolecular Research Faculty of Science Masaryk University Kamenice 5 625 00 Brno Czech Republic

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Akagi T, Fujita N, Masuda K, et al. 2023. Rapid and dynamic evolution of a giant Y chromosome in DOI

Aravind L, Balasubramanian S, Rao A.. 2019. Unusual activity of a PubMed PMC

Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A, Balasubramanian S.. 2015. 5-Formylcytosine can be a stable DNA modification in mammals. Nature Chemical Biology 11, 555–557. PubMed PMC

Bačovský V, Čegan R, Tihlaříková E, Neděla V, Hudzieczek V, Smrža L, Janíček T, Beneš V, Hobza R.. 2022. Chemical genetics in PubMed

Bačovský V, Houben A, Kumke K, Hobza R.. 2019. The distribution of epigenetic histone marks differs between the X and Y chromosomes in PubMed

Bergero R, Forrest A, Kamau E, Charlesworth D.. 2007. Evolutionary strata on the X chromosomes of the dioecious plant PubMed PMC

Blavet N, Blavet H, Muyle A, et al. 2015. Identifying new sex-linked genes through BAC sequencing in the dioecious plant PubMed PMC

Bogomazova AN, Lagarkova MA, Panova AV, Nekrasov ED, Kiselev SL.. 2014. Reactivation of Х chromosome upon reprogramming leads to changes in the replication pattern and 5hmC accumulation. Chromosoma 123, 117–128. PubMed

Cao X, Jacobsen SE.. 2002. Locus-specific control of asymmetric and CpNpG methylation by the PubMed PMC

Cermak T, Kubat Z, Hobza R, Koblizkova A, Widmer A, Macas J, Vyskot B, Kejnovsky E.. 2008. Survey of repetitive sequences in PubMed

Chavez L, Huang Y, Luong K, et al. 2014. Simultaneous sequencing of oxidized methylcytosines produced by TET/JBP dioxygenases in PubMed PMC

De La Rica L, Deniz O, Cheng KCL, Todd CD, Cruz C, Houseley J, Branco MR.. 2016. TET-dependent regulation of retrotransposable elements in mouse embryonic stem cells. Genome Biology 17, 234. PubMed PMC

Deniz O, Frost JM, Branco MR.. 2019. Regulation of transposable elements by DNA modifications. Nature Reviews. Genetics 20, 417–431. PubMed

Erdmann RM, Souza AL, Clish CB, Gehring M.. 2015. 5-hydroxymethylcytosine is not present in appreciable quantities in PubMed PMC

Fransz P, de Jong JH, Lysak M, Castiglione MR, Schubert I.. 2002. Interphase chromosomes in PubMed PMC

Gackowski D, Zarakowska E, Starczak M, Modrzejewska M, Olinski R.. 2015. Tissue-specific differences in DNA modifications (5-hydroxymethylcytosine, 5-formylcytosine, 5-carboxylcytosine and 5-hydroxymethyluracil) and their interrelationships. PLoS One 10, e0144859. PubMed PMC

He Y-F, Li B-Z, Li Z, et al. 2011. Tet-mediated formation of 5-carboxylcytosine and its excision by TDG in mammalian DNA. Science 333, 1303–1307. PubMed PMC

Hobza R, Cegan R, Jesionek W, Kejnovsky E, Vyskot B, Kubat Z.. 2017. Impact of repetitive elements on the Y chromosome formation in plants. Genes 8, 302. PubMed PMC

Hobza R, Kubat Z, Cegan R, Jesionek W, Vyskot B, Kejnovsky E.. 2015. Impact of repetitive DNA on sex chromosome evolution in plants. Chromosome Research 23, 561–570. PubMed

Hobza R, Lengerova M, Svoboda J, Kubekova H, Kejnovsky E, Vyskot B.. 2006. An accumulation of tandem DNA repeats on the Y chromosome in PubMed

Houben A, Demidov D, Gernand D, Meister A, Leach CR, Schubert I.. 2003. Methylation of histone H3 in euchromatin of plant chromosomes depends on basic nuclear DNA content: methylation of histone H3 in euchromatin. The Plant Journal 33, 967–973. PubMed

Hubinský M, Hobza R, Starczak M, Gackowski D, Kubat Z, Janíček T, Horáková L, Luis Lorenzo JL.. 2024. Data from: Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant PubMed DOI PMC

Inoue A, Matoba S, Zhang Y.. 2012. Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3-mediated 5-methylcytosine oxidation. Cell Research 22, 1640–1649. PubMed PMC

Iyer LM, Zhang D, de Souza RF, Pukkila PJ, Rao A, Aravind L.. 2014. Lineage-specific expansions of TET/JBP genes and a new class of DNA transposons shape fungal genomic and epigenetic landscapes. Proceedings of the National Academy of Sciences, USA 111, 1676–1683. PubMed PMC

Ji L, Jordan WT, Shi X, Hu L, He C, Schmitz RJ.. 2018. TET-mediated epimutagenesis of the PubMed PMC

Kalinka A, Starczak M, Gackowski D, Stępień E, Achrem M.. 2023. Global DNA 5-hydroxymethylcytosine level and its chromosomal distribution in four rye species. Journal of Experimental Botany 74, 3488–3502. PubMed

Kejnovsky E, Hawkins JS, Feschotte C.. 2012. Plant transposable elements: biology and evolution. In: Wendel JF, Greilhuber J, Dolezel J, Leitch IJ, eds. Plant genome diversity. Vienna: Springer Vienna, 17–34.

Kejnovsky E, Hobza R, Cermak T, Kubat Z, Vyskot B.. 2009. The role of repetitive DNA in structure and evolution of sex chromosomes in plants. Heredity 102, 533–541. PubMed

Kejnovsky E, Vyskot B.. 2010. PubMed

Kralova T, Cegan R, Kubat Z, Vrana J, Vyskot B, Vogel I, Kejnovsky E, Hobza R.. 2014. Identification of a novel retrotransposon with sex chromosome-specific distribution in PubMed

Krasovec M, Kazama Y, Ishii K, Abe T, Filatov DA.. 2019. Immediate dosage compensation is triggered by the deletion of Y-linked genes in PubMed PMC

Kriaucionis S, Heintz N.. 2009. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science 324, 929–930. PubMed PMC

Kubat Z, Hobza R, Vyskot B, Kejnovsky E.. 2008. Microsatellite accumulation on the Y chromosome in PubMed

Kubat Z, Zluvova J, Vogel I, Kovacova V, Cermak T, Cegan R, Hobza R, Vyskot B, Kejnovsky E.. 2014. Possible mechanisms responsible for absence of a retrotransposon family on a plant Y chromosome. New Phytologist 202, 662–678. PubMed

Kubiura M, Okano M, Kimura H, Kawamura F, Tada M.. 2012. Chromosome-wide regulation of euchromatin-specific 5mC to 5hmC conversion in mouse ES cells and female human somatic cells. Chromosome Research 20, 837–848. PubMed PMC

Lengerova M, Kejnovsky E, Hobza R, Macas J, Grant SR, Vyskot B.. 2004. Multicolor FISH mapping of the dioecious model plant, PubMed

Li Y, Kumar S, Qian W.. 2018. Active DNA demethylation: mechanism and role in plant development. Plant Cell Reports 37, 77–85. PubMed PMC

Ličytė J, Kvederavičiūtė K, Rukšėnaitė A, Godliauskaitė E, Gibas P, Tomkutė V, Petraitytė G, Masevičius V, Klimašauskas S, Kriukienė E.. 2022. Distribution and regulatory roles of oxidized 5-methylcytosines in DNA and RNA of the basidiomycete fungi PubMed PMC

Marais GAB, Nicolas M, Bergero R, Chambrier P, Kejnovsky E, Monéger F, Hobza R, Widmer A, Charlesworth D.. 2008. Evidence for degeneration of the Y chromosome in the dioecious plant PubMed

Martin A, Troadec C, Boualem A, Rajab M, Fernandez R, Morin H, Pitrat M, Dogimont C, Bendahmane A.. 2009. A transposon-induced epigenetic change leads to sex determination in melon. Nature 461, 1135–1138. PubMed

Moroz LL, Kocot KM, Citarella MR, et al. 2014. The ctenophore genome and the evolutionary origins of neural systems. Nature 510, 109–114. PubMed PMC

Muyle A, Zemp N, Deschamps C, Mousset S, Widmer A, Marais GAB.. 2012. Rapid de novo evolution of X chromosome dosage compensation in PubMed PMC

Muyle A, Zemp N, Fruchard C, et al. 2018. Genomic imprinting mediates dosage compensation in a young plant XY system. Nature Plants 4, 677–680. PubMed

Muyle A, Marais GAB, Bačovský V, Hobza R, Lenormand T.. 2022. Dosage compensation evolution in plants: theories, controversies and mechanisms. Philosophical Transactions of the Royal Society B: Biological Sciences 377, 20210222. PubMed PMC

Neri F, Incarnato D, Krepelova A, Rapelli S, Anselmi F, Parlato C, Medana C, Dal Bello F, Oliviero S.. 2015. Single-base resolution analysis of 5-formyl and 5-carboxyl cytosine reveals promoter DNA methylation dynamics. Cell Reports 10, 674–683. PubMed

Pfaffeneder T, Hackner B, Truß M, Münzel M, Müller M, Deiml CA, Hagemeier C, Carell T.. 2011. The discovery of 5-formylcytosine in embryonic stem cell DNA. Angewandte Chemie International Edition 50, 7008–7012. PubMed

Pfeifer GP. 2023. 5-hydroxymethylcytosine stabilizes transcription by preventing aberrant initiation in gene bodies. Nature Genetics 55, 2–3. PubMed

Pikaard CS, Mittelsten Scheid O.. 2014. Epigenetic regulation in plants. Cold Spring Harbor Perspectives in Biology 6, a019315. PubMed PMC

Puterova J, Kubat Z, Kejnovsky E, Jesionek W, Cizkova J, Vyskot B, Hobza R.. 2018. The slowdown of Y chromosome expansion in dioecious PubMed PMC

Raiber E-A, Beraldi D, Ficz G, Burgess HE, Branco MR, Murat P, Oxley D, Booth MJ, Reik W, Balasubramanian S.. 2012. Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase. Genome Biology 13, R69. PubMed PMC

Rodríguez Lorenzo JL, Hobza R, Vyskot B.. 2018. DNA methylation and genetic degeneration of the Y chromosome in the dioecious plant PubMed PMC

Rodríguez Lorenzo JL, Hubinský M, Vyskot B, Hobza R.. 2020. Histone post-translational modifications in PubMed

RStudio Team. 2022. RStudio: integrated development environment for R. Boston, MA: RStudio, PBC.

Ruijter JM, Ramakers C, Hoogaars WMH, Karlen Y, Bakker O, van den Hoff MJB, Moorman AFM.. 2009. Amplification efficiency: linking baseline and bias in the analysis of quantitative PCR data. Nucleic Acids Research 37, e45–e45. PubMed PMC

Schindelin J, Arganda-Carreras I, Frise E, et al. 2012. Fiji: an open-source platform for biological-image analysis. Nature Methods 9, 676–682. PubMed PMC

Siroky J, Castiglione MR, Vyskot B.. 1998. DNA methylation patterns of PubMed

Slotkin RK, Martienssen R.. 2007. Transposable elements and the epigenetic regulation of the genome. Nature Reviews. Genetics 8, 272–285. PubMed

Starczak M, Gawronski M, Olinski R, Gackowski D.. 2021. Quantification of DNA modifications using two-dimensional ultraperformance liquid chromatography tandem mass spectrometry (2D-UPLC-MS/MS). Methods in Molecular Biology 2198, 91–108. PubMed

Stoyanova E, Riad M, Rao A, Heintz N.. 2021. 5-Hydroxymethylcytosine-mediated active demethylation is required for mammalian neuronal differentiation and function. eLife 10, e66973. PubMed PMC

Szulwach KE, Li X, Li Y, et al. 2011. Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genetics 7, e1002154. PubMed PMC

Tahiliani M, Koh KP, Shen Y, et al. 2009. Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in mammalian DNA by MLL partner TET1. Science 324, 930–935. PubMed PMC

Tang Y, Xiong J, Jiang H-P, Zheng S-J, Feng Y-Q, Yuan B-F.. 2014. Determination of oxidation products of 5-methylcytosine in plants by chemical derivatization coupled with liquid chromatography/tandem mass spectrometry analysis. Analytical Chemistry 86, 7764–7772. PubMed

Tariq M, Saze H, Probst AV, Lichota J, Habu Y, Paszkowski J.. 2003. Erasure of CpG methylation in PubMed PMC

Wang X, Song S, Wu Y-S, et al. 2015. Genome-wide mapping of 5-hydroxymethylcytosine in three rice cultivars reveals its preferential localization in transcriptionally silent transposable element genes. Journal of Experimental Botany 66, 6651–6663. PubMed PMC

Wossidlo M, Nakamura T, Lepikhov K, Marques CJ, Zakhartchenko V, Boiani M, Arand J, Nakano T, Reik W, Walter J.. 2011. 5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nature Communications 2, 241. PubMed

Wu F, Li X, Looso M, et al. 2023. Spurious transcription causing innate immune responses is prevented by 5-hydroxymethylcytosine. Nature Genetics 55, 100–111. PubMed PMC

Wu H, D’Alessio AC, Ito S, Wang Z, Cui K, Zhao K, Sun YE, Zhang Y.. 2011. Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells. Genes & Development 25, 679–684. PubMed PMC

Wu X, Zhang Y.. 2017. TET-mediated active DNA demethylation: mechanism, function and beyond. Nature Reviews. Genetics 18, 517–534. PubMed

Yakovlev IA, Gackowski D, Abakir A, Viejo M, Ruzov A, Olinski R, Starczak M, Fossdal CG, Krutovsky KV.. 2019. Mass spectrometry reveals the presence of specific set of epigenetic DNA modifications in the Norway spruce genome. Scientific Reports 9, 19314. PubMed PMC

Zhang H, Lang Z, Zhu J-K.. 2018. Dynamics and function of DNA methylation in plants. Nature Reviews. Molecular Cell Biology 19, 489–506. PubMed

Zhang L, Chen W, Iyer LM, Hu J, Wang G, Fu Y, Yu M, Dai Q, Aravind L, He C.. 2014. A TET homologue protein from PubMed PMC

Zhang Y, Zhou C.. 2019. Formation and biological consequences of 5-formylcytosine in genomic DNA. DNA Repair 81, 102649. PubMed

Zluvova J, Georgiev S, Janousek B, Charlesworth D, Vyskot B, Negrutiu I.. 2007. Early events in the evolution of the PubMed PMC

Non-canonical bases differentially represented in the sex chromosomes of the dioecious plant Silene latifolia