Dynamic DNA methylation reconfiguration during seed development and germination
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA373832 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5239970.fastq.gz | Fastqsanger.gz | |||
| SRR5239980.fastq.gz | Fastqsanger.gz | |||
| SRR5239990.fastq.gz | Fastqsanger.gz | |||
| SRR5239971.fastq.gz | Fastqsanger.gz | |||
| SRR5239981.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
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: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:This SuperSeries is composed of the SubSeries listed below.
2017-08-31 | GSE94712 | GEO
Project description:Seed maturation, dormancy and germination are distinct physiological processes. Transition from maturation to dormancy, and from dormancy into germination are not only critical developmental phases in the plant life cycle but are also important agricultural traits. These developmental processes and their phase transitions are fine determined and coordinately regulated by genetic makeup and environmental cues. SCARECROW-LIKE15 (SCL15) has been demonstrated to be essential for repressing the seed maturation programme in vegetative tissues (Gao et al., Nat Commun, 2015, 6:7243). Here we report that SCL15 is also important for seed dormancy maintenance, germination timing and seed vigor performance based on the effects of SCL15 mutation on plant germination, growth and reproduction when compared with wild type Arabidopsis and over-expression lines 35S:SCL15 and Napin:SCL15. Seed dormancy is enhanced by the mutation of SCL15 in a GA signaling dependent way, indicating that SCL15 plays a negative role for primary dormancy release. Seed germination is positively regulated by SCL15 through interaction with ABA, GA and auxin signaling. SCL15 acts as positive regulator of seed vigor and effect of SCL15 mRNA abundance on seed reserve accumulation and seed development during late embryogenesis may contribute to the seed vigor performance.
2020-11-04 | GSE160707 | 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:Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we measured gene expression levels of Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using. We mapped the eQTL of the gene expression and the result displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.
2020-06-24 | E-MTAB-9080 | biostudies-arrayexpress
Project description:In addition to the evolutionarily-conserved Ca2+ sensor, calmodulin (CaM), plants possess a large family of CaM-related proteins (CMLs). Using a cml39 loss-of-function mutant, we investigated the roles of CML39 in Arabidopsis and discovered a range of phenotypes across developmental stages and in different tissues. In mature plants, loss of CML39 results in shorter siliques, reduced seed number per silique, and reduced number of ovules per pistil. We also observed changes in seed development, germination, and seed coat properties in cml39 mutants in comparison to wild-type plants. Using radicle emergence as a measure of germination, cml39 mutants showed more rapid germination than wild-type plants. In marked contrast to wild-type seeds, the germination of developing, immature cml39 seeds was not sensitive to cold-stratification. In addition, germination of cml39 seeds was less sensitive than wild-type to inhibition by ABA or by treatments that impaired gibberellic acid biosynthesis. Tetrazolium red staining indicated that the seed-coat permeability of cml39 seeds is greater than that of wild-type seeds. RNA sequencing analysis of cml39 seedlings suggests that changes in chromatin modification may underlie some of the phenotypes associated with cml39 mutants, consistent with previous reports that orthologs of CML39 participate in gene silencing. Aberrant ectopic expression of transcripts for seed storage proteins in 7-day old cml39 seedlings was observed, suggesting mis-regulation of early developmental programs. Collectively, our data support a model where CML39 serves as an important Ca2+ sensor during ovule and seed development, as well as during germination and seedling establishment.
2018-05-01 | GSE108898 | GEO
Project description:Histone acetylation is involved in the regulation of gene expression in plants and eukaryotes. Histone deacetylases (HDACs) are enzymes that catalyze the removal of acetyl groups from histones, which is associated with the repression of gene expression. To study the role of histone acetylation in the regulation of gene expression during seed germination, trichostatin A (TSA), a specific inhibitor of histone deacetylase, was used to treat imbibing Arabidopsis thaliana seeds. GeneChip arrays were used to show that TSA induces up-regulation of 45 genes and down-regulation of 27 genes during seed germination. Eight TSA-up-regulated genes were selected for further analysis - RAB18, RD29B, ATEM1, HSP70 and four late embryogenesis abundant protein genes (LEA). A gene expression time course shows that these eight genes are expressed at high levels in the dry seed and repressed upon seed imbibition at an exponential rate. In the presence of TSA, the onset of repression of the eight genes is not affected but the final level of repressed expression is elevated. Chromatin immunoprecipitation and HDAC assays show that there is a transient histone deacetylation event during seed germination at one day after imbibition, which serves as a key developmental signal that affects the repression of the eight genes. This SuperSeries is composed of the SubSeries listed below.
2005-12-10 | GSE3799 | GEO
Project description:How epigenetics is involved in the transition from seed maturation to seed germination largely remains elusive. To uncover the possible role of epigenetics in gene expression during the transition from seed maturation to seed germination in soybean, the transcriptome of cotyledons from four stages of soybean seed maturation and germination, including mid-late maturation, late maturation, seed dormancy and seed germination, were profiled by Illumina sequencing. For the genes that are quantitatively regulated at the four stages, two antagonistic epigenetic marks, H3K4me3 and H3K27me3, together with the binding of RNA polymerase II, were investigated at the four stages by chromatin immunoprecipitation (ChIP). For 10 out of 16 genes examined, the relative enrichment of histone modification marks (H3K4me3 and H3K27me3) and RNA polymerase II binding on their promoter regions correlates well with their relative expression levels at four stages, suggesting the involvement of epigenetics in transcriptional regulation. A striking finding is that seed germination-specific genes start to show open chromatin (H3K4me3) during late seed maturation although their transcripts do not accumulate, which is further supported by RNA polymerase II binding. Together, our results provide the first evidence that seed germination genes can be primed for transcription (open chromatin and RNA polymerase II binding) during seed maturation, highlighting that the transition from seed maturation to seed germination starts at late seed maturation stages at both the genetic and epigenetic levels.
2011-05-10 | GSE29134 | GEO