ArticleScientific reports2017
Dynamic Changes of Genome-Wide DNA Methylation during Soybean Seed Development.
Article in Scientific reports, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 57 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
57 citing papers in PubMed, 112 citations in OpenAlex.
- Grain-maturing temperature induces seed epi-memory via DNA methylation for subsequent development in rice (Oryza sativa L.).Plant physiology · 2026Article
- Genotype-dependent DNA methylation patterns are negatively associated with allelic variation rather than heat-induced gene expression in two contrasting potato genotypes.The Plant journal : for cell and molecular biology · 2026Article
- Features of DNA methylome in Capsicum spp.Epigenetics & chromatin · 2025Article
- Epigenomics and Non-Coding RNAs in Soybean Adaptation to Abiotic Stresses.International journal of molecular sciences · 2025Review
- Genome-Wide Identification and Expression Pattern Analysis of the DNA Methyltransferase Gene Family Revealed the DNA Methylation Response to Tapping in Rubber Tree.Plants (Basel, Switzerland) · 2025Article
- Site-Specific Changes in Cytosine Methylation in Promoters of the Genes Encoding the Membrane Subunits of Succinate Dehydrogenase During Germination of Maize Seeds.International journal of molecular sciences · 2025Article
- Regulation of seed germination: ROS, epigenetic, and hormonal aspects.Journal of advanced research · 2025Review
- The dynamic epigenetic atlas and its effects on instability of starch and seed storage protein quality traits in wheat (Frontiers in plant science · 2025Article
- Omics-Driven Strategies for Developing Saline-Smart Lentils: A Comprehensive Review.International journal of molecular sciences · 2024Review
- Single-Base Methylome Analysis of Sweet Cherry (International journal of molecular sciences · 2024Article
- Harnessing Multi-Omics Strategies and Bioinformatics Innovations for Advancing Soybean Improvement: A Comprehensive Review.Plants (Basel, Switzerland) · 2024Review
- DNA methylation variations underlie lettuce domestication and divergence.Genome biology · 2024Article
- Involvement of Abscisic Acid in Transition of Pea (Plants (Basel, Switzerland) · 2024Article
- Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce.GigaScience · 2024Article
- Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean.Frontiers in plant science · 2024Article
- Changes in epigenetic features in legumes under abiotic stresses.The plant genome · 2023Review
- Small RNA-mediated DNA methylation during plant reproduction.The Plant cell · 2023Review
- Epigenetic Regulation During Plant Development and the Capacity for Epigenetic Memory.Annual review of plant biology · 2023Review
- Elucidating the importance of the catabolic enzyme, methionine-gamma-lyase, in stresses during Arabidopsis seed development and germination.Frontiers in plant science · 2023Article
- Tris(1,3-dichloro-2-propyl) phosphate disrupts the trajectory of cytosine methylation within developing zebrafish embryos.Environmental research · 2022Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Seed development is programmed by expression of many genes in plants. Seed maturation is an important developmental process to soybean seed quality and yield. DNA methylation is a major epigenetic modification regulating gene expression. However, little is known about the dynamic nature of DNA methylation and its effects on gene expression during plant development. Through whole-genome bisulfite sequencing, we showed that DNA methylation went through dynamic changes during seed maturation. An average of 66% CG, 45% CHG and 9% CHH contexts was methylated in cotyledons. CHH methylation levels in cotyledons changed greatly from 6% at the early stage to 11% at the late stage. Transcribed genes were approximately two-fold more likely to be differentially methylated than non-transcribed genes. We identified 40, 66 and 2136 genes containing differentially methylated regions (DMRs) with negative correlation between their expression and methylation in the CG, CHG and CHH contexts, respectively. The majority of the DMR genes in the CHH context were transcriptionally down-regulated as seeds mature: 99% of them during early maturation were down-regulated, and preferentially associated with DNA replication and cell division. The results provide novel insights into the dynamic nature of DNA methylation and its relationship with gene regulation in seed development.
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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.