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ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development [RNA-Seq]

ABSTRACT: 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.

ORGANISM(S): Zea mays

PROVIDER: GSE292616 | GEO | 2025/06/30

REPOSITORIES: GEO

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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. To obtain the global gene expression profile during maize kernel development, a microarray with approximately 58,000 probes was used. The maize inbred line X178 was planted on the field. Each plant was self-pollinated by hand. The ears were harvested from healthy plants at 1, 5, 10, 15, 25 and 35 days after pollination (DAP), respectively. In order to increase the consistency & uniformity of the isolated kernels, the upper half and about one sixth of ears from the bottom were cut and discarded, the kernels were isolated from the rest part of the ears. Samples at each time-point were collected from at least thirty ears and pooled to represent the line characteristics of X178. Two sub-samples for replication in the microarray analysis were randomly drawn. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. 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.

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ZmEMF1a is required for the maintenance of H2Aub and H3K27me3 modifications in maize kernel development [RNA-Seq]

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