Opaque-2 regulates a complex gene network associated with cell differentiation and storage function of maize endosperm
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ABSTRACT:
PROVIDER: PRJNA471036 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7153130_1.fastq.gz | Fastqsanger.gz | |||
| SRR7153130_2.fastq.gz | Fastqsanger.gz | |||
| SRR7153131_1.fastq.gz | Fastqsanger.gz | |||
| SRR7153131_2.fastq.gz | Fastqsanger.gz | |||
| SRR7153132_1.fastq.gz | Fastqsanger.gz |
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Project description:Development of the cereal endosperm involves cell differentiation processes that enable nutrient uptake from the maternal plant, accumulation of storage products and their utilization during germination. However, little is known about the regulatory mechanisms that link cell differentiation processes with those controlling storage product synthesis and deposition, including the activation of zein genes by the maize (Zea mays) bZIP transcription factor Opaque-2 (O2). In this study, we mapped in vivo binding sites of O2 in B73 endosperm, and compared the results with genes differentially expressed in B73 and B73o2. We identified 186 putative direct O2 targets and 1,677 indirect targets, encoding a broad set of gene functionalities. Examination of the temporal expression patterns of O2 targets using real-time RT-PCR experiments revealed at least two distinct modes of O2-mediated gene activation. We also showed that two O2-activated genes, bZIP17 and NAKED ENDOSPERM2 (NKD2) encoded transcription factors, which can in turn co-activate other O2-network genes with O2. NKD2 (with its paralog NKD1) was previously shown to be involved in regulation of aleurone development. Collectively, our results provide novel insights into the complexity of the O2-regulated network and its role in regulation of endosperm cell differentiation and function.
2018-09-14 | GSE114343 | GEO
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:Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
2024-06-21 | GSE262337 | GEO
Project description:Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
2024-06-21 | GSE262335 | GEO
Project description:Grain filling in maize (Zea mays L.) is intricately linked to cell development, involving the regulation of genes responsible for the biosynthesis of storage reserves (starch, proteins, and lipids) and phytohormones. However, the regulatory network coordinating these biological functions remains unclear. In this study, we identified 1,744 high-confidence target genes co-regulated by the transcription factors (TFs) ZmNAC128 and ZmNAC130 (ZmNAC128/130) through chromatin immunoprecipitation sequencing coupled with RNA-seq analysis in the zmnac128/130 loss-of-function mutants. We further constructed a hierarchical regulatory network using DNA affinity purification sequencing analysis of downstream TFs regulated by ZmNAC128/130. In addition to target genes involved in the biosynthesis of starch and zeins, we discovered novel target genes of ZmNAC128/130 involved in the biosynthesis of lipids and indole-3-acetic acid (IAA). Consistently, the number of oil bodies, as well as the contents of triacylglycerol and IAA were significantly reduced in zmnac128/130. The hierarchical regulatory network centered by ZmNAC128/130 revealed a significant overlap between the direct target genes of ZmNAC128/130 and their downstream TFs, particularly in regulating the biosynthesis of storage reserves and IAA. Our results indicated that the biosynthesis of storage reserves and IAA is coordinated by a multi-TFs hierarchical regulatory network in maize endosperm.
2024-06-21 | GSE262336 | GEO
Project description:Investigation of Gene Network of NKD1, NKD2 and OPAQUE-2 Associated with Maize Endosperm Development
| PRJNA728077 | ENA
Project description:The transcriptomic analysis of nkd1, nkd2 and o2 homozygous mutant set (including 1 WT, 3 single mutants, 3 double mutants and 1 triple mutant) at 8, 12 and 16 DAP revealed temporal regulatory landscape in endosperm grain-filling stage. The data also showed NKD1, NKD2 and O2 interactively regulate gene network overtime in several processes, such as hormone response, cell wall organization, nutrient storage and endoreduplication, etc.
2023-10-09 | GSE174059 | GEO
Project description:The cereal endosperm consists of starchy endosperm (ST) cells, which accumulate storage proteins and starch, the peripheral aleurone (AL) cells, which mobilize these storage compounds during germination, and transfer cells in contact with the maternal vascular tissues, and the embryo-surrounding region. We conducted RNA-sequencing and analyzed transcript profiles of AL and ST tissues at 18 and 22 days after pollination (DAP), when storage compounds such as proteins, starch, triacylglycerols, specialized metabolites, and minerals are actively synthesized in the maize endosperm. We combined published RNA-seq datasets from other kernel tissues at different developmental stages to analyze gene expression connected to synthesis and accumulation of storage compounds and metabolites. Using weighted correlation network analysis (WGCNA), we identified gene modules associated with metabolic pathways related to nutritional properties of the maize endosperm. We also provide information of novel marker genes specifically expressed in AL and ST, at either early or late developmental stages. This study is important for understanding maize endosperm development and for developing strategies to improve nutritional quality of maize kernels.
2017-05-02 | GSE95678 | GEO
Project description:Quality Protein Maize (QPM) was created by selecting for genetic modifiers that convert the starchy endosperm of an opaque2 (o2) mutant to a hard, vitreous phenotype. Genetic analysis has shown there are multiple, unlinked o2 modifiers (Opm), but their identity and mode of action are unknown. A microarray hybridization performed with RNA obtained from true breeding o2 progeny with vitreous and opaque kernel phenotypes identified a small group of differentially expressed genes, some of which map at or near the Opm QTLs. Compared 18 days after pollination endosperm transcript profiles in true breeding modified (vitreous; V) and non-modified (opaque; O) opaque 2 kernels. Used four vitreous biological reps (V1-V4) and four opaque biological reps (O1-O4). Each biological rep is a pool of 25 kernels representing 5 kernels form each of 5 uniform phenotype ears (vitreous or opaque). Four arrays used: Array 1= V1 vs O1, Array 2 = V2 vs O2, Array 3 = V3 vs O3, Array 4 = V4 vs O4
2010-05-26 | E-GEOD-10449 | biostudies-arrayexpress
Project description:The endosperm of cereal grains feeds the entire world as major food supply, however little is known for its defense responses during endosperm development. Inducer of CBF Expression 1 (ICE1) is a known regulator of cold tolerance in plants. ICE1 has a monocot-specific homologue that is preferentially expressed in cereal grains but with an unclear regulatory function. Here, we characterized the function of monocot-specific ZmICE1 (ZmICE1a) in maize (Zea mays) kernel. mRNA in situ hybridization (ISH) revealed that ZmICE1a is predominantly expressed in the peripheral endosperm (AL, SAL, and BETL). Loss-of-function of ZmICE1a reduced starch content and kernel weight. RNA-seq analysis revealed contradicted expression patterns between starch synthesis genes and genes involved in defense and phytohormone synthesis in zmice1a developing endosperm. Coupled with CUT&Tag-seq analysis, we found that ZmICE1a positively regulates genes in starch synthesis, while negatively regulates genes in AL-specific defense and the synthesis of IAA and JA. Explant assays revealed that exogenous IAA or JA induces the expression of numerous defense genes. mRNA ISH assays revealed that the defense genes induced by IAA and JA, exhibit distinct spatial specific expression in BETL and SAL, respectively. Moreover, we dissected a JA-ZmJAZ9-ZmICE1a-MPI signaling axis involved in JA-mediated defense regulation. Overall, our study revealed ZmICE1a as a key regulatory for endosperm defense responses, and coordinates defense-storage tradeoffs during endosperm development.
2024-09-19 | GSE254177 | GEO