Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi
Abstract 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 evolution...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2025-04-01
|
| Series: | Molecular Horticulture |
| Subjects: | |
| Online Access: | https://doi.org/10.1186/s43897-025-00145-3 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850265714782371840 |
|---|---|
| author | Min Ma Yuanda Wang Zhenfei Sun Ranze Zhao Honghua Li Xiaoxuan Li Hongfang Zhu Xuedong Yang Changwei Zhang Yuda Fang |
| author_facet | Min Ma Yuanda Wang Zhenfei Sun Ranze Zhao Honghua Li Xiaoxuan Li Hongfang Zhu Xuedong Yang Changwei Zhang Yuda Fang |
| author_sort | Min Ma |
| collection | DOAJ |
| description | Abstract 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. |
| format | Article |
| id | doaj-art-308c0dcddf874bce82bf363f43328a3a |
| institution | OA Journals |
| issn | 2730-9401 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | BMC |
| record_format | Article |
| series | Molecular Horticulture |
| spelling | doaj-art-308c0dcddf874bce82bf363f43328a3a2025-08-20T01:54:20ZengBMCMolecular Horticulture2730-94012025-04-015111710.1186/s43897-025-00145-3Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choiMin Ma0Yuanda Wang1Zhenfei Sun2Ranze Zhao3Honghua Li4Xiaoxuan Li5Hongfang Zhu6Xuedong Yang7Changwei Zhang8Yuda Fang9Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityShanghai Key Laboratory of Facility Horticulture Technology, Shanghai Academy of Agricultural SciencesShanghai Key Laboratory of Facility Horticulture Technology, Shanghai Academy of Agricultural SciencesCollege of Horticulture, Nanjing Agricultural UniversityJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong UniversityAbstract 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.https://doi.org/10.1186/s43897-025-00145-3AutopolyploidPak choiTranscriptional regulationTransposable elementDNA methylation |
| spellingShingle | Min Ma Yuanda Wang Zhenfei Sun Ranze Zhao Honghua Li Xiaoxuan Li Hongfang Zhu Xuedong Yang Changwei Zhang Yuda Fang Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi Molecular Horticulture Autopolyploid Pak choi Transcriptional regulation Transposable element DNA methylation |
| title | Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi |
| title_full | Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi |
| title_fullStr | Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi |
| title_full_unstemmed | Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi |
| title_short | Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi |
| title_sort | regulation of transcriptional homeostasis by dna methylation upon genome duplication in pak choi |
| topic | Autopolyploid Pak choi Transcriptional regulation Transposable element DNA methylation |
| url | https://doi.org/10.1186/s43897-025-00145-3 |
| work_keys_str_mv | AT minma regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT yuandawang regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT zhenfeisun regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT ranzezhao regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT honghuali regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT xiaoxuanli regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT hongfangzhu regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT xuedongyang regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT changweizhang regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi AT yudafang regulationoftranscriptionalhomeostasisbydnamethylationupongenomeduplicationinpakchoi |