ArticleBMC genomics2020
DNA methylation and its effects on gene expression during primary to secondary growth in poplar stems.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 45 citations in OpenAlex.
- Article
- A comparative study of phyllostachys edulis and its dwarf variant phyllostachys edulis 'Tubaeformis' at the anatomical, transcriptomic, and DNA methylation levels.Frontiers in plant science · 2026Article
- Roles for epigenetics in wood formation and stress response intrees-from basic biology to forest management.Frontiers in epigenetics and epigenomics · 2025Review
- Single-Base Methylome Analysis of Sweet Cherry (International journal of molecular sciences · 2024Article
- DNA methylation analysis reveals local changes in resistant and susceptible soybean lines in response to Phytophthora sansomeana.G3 (Bethesda, Md.) · 2024Article
- Methylation of microRNA genes and its effect on secondary xylem development of stem in poplar.The plant genome · 2024Article
- Increased DNA methylation contributes to the early ripening of pear fruits during domestication and improvement.Genome biology · 2024Article
- Allele-specific DNA methylation and gene expression during shoot organogenesis in tissue culture of hybrid poplar.Horticulture research · 2024Article
- Deciphering the intricate hierarchical gene regulatory network: unraveling multi-level regulation and modifications driving secondary cell wall formation.Horticulture research · 2024Article
- Methylome-wide analysis in systemic microbial-induced experimental periodontal disease in mice with different susceptibility.Frontiers in cellular and infection microbiology · 2024Article
- Identification and validation of functional roles for three MYC-associated genes in hepatocellular carcinoma.Journal of advanced research · 2023Article
- Transgressive and parental dominant gene expression and cytosine methylation during seed development in Brassica napus hybrids.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- The methylation landscape of giga-genome and the epigenetic timer of age in Chinese pine.Nature communications · 2023Article
- Revealing the transitory and local effect of zebularine on development and on proteome dynamics ofFrontiers in plant science · 2023Article
- Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment inInternational journal of molecular sciences · 2023Article
- Plasticity across levels: Relating epigenomic, transcriptomic, and phenotypic responses to osmotic stress in a halotolerant microalga.Molecular ecology · 2022Article
- DNA methylation and histone modifications induced by abiotic stressors in plants.Genes & genomics · 2022Review
- Article
- Review
- Transcriptome-wide identification and characterization of microRNAs in diverse phases of wood formation in Populus trichocarpa.G3 (Bethesda, Md.) · 2021Article
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Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
Abstract
backgroundAs an important epigenetic mark, 5-methylcytosine (5mC) methylation is involved in many DNA-dependent biological processes and plays a role during development and differentiation of multicellular organisms. However, there is still a lack of knowledge about the dynamic aspects and the roles of global 5mC methylation in wood formation in tree trunks. In this study, we not only scrutinized single-base resolution methylomes of primary stems (PS), transitional stems (TS), and secondary stems (SS) of Populus trichocarpa using a high-throughput bisulfite sequencing technique, but also analyzed the effects of 5mC methylation on the expression of genes involved in wood formation.
resultsThe overall average percentages of CG, CHG, and CHH methylation in poplar stems were ~ 53.6%, ~ 37.7%, and ~ 8.5%, respectively, and the differences of 5mC in genome-wide CG/CHG/CHH contexts among PS, TS, and SS were statistically significant (p < 0.05). The evident differences in CG, CHG, and CHH methylation contexts among 2 kb proximal promoters, gene bodies, and 2 kb downstream regions were observed among PS, TS, and SS. Further analysis revealed a perceptible global correlation between 5mC methylation levels of gene bodies and transcript levels but failed to reveal a correlation between 5mC methylation levels of proximal promoter regions and transcript levels. We identified 653 and 858 DMGs and 4978 and 4780 DEGs in PS vs TS and TS vs SS comparisons, respectively. Only 113 genes of 653 DMGs and 4978 DEGs, and 114 genes of 858 DMGs and 4780 DEG were common. Counterparts of some of these common genes in other species, including Arabidopsis thaliana, are known to be involved in secondary cell wall biosynthesis and hormone signaling. This indicates that methylation may directly modulate wood formation genes and indirectly attune hormone signaling genes, which in turn impact wood formation.
conclusionsDNA methylation only marginally affects pathway genes or regulators involved in wood formation, suggesting that further studies of wood formation should lean towards the indirect effects of methylation. The information and data we provide here will be instrumental for understanding the roles of methylation in wood formation in tree species.
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