Regulation of flowering time by autophagy in rice
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ABSTRACT:
PROVIDER: PRJNA732680 | ENA |
REPOSITORIES: ENA
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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: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 circadian clock enables organisms to rapidly adapt to the ever-changing environmental conditions that are caused by daily light/dark cycles. Circadian clock genes universally affect key agricultural traits, particularly flowering time. Here, we show that OsPRR37, a circadian clock gene, delays rice flowering time in an expression level-dependent manner. Using high-throughput mRNA sequencing on an OsPRR37 overexpressing transgenic line (OsPRR37-OE5) and the recipient parent Guangluai4 that contains the loss-of-function Osprr37, we identify 14,992 genes that display diurnal rhythms, which account for 52.9% of the transcriptome. Overexpressing OsPRR37 weakens the transcriptomic rhythms and alters the phases of rhythmic genes. In total, 3,210 differentially expressed genes (DEGs) are identified, among which 1,863 rhythmic DEGs show a correlation between the change of absolute amplitudes and the mean expression levels. We further reveal that OsPRR37 functions as a transcriptional repressor to repress the expression levels and amplitudes of day-phased clock genes. More importantly, OsPRR37 confers expanded regulation on the evening-phased rhythmic DEGs by repressing the morning-phased rhythmic DEGs. Further study shows that OsPRR37 expands its regulation on flowering pathways by repressing Ehd1. Thus, our results demonstrate an expanded regulation mechanism of the circadian clock on the diurnal rhythms of the transcriptome.
2018-05-10 | GSE114188 | 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 | 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:A great majority of plants synchronize flowering with day length. In rice, the most important environmental cue that triggers flowering is the photoperiod. Here, we show that the s73 mutant, identified in a gamma irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the SE5 gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants showed a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of Hd3a, the most important floral integrator. Ehd1, an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds implies that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering affecting both Hd1 and Ehd1 flowering pathways.
2009-12-31 | GSE16796 | GEO
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
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:A great majority of plants synchronize flowering with day length. In rice, the most important environmental cue that triggers flowering is the photoperiod. Here, we show that the s73 mutant, identified in a gamma irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the SE5 gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants showed a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of Hd3a, the most important floral integrator. Ehd1, an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds implies that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering affecting both Hd1 and Ehd1 flowering pathways. Four biological replicates from each genotype (s73 mutant and Bahia wt) were labelled with Cy3 and Cy5 alternatively (2+2) following a dye-swap design. In total, 4 microarrays were hybridized. The supplementary file 'GSE16796_stat_analysis.txt' contains the final statistical analysis of study GSE16796.
2010-05-16 | E-GEOD-16796 | biostudies-arrayexpress