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3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIA-PET]

ABSTRACT: 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.

ORGANISM(S): Oryza sativa Japonica Group Oryza sativa Indica Group

PROVIDER: GSE214050 | GEO | 2022/09/28

REPOSITORIES: GEO

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3D epigenome architecture orchestrates cis and trans regulation of flowering time in rice [ChIP-seq]

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

Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice

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

Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice

2009-12-31 | GSE16796 | GEO

A common set of genes responding to florigenic and photoperiodic induction at the shoot apical meristem of rice

Project description:Flowering of rice is triggered by transcriptional reprogramming at the shoot apical meristem (SAM) mediated by florigenic proteins produced in leaves in response to changes in the photoperiod. Florigens are more rapidly expressed under short day (SD) and include the HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1) Phosphatidyl Ethanolamine Binding Proteins (PEBP). Hd3a and RFT1 are largely redundant at converting the SAM into an inflorescence, but whether they activate the same target genes and convey all photoperiodic information that modifies gene expression at the SAM is currently unclear. We uncoupled the contribution of Hd3a, RFT1 and SD to transcriptome reprogramming at the SAM, by RNA-sequencing of dex-inducible over-expressors of single florigens and wild type plants exposed to photoperiodic induction. Fifteen highly differentially expressed genes common to Hd3a, RFT1 and SD were retrieved, ten of which still uncharacterized. Detailed functional studies on some candidates revealed a role for LOC_Os04g13150 in determining tiller angle and bract development and the gene was renamed BROADER TILLER ANGLE 1 (BRT1). We identified a core set of genes common to florigenic and photoperiodic induction and defined the function of a novel florigen target controlling tiller angle.

2024-02-01 | GSE226057 | GEO

Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

Project description:Plants show a high degree of developmental plasticity in response to external cues, including day length and environmental stress. Water scarcity in particular can interfere with photoperiodic flowering, resulting in the acceleration of the switch to reproductive growth in several species, a process called drought escape. However, other strategies are possible and drought stress can also delay flowering, albeit the underlying mechanisms have never been addressed at the molecular level. We investigated these interactions in rice, a short day species in which drought stress delays flowering. A protocol that allows the synchronization of drought with the floral transition was set up to profile the transcriptome of leaves subjected to stress under distinct photoperiods. We identified clusters of genes that responded to drought differently depending on day length. Exposure to drought stress under floral-inductive photoperiods strongly reduced transcription of EARLY HEADING DATE 1 (Ehd1), HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), primary integrators of day length signals, providing a molecular connection between stress and the photoperiodic pathway. However, phenotypic and transcriptional analyses suggested that OsGIGANTEA (OsGI) does not integrate drought and photoperiodic signals as in Arabidopsis, highlighting molecular differences between between long and short day model species.

2017-03-01 | GSE78972 | GEO

Microarray comparative analysis of wild-type and hd1-3 mutant rice

Project description:Heading date1(Hd1) is a critical regulator controlling rice flowering time, which promotes flowering under short-day (SD) conditions and represses flowering under long-day (LD) conditions. In our previous study (Luan et al., 2009), we identified a rice mutant, hd1-3, in which the Hd1 gene was deficient due to several insertions/deletions in the coding region. To search for downstream genes regulated by Hd1, we performed microarray analysis of hd1-3 mutant and the wild-type Zhonghua11 under both SD and LD conditions. According to the microarray results, SDG712 gene was significantly downregulated in the hd1-3 mutant, indicating that SDG712 gene may acts downstream of Hd1, and may functions in rice flowering time regulation.

2021-02-04 | GSE166053 | GEO

Oryza sativa

Project description:Hd3a, RFT1 and Ehd1 integrate photoperiodic and drought stress signals to delay the floral transition in rice

| PRJNA314526 | ENA

PREMATURE INTERNODE ELONGATION 1 coordinates internode elongation in response to florigenic signals at the shoot apex of rice

Project description:Flowering of several plant species is induced by exposure to specific photoperiods that promote the expression of florigenic proteins in the leaves and their subsequent translocation to the shoot apex, where they commit the meristem to a reproductive fate. Transition to reproductive growth at the apex is often accompanied by stem elongation, to expose flowers above the leaves and facilitate fertilization. However, how growth and inflorescence formation are coupled and how photoperiodic signals coordinate these processes at the apex is still unclear. We studied these mechanisms in rice, a short day plant. Here, we show that HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1), encoding components of the rice florigenic signal, are sufficient to repress expression of PREMATURE INTERNODE ELONGATION 1 (PINE1) at the shoot apex during the transition to flowering, thus promoting culm elongation. PINE1 encodes a nuclear C2H2 zinc finger transcriptional repressor that controls the mRNA abundance of GA3ox2, a gibberellin (GA) biosynthetic gene. These data uncover the existence of a regulatory network coordinating multiple aspects of phase transition, and indicate that GA-induced growth and activity of florigenic proteins at the shoot apex need to be strictly coupled.

2018-11-30 | GSE90493 | GEO

The Evening Complex integrates photoperiod signals to control flowering in rice [RNA-Seq]

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

The Evening Complex integrates photoperiod signals to control flowering in rice [ChIP-Seq]

2022-05-24 | GSE181831 | GEO

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