The Nhd1–MYB110–MADS15 transcription factor module regulates flowering time in rice
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PROVIDER: PRJNA1284265 | ENA |
REPOSITORIES: ENA
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Project description:The precise regulation of flowering time, known as heading date in rice (Oryza sativa L.), is critical for regional adaptation, agricultural productivity, and crop rotation practices. In rice, the florigen activation complex (FAC) and its downstream effectors are well-characterized mediators of the floral transition in the shoot apical meristem (SAM). Here, we characterized OsMYB110 as a SAM-localized transcription factor that promotes flowering, exhibiting functional similarity to the established flowering regulator Nhd1 (N-mediated heading date-1). Through integrated molecular and genetic analyses, we demonstrate that: (1) Nhd1 directly binds to the OsMYB110 promoter to activate its expression, while OsMYB110 in turn binds to and activates the OsMADS15 promoter to control flowering progression, and (2) genetic epistasis places OsMYB110 downstream of Nhd1 but upstream of OsMADS15 in the flowering regulation hierarchy. Furthermore, while elevated phosphate accelerates flowering, this response is abolished in myb110 and mads15 mutants but maintained in nhd1 mutants. These results define a previously unrecognized Nhd1–OsMYB110–OsMADS15 regulatory module that integrates developmental and nutrient signaling pathways to control rice flowering time.
2025-07-04 | GSE301208 | GEO
Project description:This study investigated the effect of autophagy on flowering time in rice. Results provide important information of the response of flowering time to autophagy, such as specific flowerig time genes, up- or down-regulated specific flowering time functions.
2022-05-06 | GSE175519 | GEO
Project description:Regulation of flowering time by autophagy in rice
| PRJNA732680 | ENA
Project description:Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.
2022-09-28 | GSE214069 | GEO
Project description:Repressive epigenetic modification histone H3 lysine 27 tri-methylation (H3K27me3) marks many agronomically important genes in plants. However, H3K27me3-associated three-dimensional (3D) genome architecture and its regulatory functions in rice flowering time remain unclear. In this study, we map H3K27me3-associated genome topology using long-read ChIA-PET and reveal extensive chromatin loops among H3K27me3-marked regions in different rice varieties and tissues. Multiple H3K27me3-associated chromatin loops usually tether together and further form repressive chromatin interacting domains (RIDs), which provide structural bases for the regulation of the co-modification and co-expression of interacting genes. Surprisingly, we identified extensive chromatin loops between the rice florigen genes Hd3a and RFT1, and frequent chromatin interactions between the positive flowering regulator Ehd1 on the chromosome 10 and Hd3a/ RFT1 loci on the chromosome 6. These results suggest that flowering genes might form a Ehd1-Hd3a/RFT1-centered spatial gene cluster in rice. We also demonstrate the flowering regulator protein complexes comprising Ghd7, Ghd8, and Hd1 could bind to the Ehd1-Hd3a/RFT1 spatial gene cluster. In addition, liquid-liquid phase separation of Ghd7 and Hd1, as well as the essentially synchronous expression of Ehd1 and Hd3a suggest that this spatial gene cluster acts as a regulatory hub to coordinately regulates the expression of Ehd1-Hd3a. This work uncovers the frame of integrated cis and trans molecular mechanism underlying transcriptional regulation of florigen genes in rice.
2022-09-28 | GSE214050 | GEO
Project description:The timing of flowering is a critical agronomic trait governed by a number of different internal and external events, such as temperature, light and photoperiod. Despite a firm understanding of flowering time from a genetic standpoint, there exists a limited understanding of how post-translational modifications may influence flowering, and what molecular PTM machinery is responsible for catalyzing these events. Here, we identify and characterize a novel B4 Raf-like MAPKKK protein kinase called RAF24, which exhibits an early flowering phenotype. Analysis of closely-related B4 Raf-like MAPKKK protein kinases RAF18 and RAF20, indicate that RAF24 is the only B4 RAF to possess an early flowering phenotype. Through quantitative proteomics, we then found that RAF24 impacts the phosphorylation status of numerous flowering related proteins related to the autonomous flowering pathway, with changes in the phosphorylation status of HISTONE MONO-UBIQUITINATION 2 (HUB2) representing the largest fold-change. Subsequent analysis of the HUB2 protein interactome by quantitative affinity purification mass spectrometry (AP-MS) revealed a relationship between HUB2 phosphorylation at S314 phosphorylation status and HUB2 function that manifest as changes in activity and protein-protein interactions. Use of phospho-memetic and -ablative mutants validate the importance of S314, directly linking this HUB2 phosphorylation event to the proper control of flowering time. Collectively, our findings implicate RAF24 as a higher-order regulator of flowering, while further implicating HUB2 as a centerpiece of flowering time regulation in plants.
2025-05-09 | PXD038688 | Pride
Project description:This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.
2022-05-24 | GSE181833 | GEO
Project description:This study aim to understand how the long and short day flowering pathways are integrated and the mechanism of photoperiod perception in rice. Trascriptome at different time points under LD and SD conditions reveal that photoperiodism in rice is controlled by the evening complex. Mutants in LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) orthologs abolish flowering. We show that light causes a rapid and sustained degradation of ELF3-1, and this response is dependent on phyB. ChIP-seq of ELF3 and LUX reveal that EC controls both LD and SD flowering pathways by directly binding and suppressing the expression of key floral repressors, including PRR7 orthologs and Ghd7.
2022-05-24 | GSE181831 | GEO
Project description:Proteome analysis of developing grain in indica rice "Naba" (S1) and "Puluik Arang" (S2). Ovary samples at 10 days after flowering were used.
2019-10-18 | PXD015105 | JPOST Repository
Project description:Using a yeast to hybrid screen, it was found that PHO2, a key regulator of phosphate homeostasis, could interact with GIGANTEA, a key regulator of flowering time. In addition, mutant analysis revealed that both the pho2 and gi mutants shared similar phenotypes, both at the phosphate and flowering time levels. We used microarrays to analyse the effects of each mutation (pho2 or gi) on global gene expression, and assessed the proportion of genes similalry regulated in both mutants, in both shoots and roots. Wild-type (Nipponbare), pho2 and gi knock-out rice plants were grown to 21-days before harvesting root and shoot separately.
2013-07-01 | E-GEOD-46867 | biostudies-arrayexpress