{"title":"小白菜基因组复制时DNA甲基化对转录稳态的调控。","authors":"Min Ma, Yuanda Wang, Zhenfei Sun, Ranze Zhao, Honghua Li, Xiaoxuan Li, Hongfang Zhu, Xuedong Yang, Changwei Zhang, Yuda Fang","doi":"10.1186/s43897-025-00145-3","DOIUrl":null,"url":null,"abstract":"<p><p>Polyploidy occurs frequently in plants and is an important force in plant evolution and crop breeding. New polyploids face various challenges due to genome duplication and subsequent changes in epigenetic modifications, nucleus/cell size and gene expression. How polyploids produce evolutionary novelty remains to be understood. In this study, a transcriptome comparison between 21-day-old diploid and autotetraploid pak choi seedlings revealed that there are few differentially expressed genes (DEGs), with a greater proportion of DEGs downregulated in response to genome duplication. Genome-wide DNA methylation analysis indicated that the level of DNA methylation is obviously increased, especially in transposable elements (TEs) and 1 kb flanking regions, upon genome doubling. The differentially methylated regions between diploid and autotetraploid pak choi were related to 12,857 differentially hypermethylated genes and 8,451 hypomethylated genes, and the DEGs were negatively correlated with the differential methylation in the regions across the DEGs. Notably, TE methylation increases significantly in regions flanking neighboring non-DEGs rather than those flanking DEGs. These results shed light on the role of DNA methylation in the transcriptional regulation of genes in polyploids and the mechanism of coping with \"genome shock\" due to genome doubling in cruciferous plants.</p>","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"22"},"PeriodicalIF":10.6000,"publicationDate":"2025-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971760/pdf/","citationCount":"0","resultStr":"{\"title\":\"Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.\",\"authors\":\"Min Ma, Yuanda Wang, Zhenfei Sun, Ranze Zhao, Honghua Li, Xiaoxuan Li, Hongfang Zhu, Xuedong Yang, Changwei Zhang, Yuda Fang\",\"doi\":\"10.1186/s43897-025-00145-3\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>Polyploidy occurs frequently in plants and is an important force in plant evolution and crop breeding. New polyploids face various challenges due to genome duplication and subsequent changes in epigenetic modifications, nucleus/cell size and gene expression. How polyploids produce evolutionary novelty remains to be understood. In this study, a transcriptome comparison between 21-day-old diploid and autotetraploid pak choi seedlings revealed that there are few differentially expressed genes (DEGs), with a greater proportion of DEGs downregulated in response to genome duplication. Genome-wide DNA methylation analysis indicated that the level of DNA methylation is obviously increased, especially in transposable elements (TEs) and 1 kb flanking regions, upon genome doubling. The differentially methylated regions between diploid and autotetraploid pak choi were related to 12,857 differentially hypermethylated genes and 8,451 hypomethylated genes, and the DEGs were negatively correlated with the differential methylation in the regions across the DEGs. Notably, TE methylation increases significantly in regions flanking neighboring non-DEGs rather than those flanking DEGs. These results shed light on the role of DNA methylation in the transcriptional regulation of genes in polyploids and the mechanism of coping with \\\"genome shock\\\" due to genome doubling in cruciferous plants.</p>\",\"PeriodicalId\":29970,\"journal\":{\"name\":\"Molecular Horticulture\",\"volume\":\"5 1\",\"pages\":\"22\"},\"PeriodicalIF\":10.6000,\"publicationDate\":\"2025-04-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11971760/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Horticulture\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.1186/s43897-025-00145-3\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"HORTICULTURE\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Horticulture","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.1186/s43897-025-00145-3","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"HORTICULTURE","Score":null,"Total":0}
Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.
Polyploidy occurs frequently in plants and is an important force in plant evolution and crop breeding. New polyploids face various challenges due to genome duplication and subsequent changes in epigenetic modifications, nucleus/cell size and gene expression. How polyploids produce evolutionary novelty remains to be understood. In this study, a transcriptome comparison between 21-day-old diploid and autotetraploid pak choi seedlings revealed that there are few differentially expressed genes (DEGs), with a greater proportion of DEGs downregulated in response to genome duplication. Genome-wide DNA methylation analysis indicated that the level of DNA methylation is obviously increased, especially in transposable elements (TEs) and 1 kb flanking regions, upon genome doubling. The differentially methylated regions between diploid and autotetraploid pak choi were related to 12,857 differentially hypermethylated genes and 8,451 hypomethylated genes, and the DEGs were negatively correlated with the differential methylation in the regions across the DEGs. Notably, TE methylation increases significantly in regions flanking neighboring non-DEGs rather than those flanking DEGs. These results shed light on the role of DNA methylation in the transcriptional regulation of genes in polyploids and the mechanism of coping with "genome shock" due to genome doubling in cruciferous plants.
期刊介绍：
Aims
Molecular Horticulture aims to publish research and review articles that significantly advance our knowledge in understanding how the horticultural crops or their parts operate mechanistically. Articles should have profound impacts not only in terms of high citation number or the like, but more importantly on the direction of the horticultural research field.
Scope
Molecular Horticulture publishes original Research Articles, Letters, and Reviews on novel discoveries on the following, but not limited to, aspects of horticultural plants (including medicinal plants):
▪ Developmental and evolutionary biology
▪ Physiology, biochemistry and cell biology
▪ Plant-microbe and plant-environment interactions
▪ Genetics and epigenetics
▪ Molecular breeding and biotechnology
▪ Secondary metabolism and synthetic biology
▪ Multi-omics dealing with data sets of genome, transcriptome, proteome, metabolome, epigenome and/or microbiome.
The journal also welcomes research articles using model plants that reveal mechanisms and/or principles readily applicable to horticultural plants, translational research articles involving application of basic knowledge (including those of model plants) to the horticultural crops, novel Methods and Resources of broad interest.
In addition, the journal publishes Editorial, News and View, and Commentary and Perspective on current, significant events and topics in global horticultural fields with international interests.
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