MiR394 modulates brassinosteroid signaling to regulate hypocotyl elongation in Arabidopsis
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ABSTRACT:
PROVIDER: PRJNA649706 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12352188.fastq.gz | Fastqsanger.gz | |||
| SRR12352189.fastq.gz | Fastqsanger.gz | |||
| SRR12352190.fastq.gz | Fastqsanger.gz | |||
| SRR12352191.fastq.gz | Fastqsanger.gz | |||
| SRR12352192.fastq.gz | Fastqsanger.gz |
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Project description:miR394 and its target gene LEAF CURLING RESPONSIVENESS are involved in BR signaling by affecting BRASSINOSTEROID INSENSITIVE2 accumulation.
2024-05-01 | GSE155422 | GEO
Project description:MicroRNAs and phytophormes are all small molecular signals that play important roles in regulating development and environmental responses in plants. The interplay between them allow the plants to better converge multiple inner and outer signals to optimizing their survival strategy. So far, the knowledge of how miRNAs are involved in brassinosteroid (BR) signaling is lacking. Here, we report the finding of miR394 and its target gene LEAF CURLING RESPONSENESS (LCR), which were transcriptionally responsive to BR, participate in BR signaling in regulating hypocotyls elongation in Arabidopsis. By phenotypic analyzing of a set of transgenic and mutants, miR394 was found to act as a negative regulator in BR signaling in hypocotyls elongation, while its target gene on the contrary. Genetically, miR394 functions upstream of BIN2 and BZR1/BES1, but partially downstream or independent with BRI1 and BSU1. RNA-seq analysis further supports that miR394 inhibits BR signaling through BIN2 because miR394 co-regulate significant number of genes together with BIN2. Additionally, miR394 improved the accumulation of BIN2 but decreased the protein amount of BZR1 and BES1, which can be phosphorylated by BIN2. miR394 also repressed the transcription of PRE1/5/6 and EXP8, the key hypocotyls elongation regulating genes, which had been reported to be BZR1/BES1 targets. These findings revealed a new pathway that miRNA involved in BR signaling in Arabidopsis.
2019-08-01 | GSE114214 | GEO
Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5. Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day. Seedlings were then collected during periods of hypocotyl elongation and stasis for three days. There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates. In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study. Each sample consists of multiple pooled seedlings.
2011-03-31 | E-GEOD-21684 | biostudies-arrayexpress
Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5.
2011-03-31 | GSE21684 | GEO
Project description:Driven by cell elongation, hypocotyl growth is tightly controlled by light and responds to both external stimuli and endogenous hormonal pathways. Hypocotyls are responsive to the stress signalling hormone abscisic acid (ABA), which effectively inhibits cell elongation. However, how this regulation is connected to light signalling has been a subject of limited studies. Here, we show that, contrary to light-grown seedlings, hypocotyl elongation of dark-grown seedlings is ABA-insensitive. In the dark, hypocotyl sensitivity to ABA is restored in the constitutive photomorphogenic pifq and cop1-4 mutants, suggesting that an active light signalling pathway is necessary for hypocotyl responsiveness to ABA. Surprisingly, etiolated hypocotyls retain an intact ABA signalling pathway, as could be detected by the induction of ABI1 and RD29B transcripts in response to exogenous ABA, suggesting that inhibition of hypocotyl elongation occurs through a divergent path that can be inhibited by PIFs. Here, using RNA-seq analysis we identified a number of ABA differentially expressed genes (DEGs) that correlate with ABA inhibition of hypocotyl elongation. Among these DEGs a number of SMALL AUXIN-UP RNA (SAUR) genes that are known to directly repress D-CLADE TYPE 2C PROTEIN PHOSPHATASES (PP2C.D) were found. The abrogation of PP2CD.D2-SAUR interaction in the pp2c.d2/PP2C.D2M331K -GFP line, restored ABA sensitivity in the dark, suggesting that SAUR proteins, upregulated by PIFs, are sufficient to render hypocotyls insensitive to ABA. This hypocotyl-specific mechanism enables to promote growth towards the light at all costs, overriding ABA inhibition of cell elongation, to ensure subsequent seedling establishment and survival.
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2021-04-28 | GSE173421 | GEO
Project description:Glucose regulates cotton fiber elongation by interacting with brassinosteroid
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Project description:Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape and functionality. During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ.
2016-06-30 | GSE79881 | GEO
Project description:SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that SOB3 inhibits hypocotyl growth in SD, similar to its effects in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-Seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes affected by SOB3 were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data indicate that SOB3 mostly binds to similar genes throughout the day. Collectively, these data indicate that SOB3 affects gene expression in a time point-specific manner irrespective of changes in binding throughout SD.
2022-08-24 | GSE189264 | GEO
Project description:SUPPRESSOR OF PHYTOCHROME B4-#3 (SOB3) is a member of the AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) family of transcription factors that are involved in light-mediated growth in Arabidopsis thaliana, affecting processes such as hypocotyl elongation. The majority of the research on the AHLs has been conducted in continuous light. However, there are unique molecular events that promote growth in short days (SD) compared to constant light conditions. Therefore, we investigated how AHLs affect hypocotyl elongation in SD. Firstly, we observed that SOB3 inhibits hypocotyl growth in SD, similar to its effects in constant light. Next, we identified AHL-regulated genes in SD-grown seedlings by performing RNA-Seq in two sob3 mutants at different time points. Our transcriptomic data indicate that PHYTOCHROME INTERACTING FACTORS (PIFs) 4, 5, 7, and 8 along with PIF-target genes are repressed by AHLs. We also identified PIF target genes that are repressed and have not been previously described as AHL-regulated, including PRE1, PIL1, HFR1, CDF5, and XTR7. Interestingly, our RNA-seq data also suggest that AHLs activate the expression of growth repressors to control hypocotyl elongation, such as HY5 and IAA17. Notably, many growth-regulating and other genes affected by SOB3 were differentially regulated between these two sob3 mutants at the time points tested. Surprisingly, our ChIP-seq data indicate that SOB3 mostly binds to similar genes throughout the day. Collectively, these data indicate that SOB3 affects gene expression in a time point-specific manner irrespective of changes in binding throughout SD.
2022-08-24 | GSE189262 | GEO