ArticleJournal of advanced research2022
DNA methylation in transposable elements buffers the connection between three-dimensional chromatin organization and gene transcription upon rice genome duplication.
Article in Journal of advanced research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 32 citations in OpenAlex.
- Epigenetic regulation and ROS signaling in plant stress adaptation: an integrated framework.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- The Association Between DNA Methylation and Three-Dimensional Genome During Whole Genome Doubling inPlants (Basel, Switzerland) · 2025Article
- Epigenetic maps of pearl millet reveal a prominent role for CHH methylation in regulating tissue-specific gene expression.aBIOTECH · 2025Article
- Regulation of transcriptional homeostasis by DNA methylation upon genome duplication in pak choi.Molecular horticulture · 2025Article
- Advancements and strategies of genetic improvement in cassava (Horticulture research · 2025Article
- Article
- Chromatin Accessibility and Gene Expression Vary Between a New and Evolved Autopolyploid of Arabidopsis arenosa.Molecular biology and evolution · 2024Article
- Autotetraploidy of rice does not potentiate the tolerance to drought stress in the seedling stage.Rice (New York, N.Y.) · 2024Article
- The high-resolution three-dimensional (3D) chromatin map of the tea plant (Horticulture research · 2023Article
- Maternal pre-pregnancy BMI, offspring epigenome-wide DNA methylation, and childhood obesity: findings from the Boston Birth Cohort.BMC medicine · 2023Article
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12 authors at 4 institutions in 1 country.
Funding
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Abstract
introductionPolyploidy is a major force in plant evolution and the domestication of cultivated crops.
objectivesThe study aimed to explore the relationship and underlying mechanism between three-dimensional (3D) chromatin organization and gene transcription upon rice genome duplication.
methodsThe 3D chromatin structures between diploid (2C) and autotetraploid (4C) rice were compared using high-throughput chromosome conformation capture (Hi-C) analysis. The study combined genetics, transcriptomics, whole-genome bisulfite sequencing (WGBS-seq) and 3D genomics approaches to uncover the mechanism for DNA methylation in modulating gene transcription through 3D chromatin architectures upon rice genome duplication.
resultsWe found that 4C rice presents weakened intra-chromosomal interactions compared to its 2C progenitor in some chromosomes. In addition, we found that changes of 3D chromatin organizations including chromatin compartments, topologically associating domains (TADs), and loops, are uncorrelated with gene transcription. Moreover, DNA methylations in the regulatory sequences of genes in compartment A/B switched regions and TAD boundaries are unrelated to their expression. Importantly, although there was no significant difference in the methylation levels in transposable elements (TEs) in differentially expressed gene (DEG) and non-DEG promoters between 2C and 4C rice, we found that the hypermethylated TEs across genes in compartment A/B switched regions and TAD boundaries may suppress the expression of these genes.
conclusionThe study proposed that the rice genome doubling might modulate TE methylation to buffer the effects of chromatin architecture on gene transcription in compartment A/B switched regions and TAD boundaries, resulting in the disconnection between 3D chromatin structure alteration and gene transcription upon rice genome duplication.
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