Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1149556 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Polycomb group (PcG) proteins are known to silence gene expression by modifying histones, such as H2Aub and H3K27me3, which is essential for maintaining cell type and tissue-specific gene expression patterns. However, the impact of PcG proteins on gene regulation through H2Aub and H3K27me3 during maize kernel development remains poorly understood. Here, we characterized a maize miniature seed mutant, mn8, and identified the underlying gene through map-based cloning. We found that Mn8 encodes ZmEMF1a, a plant-specific PcG protein. Mutation in ZmEMF1a leads to significantly reduced kernel size and weight. Molecular analyses showed that ZmEMF1a interacts with PRC1 component ZmRING1 and PRC2 subunit ZmMSI1, which are crucial for the establishment of H2Aub and H3K27me3 modifications. The deficiency of ZmEMF1a resulted in significant reduction in genomic levels of H2Aub and H3K27me3. Combined ChIP-seq and RNA-seq analyses showed that H2Aub is negatively correlated with gene expression in maize, contrasting with the positive correlation observed in Arabidopsis. Compared with wild-type (WT) endosperms, mn8 endosperms exhibited elevated expressions of homology genes of cell proliferation repressors, such as ZmDA1, ZmBB1, ZmES22, ZmMADS8, and ZmMADS14, accompanied with decreased levels of 3K27me3 or H2Aub at these loci. These findings indicate that lack of ZmEMF1a impairs the deposition of H3K27me3 and H2Aub marks at cell division repressor genes. Taken together, our results demonstrate that ZmEMF1a plays a crucial role in regulating maize kernel development by maintaining the levels of H2Aub and H3K27me3 modifications.
2025-06-30 | GSE292615 | GEO
Project description:Polycomb group (PcG) proteins are known to silence gene expression by modifying histones, such as H2Aub and H3K27me3, which is essential for maintaining cell type and tissue-specific gene expression patterns. However, the impact of PcG proteins on gene regulation through H2Aub and H3K27me3 during maize kernel development remains poorly understood. Here, we characterized a maize miniature seed mutant, mn8, and identified the underlying gene through map-based cloning. We found that Mn8 encodes ZmEMF1a, a plant-specific PcG protein. Mutation in ZmEMF1a leads to significantly reduced kernel size and weight. Molecular analyses showed that ZmEMF1a interacts with PRC1 component ZmRING1 and PRC2 subunit ZmMSI1, which are crucial for the establishment of H2Aub and H3K27me3 modifications. The deficiency of ZmEMF1a resulted in significant reduction in genomic levels of H2Aub and H3K27me3. Combined ChIP-seq and RNA-seq analyses showed that H2Aub is negatively correlated with gene expression in maize, contrasting with the positive correlation observed in Arabidopsis. Compared with wild-type (WT) endosperms, mn8 endosperms exhibited elevated expressions of homology genes of cell proliferation repressors, such as ZmDA1, ZmBB1, ZmES22, ZmMADS8, and ZmMADS14, accompanied with decreased levels of 3K27me3 or H2Aub at these loci. These findings indicate that lack of ZmEMF1a impairs the deposition of H3K27me3 and H2Aub marks at cell division repressor genes. Taken together, our results demonstrate that ZmEMF1a plays a crucial role in regulating maize kernel development by maintaining the levels of H2Aub and H3K27me3 modifications.
2025-06-30 | GSE292616 | GEO
Project description:Kernel development is accompanied by complex gene networks. Expression quantitative trait loci (eQTL) analysis is an efficient way to detect the regulatory elements of genes, especially the trans-eQTLs help to construct the regulatory networks of genes and contribute to a better understanding of the intrinsic mechanisms of biological processes. Till now, the 15 DAP (day after pollination) eQTL has been elucidated in maize kernel, but little is known about the early stage. Here, we conduct eQTL analysis for 5 DAP maize kernel using 318 maize inbred lines. The results will provide insights into the genetic basis of early kernel development.
2019-10-01 | GSE110315 | GEO
Project description:The kernel serves as a storage organ for various nutrients and determines the yield and quality of maize. Understanding the mechanisms regulating kernel development is important for maize production. In this study, a small kernel mutant smk7a of maize was characterized. Cytological observation suggested that the development of the endosperm and embryo was arrested in smk7a in the early development stage. Biochemical tests revealed that the starch, zein protein, and indole-3-acetic acid (IAA) contents were significantly lower in smk7a compared with wild-type (WT). Consistent with the defective development phenotype, transcriptome analysis of the kernels 12 and 20 days after pollination (DAP) revealed that the starch, zein, and auxin biosynthesis related genes were dramatically downregulated in smk7a. Genetic mapping indicated that the mutant was controlled by a recessive gene located on chromosome 2. Our results suggest that disrupted nutrition accumulation and auxin synthesis cause the defective endosperm and embryo development of smk7a.
2023-01-25 | GSE221594 | GEO
Project description:We performed a molecular characterization of the maize small kernel mutant with endosperm developmental deficiency phenotypes.To elucidate how SMK8 affects kernel development, we performed RNA sequencing (RNA-seq), and the results revealed numerous differentially expressed genes related to storage proteins and starch biosynthesis and biosynthesis of amino acids.
2020-07-09 | GSE154016 | GEO
Project description:Maize kernels are susceptible to infection by the opportunistic pathogen Aspergillus flavus. Infection results in reduction of grain quality and contamination of kernels with the highly carcinogenic mycotoxin, aflatoxin. To understand host response to infection by the fungus, transcription of approximately 9,000 maize genes were monitored during the host-pathogen interaction with a custom-designed Affymetrix GeneChip® DNA array. More than 1,000 maize genes were found differentially expressed at a fold change of 2 or greater. This included the up regulation of defense-related genes and signaling pathways. Transcriptional changes also were observed in primary metabolism genes. Starch biosynthetic genes were down regulated during infection, while genes encoding maize hydrolytic enzymes, presumably involved in the degradation of host reserves, were up regulated. These data indicate that infection of the maize kernel A. flavus induced metabolic changes in the kernel, including the production of a defense response, as well as a disruption in kernel development.
2014-05-14 | GSE57629 | GEO
Project description:Maize kernel is an important source of food, feed and industrial raw materials. The illustration of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. Although a great many researches based on molecular biology and gecetics have greatly increased our understanding on the kernel development, many of the mechanisms controlling this important process remain elusive. In current study, a microarray with approximately 58,000 probes was used to study the dynamic gene expression during kernel development from the fertilization to physiological maturity. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. Hybridization of slides was performed according to the manufacturer’s instructions (http://www.maizearray.org/). The hybridized slides were scanned by a Genepix 4000B (Axon, USA). A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations. By comparing six consecutive time-points, namely 1, 5, 10, 15, 25 and 35 days after pollination (DAP), 3,445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes expanded our understanding of the regulation mechanism underlying the important developmental processes, cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process. Keywords: Time course, development
2008-04-09 | GSE9386 | 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:Maize kernels are susceptible to infection by the opportunistic pathogen Aspergillus flavus. Infection results in reduction of grain quality and contamination of kernels with the highly carcinogenic mycotoxin, aflatoxin. To understand host response to infection by the fungus, transcription of approximately 9,000 maize genes were monitored during the host-pathogen interaction with a custom-designed Affymetrix GeneChip® DNA array. More than 1,000 maize genes were found differentially expressed at a fold change of 2 or greater. This included the up regulation of defense-related genes and signaling pathways. Transcriptional changes also were observed in primary metabolism genes. Starch biosynthetic genes were down regulated during infection, while genes encoding maize hydrolytic enzymes, presumably involved in the degradation of host reserves, were up regulated. These data indicate that infection of the maize kernel A. flavus induced metabolic changes in the kernel, including the production of a defense response, as well as a disruption in kernel development. Maize kernels were mock inoculated at the blister (R2) or dough (R4) stage or inoculated with A. flavus at the blister (R2), milk (R3), dough (R4), or dent (R5) stage, and harvested 4 days later. Each treatment consisted of three biological replications. For each biological replication, 8 kernels were ground and RNA was isolated and further processed.
2014-05-14 | E-GEOD-57629 | biostudies-arrayexpress