Transcriptome analysis of nkd1 and nkd2 mutants in W22 maize endosperm
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ABSTRACT:
PROVIDER: PRJNA835317 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR19091815_1.fastq.gz | Fastqsanger.gz | |||
| SRR19091815_2.fastq.gz | Fastqsanger.gz | |||
| SRR19091816_1.fastq.gz | Fastqsanger.gz | |||
| SRR19091816_2.fastq.gz | Fastqsanger.gz | |||
| SRR19091817_1.fastq.gz | Fastqsanger.gz |
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Project description:The maize NAKED ENDOSPERM (NKD) genes Nkd1 and Nkd2 encode paralogous INDETERMINATE DOMAIN (IDD) transcription factors (TFs) that have previously been shown to play critical roles in regulating endosperm gene expression and development. However, the function of each individual NKD protein is unclear. To elucidate this, we performed a transcriptome analysis for nkd1-Ds and nkd2-Ds single mutant endosperm. We found that in nkd1-Ds single mutant, nkd2 gene expression is significantly lower than WT, and similar to the nkd2-Ds mutant.
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Project description:Reduced prolamin (zein) accumulation and defective ER-body formation occurs in maize opaque endosperm mutants opaque2 (o2), floury2 (fl2), defective endosperm*B30 (DeB30), and mucronate (Mc) whereas other opaque mutants such as opaque1 (o1) and floury1 (fl1) are normal in these regards. This suggests that other factors contribute to kernel texture. We used a LC-MS/MS proteomics approach to compare non-zein proteins of nearly isogenic opaque mutants. In total, 2762 proteins were identified that were enriched for biological processes such as protein transport and folding, amino acid biosynthesis, and proteolysis. Amino acid analysis of top proteins revealed qualitative changes in lysine abundance contributing to the overall lysine increase. Principal component analysis and pathway enrichment suggested that the mutants partition into three groups: Mc, DeB30, fl2 and o2; o1; and fl1. Indicator species analysis revealed mutant-specific proteins, and highlighted ER secretory pathway components that are enriched in selected groups of mutants, albeit with no common proteins across all mutants. Most significantly changed proteins were related to stress or defense and zein partitioning into the soluble fraction for Mc, DeB30, o1 and fl1 specifically. We suggest that ER stress is a universal trigger of opacity regardless of qualitative or quantitative changes in zein accumulation.
2016-01-05 | PXD002379 | Pride
Project description:The goal of this work was to identify transcripts in maize endosperm that are regulated by water stress and the transcription factor Vp1 Keywords: stress response Plants were grown from F1 hybrid seed produced from inbreds W22 and ACR5855, where both inbred parents contributed mutant vp1-R alleles. Florets were fertilized with pollen from either homozygous vp1 pollen, thus creating vp1/vp1/vp1 mutant endosperms, or Vp1 pollen, thus creating Vp1/vp1/vp1 endosperms. Water stress treatment was imposed by withholding irrigation at 5 days after pollination; endosperms were sampled at 10 d after pollination. The study had 2 X 2 factorial design with two genotypes and two watering treatments; there were 6 biological replicates.
2017-04-19 | E-GEOD-7672 | biostudies-arrayexpress
Project description:Mu transposon insertions were sequenced in the parents and offspring from 4 maize families using MuSeq2. Male parents were Mu-active while female parents were Mu-inactive, and so all new transposon activity can be associated with the male parent. Matched endosperm and leaf from each offspring were sequenced, allowing inherited insertions to be unambiguously identified as these tissues diverge prior to fertilization (each is derived from a sister sperm cell in pollen during double fertilziation). The data were analyzed to follow the transmission of de novo Mu insertions from parent to offspring.
2025-05-09 | GSE296286 | 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.
2014-06-17 | GSE58549 | GEO
Project description:Mu transposon insertion sites in matched leaf and endosperm samples from Mu-active W22 maize
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Project description:Transcription factors (TFs) play an important role in maize endosperm development regulation. The temporal RNA-seq and co-expression network analysis of maize endosperm reveals a hiararchical regulatory network architechture modulating the endosperm development. In the network, NKD1 and NKD2 are central regulators, and GBF1, HSFTF10, NACTF49 and HB115 are secondary regulators downstream of NKD1 and 2. To further test the relationship between these TFs, a DNA affinity purification and sequencing (DAP-seq) assay was performed. The result shows that the assay on NKD1 and NKD2 called 1,951 and 56,855 peaks, and 93 and 1,692 peaks are located within 3 kb distance to transcription starting site (TSS), respectively. And assays on GBF1, HSFTF10, NACTF49 and HB115 called 15,543; 38,147; 7,388 and 936 peaks, respectively.
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Project description:This was a pilot project carried out by Dr Wojciech Majeran to determine the maize pollen proteome harvested from field-grown W22 (T43) plants in plots on the Musgrave Research Farm (Cornell CALS) in Aurora (NY). To enhance proteome coverage, the pollen were separated into soluble and membrane bound protein fractions, and separated by SDS-PAGE followed by in-gel digestion and shot-gun proteomics using a nanoLC-Orbitrap system.
2023-09-11 | PXD045274 | Pride
Project description:The goals of this study are to study the regulatory network of the two maize endosperm-specific transcription factors O2 and PBF by 16-DAP endosperm transcriptome profiling (RNA-seq) of their mutants and wild type. The results utilize the expression pattern of global genes regulated by PBF and O2 to elucidate their control for storage compounds synthesis in maize kernels.
2016-03-24 | GSE79513 | 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.
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