E-MTAB-4395
Ontology highlight
ABSTRACT:
PROVIDER: E-MTAB-4395 | ExpressionAtlas | 2019-05-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-MTAB-4395-analysis-methods.tsv | Tabular | |||
| E-MTAB-4395-atlasExperimentSummary.Rdata | Rdata | |||
| E-MTAB-4395-coexpressions.tsv.gz | Tabular | |||
| E-MTAB-4395-configuration.xml | Xml | |||
| E-MTAB-4395-factors.xml | Xml |
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Project description:Maize (Zea mays) is an excellent cereal model for research on seed development because of its relatively large size for both embryo and endosperm. Despite the importance of seed in agriculture, the genome-wide transcriptome pattern throughout seed development has not been well characterized. Using high-throughput RNA sequencing, we developed a spatiotemporal transcriptome atlas of B73 maize seed development based on 53 samples from fertilization to maturity for embryo, endosperm, and whole seed tissues.
2014-08-09 | E-MTAB-4395 | biostudies-arrayexpress
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.
2014-06-17 | GSE58549 | GEO
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.
2025-04-04 | GSE270812 | GEO
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. Examination of DNA methylated modifications in 2 maize tissues.
2014-06-17 | E-GEOD-58549 | biostudies-arrayexpress
Project description:Endosperm is a product of double fertilization and functions as a nutritive tissue in the angiosperm seed to support the growth of the embryo or the germinating seedling. In cereal grains, endosperm comprises a large proportion of the mature seed and contains large amounts of carbohydrates and proteins. To identify a high-resolution temporal transcriptome of the earliest stages of endosperm development, we used laser-capture microdissection to isolate and profile mRNA populations of a developmental series of the endosperm from 0 to 4 DAP in maize inbred B73. These stages comprise the initial period of proliferation of the triploid endosperm coenocyte through cellularized endosperm that shows an overall polarity and indications of early cell differentiation. Using computational tools, we identified distinct temporal co-expression modules during this period of development. Analysis of the co-expressed transcription-factor genes and the associated cis-regulatory elements allowed us to hypothesize gene regulatory networks involved in early endosperm development in maize.
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Project description:Opaque2 (O2) is a transcription factor that plays important roles during maize endosperm development. Mutation of the O2 gene improves the nutritional value of maize seeds, but also confers pleiotropic effects that result in reduced agronomic quality. To reveal the transcriptional regulatory framework of O2, we determined O2 DNA binding targets using chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq). ChIP-Seq analysis detected 1,686 O2 DNA binding sites distributed over 1,143 genes. We identified 4 new O2 binding motifs; among them, TGACGTGG appears to be the most conserved and strongest. We confirmed that, except for the 16 kD and 18 kD zeins, O2 directly regulates expression of all other zeins. O2 directly regulates two transcription factors, genes linked to carbon and amino acid metabolism and abiotic stress resistance. Examination of 15 days after pollination(DAP) wild type maize endosperm with O2 specific antibody and IgG serves as control.
2015-03-06 | E-GEOD-63991 | biostudies-arrayexpress
Project description:Endosperm is a filial structure resulting from a second fertilization event in angiosperms. As an absorptive storage organ, endosperm plays an essential role in support of embryo development or seedling germination. The accumulation of carbohydrate and protein storage products in cereal endosperm provides humanity with a major portion of its food, feed and renewal resources. However, little is known regarding the regulatory gene networks controlling endosperm proliferation and differentiation. As a first step towards understanding these processes, we have profiled all mRNAs in kernel and endosperm of maize at eight successive stages during the first 12 days after pollination. Analysis of these gene sets has identified temporal programs of gene expression including hundreds of transcription-factor genes. We also show a close correlation of these sequentially expressed gene sets with distinct spatial programs of expression in distinct compartments of the developing endosperm. The results constitute a preliminary atlas of spatiotemproal patterns of endosperm gene expression in support of future efforts for understanding the underlying mechanisms that control seed yield and quality. The unpollinated kernels (0 DAP), the kernels of 2, 3, 4, 6 DAP and hand dissected endosperms of 8, 10, 12 DAP from the B73 were used to perform high-throughput sequencing using the SOLiD platform
2014-01-17 | E-GEOD-54131 | biostudies-arrayexpress
Project description:Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs.
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Project description:The embryo is responsible for transmitting genetic information to the next generation. However, the underlying gene expression and gene imprinting during early embryo development remain largely elusive in maize. Using high-throughput RNA sequencing, we analyzed the allelic gene expression patterns of maize embryos from reciprocal crosses between inbred lines B73 and Mo17 at six time points (3 to 13 days after pollination). A total of 9532 genes were found to be differentially expressed in developmental stage, 3512 of 9532 genes were affected by cross direction. Co-expression analysis uncovered the sequential gene activations during maize embryo development. Further, we found 64 embryo strongly imprinted genes, including 57 maternally expressed imprinted genes (MEG) and 7 paternally expressed imprinted genes (PEG) in the maize embryo. Among them, 20 genes were continuously imprinted and 36 imprinted genes were newly identified. By applying In situ hybridization, we verified that six of the differentially expressed genes showed enriched transcription in the embryo. In addition, mutant analyses indicated that three of the imprinted genes displayed reduced embryo size. Therefore, our data shed new light on our understanding of the gene expression and gene imprinting in early maize embryo development, and suggested that imprinted genes are important for proper embryo development.
2017-12-05 | GSE95399 | GEO
Project description:Endosperm is a product of double fertilization, and provides nutrients and signals to the embryo during seed development in flowering plants. Early stages of endosperm development are critical for the development of its storage capacity through synthesis and accumulation of starch and storage proteins. Here we report on the isolation and sequencing of mRNAs from the central portion of the starchy endosperm of Zea mays (maize) B73 at 6 days after pollination. We detected high correlation among the four biological replicates of RNAs isolated using laser-capture microdissection of the cell type. Because the assayed stage of development precedes the synthesis and accumulation of the major storage proteins and starch in the endosperm, our dataset likely include mRNAs for genes that are involved in control and establishment of these developmental programs. Four replicates of mRNAs from the central portion of starchy endopserm were isolated using laser-capture microdissection and sequenced using the Illumina GAIIx platform.
2014-06-17 | E-GEOD-58504 | biostudies-arrayexpress