Ontology highlight
ABSTRACT:
PROVIDER: PRJNA433275 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6679008.fastq.gz | Fastqsanger.gz |
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Project description:Embryo and endosperm gene expression profile at ripening stage
2015-06-24 | E-GEOD-39432 | ExpressionAtlas
Project description:Repression of transposable elements (TEs) by DNA methylation is necessary for host plants to maintain genome integrity and prevent from harmful mutations. However, under certain circumstances, TEs are thought to escape from the host defense system and therefore activate their transcription. In A. thaliana and O. sativa, DNA demethylase targets to the sequence derived from TEs in the central cell, a progenitor cell of endosperm in the female gametophyte. This genome-wide DNA demethylation is also observed in the endosperm after fertilization. In this study, we survey transcripts generated from TEs during the rice endosperm development and some points of the embryo as a control using custom-made microarray. We found that TE transcripts are largely different in the embryo and endosperm. The expression patterns of TEs are dynamically up- and down-regulated during the endosperm development, especially for miniature inverted-repeat transposable elements (MITEs).
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Project description:Transcription profiling by high throughput sequencing of maize embryo and endosperm during development
2019-05-15 | E-MTAB-4395 | ExpressionAtlas
Project description:Epigenetic modification plays important roles in plant and animal development. DNA methylation can impact the transposable element (TE) silencing, gene imprinting and regulate gene expression.Through a genome-wide analysis, DNA methylation peaks were respectively characterized and mapped in maize embryo and endosperm genome. Distinct methylation level across maize embryo and endosperm was observed. The maize embryo genome contained more DNA methylation peaks than endosperm. However, the endosperm chloroplast genome contained more DNA methylation peaks to compare with the embryo chloroplast genome. DNA methylation regions were characterized and mapped in genome. More CG island (CGI) shore are methylated than CGI in maize suggested that DNA methylation level is not positively correlated with CpG density. The DNA methylation occurred more frequently in the promoter sequence and transcriptional termination region (TTR) than other regions of the genes. The result showed that 99% TEs we characterized are methylated in maize embryo, but some (34.8%) of them are not methylated in endosperm. Maize embryo and endosperm exhibit distinct pattern/level of methylation. The most differentially methylated two regions between embryo and endosperm are High CpG content promoters (HCPs) and high CpG content TTRs (HCTTRs). DNA methylation peaks distinction of mitochondria and chloroplast DNA were less than the nucleus DNA. Our results indicated that DNA methylation is associated with the gene silencing or gene activation in maize endosperm and embryo. Many genes involved in embryogenesis and seed development were found differentially methylated in embryo and endosperm. We found 17 endosperm-specific expressed imprinting genes were hypomethylated in endosperm and were hypermethylated in embryo. The expression of a maize DEMETER -like (DME-like) gene and MBD101 gene (MBD4 homolog) which direct bulk genome DNA demethylation were higher in endosperm than in embryo. These two genes may be associated with the distinct methylation level across maize embryo and endosperm.The methylomes of maize embryo and endosperm was obtained by MeDIP-seq method. The global mapping of maize embryo and endosperm methylation in this study broadened our knowledge of DNA methylation patterns in maize genome, and provided useful information for future studies on maize seed development and regulation of metabolic pathways in different seed tissues.
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Project description:The endosperm is a nutritive tissue that supports the growing embryo. Endosperm life span is restricted to seed development and germination. During maize kernel development in maize, two distinct endosperm cell death processes occur. The endosperm adjacent to the embryo scutellum (EAS) undergoes a lytic cell death supposedly to allow embryo expansion, whereas the starchy endosperm (SE) dies after kernel filling producing cell corpses that store nutrients required during germination. Here, we present a detailed analysis of these divergent cell death processes. During SE cell death, mitochondria, nuclei, and the endoplasmic reticulum disintegrate, while nuclear chromatin, cell walls, starch granules, and protein bodies are preserved. In contrast, EAS cells remobilize their stored nutrients, secrete extracellular vesicles, before the cells collapse and a complex post-mortem corpse clearance process ensues. Using single-nucleus RNA-sequencing transcriptome analysis of the developing endosperm, we identified the NAC transcription factors KIL1 and KIL2 as specifically expressed in the EAS. Dominant and recessive loss-of-function approaches demonstrate that KIL1 and KIL2 redundantly promote cell death execution and corpse clearance of the EAS, but are not required for SE cell death. The reduction of EAS cell death in loss-of-function lines strongly impeded embryo growth. Interestingly, KIL1 and KIL2 expression are promoted by DED1, an imprinted paternally expressed transcription factor, suggesting a paternal control over EAS cell death and embryo growth in maize.
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