Evidence map›Paper›PMID 40186241›Full record

ArticleMolecular horticulture2025

Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.

Min Ma, Yuanda Wang, Zhenfei Sun, Ranze Zhao, Honghua Li, Xiaoxuan Li, Hongfang Zhu, Xuedong Yang, Changwei Zhang, Yuda Fang

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PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular horticulture, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

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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.

2 · The registry

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3 · Its place in the literature

Who cites it

4 citing papers in PubMed.

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4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

10 authors.

Min Ma *Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Yuanda Wang *Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Zhenfei SunJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Ranze ZhaoJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Honghua LiJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Xiaoxuan LiJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Hongfang ZhuShanghai Key Laboratory of Facility Horticulture Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
Xuedong YangShanghai Key Laboratory of Facility Horticulture Technology, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
Changwei ZhangCollege of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
Yuda FangJoint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China. yuda.fang@sjtu.edu.cn.ORCID http://orcid.org/0000-0003-1744-7928

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

AutopolyploidDNA methylationPak choiTranscriptional regulationTransposable element

Identifiers

PMID40186241
PMCPMC11971760

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.