Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA373835 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Dynamic DNA methylation reconfiguration during seed development and germination (MethylC-seq)
| PRJNA373836 | ENA
Project description:Dynamic DNA methylation reconfiguration during seed development and germination
| PRJNA373832 | ENA
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: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:RNAseq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
2017-08-15 | GSE94457 | GEO
Project description:sRNA-seq profiling of 10 time points during germination in Arabidopsis, from freshly harvested seed, through mature seed, stratification, germination and to post-germination.
2017-08-15 | GSE94458 | GEO
Project description:methylC-seq profiling of 4 time points during germination in Arabidopsis, from mature seed, through stratification, germination and to post-germination.
2017-08-15 | GSE94456 | GEO
Project description:The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in chromatin structure regulation that endows seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but the loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5’ gene end distribution, which facilities chromatin opening in seeds. During germination, this H3.3-established chromatin accessibility is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3’ gene end and restricts chromatin accessibility to prevent cryptic transcription and protect gene body DNA methylation. Our results suggest a fundamental role of H3.3 in initiating chromatin opening at regulatory regions in seed to license the embryonic to post-embryonic transition. Transcriptome, chromatin accessibility, H3.3 and H2A.Z enrichment, and DNA methylation were examined in Col or h3.3ko mutant
2022-12-01 | GSE209642 | 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
Project description:Karrikins promote seed germination in Arabidopsis thaliana. Completion of germination (protrusion of the radicle) is not observed until ~72 h in dormant wildtype seed under these conditions. We used microarrays to examine karrikin-induced transcriptional changes after 24 h of imbibition. Transcriptional changes may indicate events leading to karrikin-induced germination or karrikin-specific markers.
2010-03-01 | GSE20556 | GEO