Dynamic DNA methylation reconfiguration during seed development and germination
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE94712 | GEO | 2017/08/31
SECONDARY ACCESSION(S): PRJNA373832
REPOSITORIES: GEO
Similar Datasets
Project description:BackgroundUnlike animals, plants can pause their life cycle as dormant seeds. In both plants and animals, DNA methylation is involved in the regulation of gene expression and genome integrity. In animals, reprogramming erases and re-establishes DNA methylation during development. However, knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared time-series methylomes of dry and germinating seeds to publicly available seed development methylomes.ResultsTime-series whole genome bisulfite sequencing reveals extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during seed development depends on both RNA-directed DNA methylation and heterochromatin formation pathways, whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late seed development.ConclusionsThis study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy.
| S-EPMC5599895 | biostudies-literature
Project description:The life cycle of flowering plants ends and begins with seeds. Unlike animals, plants can pause their life cycle as dormant seeds during this transition. DNA methylation is involved in the regulation of gene expression and genome integrity. Reprogramming erases and re-establishes DNA methylation during development in animals. Knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared dry and germinating seed time-series methylomes to publicly available seed development methylomes. Time-series whole genome bisulfite sequencing (WGBS) revealed extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during embryogenesis depends on both RNA-directed DNA methylation and heterochromatin formation pathways whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late embryogenesis, which contributes to the endosperm specific methylation patterns.This study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy.
2017-08-31 | GSE94710 | GEO
Project description:The life cycle of flowering plants ends and begins with seeds. Unlike animals, plants can pause their life cycle as dormant seeds during this transition. DNA methylation is involved in the regulation of gene expression and genome integrity. Reprogramming erases and re-establishes DNA methylation during development in animals. Knowledge of reprogramming or reconfiguration in plants has been limited to pollen and the central cell. To better understand epigenetic reconfiguration in the embryo, which forms the plant body, we compared dry and germinating seed time-series methylomes to publicly available seed development methylomes. Time-series whole genome bisulfite sequencing (WGBS) revealed extensive gain of CHH methylation during seed development and drastic loss of CHH methylation during germination. These dynamic changes in methylation mainly occur within transposable elements. Active DNA methylation during embryogenesis depends on both RNA-directed DNA methylation and heterochromatin formation pathways whereas global demethylation during germination occurs in a passive manner. However, an active DNA demethylation pathway is initiated during late embryogenesis, which contributes to the endosperm specific methylation patterns.This study provides new insights into dynamic DNA methylation reprogramming events during seed development and germination and suggests possible mechanisms of regulation. The observed sequential methylation/demethylation cycle suggests an important role of DNA methylation in seed dormancy.
2017-08-31 | GSE94711 | GEO
Project description:Dynamic DNA methylation reconfiguration during seed development and germination
| PRJNA373832 | ENA
Project description:Seed development needs the coordination of multiple molecular mechanisms to promote correct tissue development, seed filling, and the acquisition of germination capacity, desiccation tolerance, longevity, and dormancy. Heat stress can negatively impact these processes and upon the increase of global mean temperatures, global food security is threatened. Here, we explored the impact of heat stress on seed physiology, morphology, gene expression, and methylation on three stages of seed development. Notably, Arabidopsis Col-0 plants under heat stress presented a decrease in germination capacity as well as a decrease in longevity. We observed that upon mild stress, gene expression and DNA methylation were moderately affected. Nevertheless, upon severe heat stress during seed development, gene expression was intensively modified, promoting heat stress response mechanisms including the activation of the ABA pathway. By analyzing candidate epigenetic markers using the mutants' physiological assays, we observed that the lack of DNA demethylation by the ROS1 gene impaired seed germination by affecting germination-related gene expression. On the other hand, we also observed that upon severe stress, a large proportion of differentially methylated regions (DMRs) were located in the promoters and gene sequences of germination-related genes. To conclude, our results indicate that DNA (de)methylation could be a key regulatory process to ensure proper seed germination of seeds produced under heat stress.
| S-EPMC8005211 | biostudies-literature
Project description: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.
| S-EPMC5613027 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below.
2021-03-23 | GSE167245 | GEO
Project description:In this study, we performed bisulphite of two stages of seed development in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. Paired-end reads were generated from 5 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.
2020-07-13 | GSE131669 | GEO
Project description:In this study, we performed bisulphite of five stages of seed development in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. Paired-end reads were generated from 11 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.
2020-07-13 | GSE131665 | GEO
Project description:What methylation changes are occurring during seed development largely remains unknown. To uncover the possible role of DNA methylation throughout all of seed development - from fertilization through dormancy and post-germination in soybean, we characterized the methylome of whole seeds representing the differentiation (GLOB and COT stages), maturation (early- [EM], mid- [B1] and late- [AA1] maturation stages), dormancy (DRY stage), and post-germination (seedling) phases of soybean seed development using Illumina sequencing. In addition, we characterized the methylome of the cotyledons of germinated seedling to examine methylation differences before and after germination.
2011-12-22 | GSE34637 | GEO