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Light- and Phytochrome-Dependent Regulation of Hypocotyl Elongation in Arabidopsis thaliana

ABSTRACT: To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT)

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE38989 | GEO | 2013/03/01

SECONDARY ACCESSION(S): PRJNA170166

REPOSITORIES: GEO

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Light- and Phytochrome-Dependent Regulation of Hypocotyl Elongation in Arabidopsis thaliana

Project description:To identify and characterize genes required for tissue-specific phytochrome responses during hypocotyl development in far-red-light grown bvr lines, we performed gene transcriptional profiling using bvr lines with mesophyll-specific phytochrome inactivation (cab3: :pBVR2). We identified several candidate genes whose expression is significantly altered in lines with mesophyll tissue-specific BVR expression (Cab3::pBVR2), compared to constitutive phytochrome inactivation lines, i.e. 35S-driven BVR lines (35S::pBVR3). No-0 is used as wild-type (WT) Seeds of No-0 WT, 35S::pBVR3 and CAB3::pBVR2 on MS plates were exposed to Red (R) light of 75 M-BM-5mol m-2 s-1 for 5 min and imbibing seeds were cold-stratified at 4 M-BM-0C in darkness for 3 d. Seedlings were grown under continuous far-red illumination for 7 d. Seven-day-old vegetative whole seedlings (300 M-bM-^@M-^S 500 mg) were quickly (<1 min) harvested and immediately frozen in liquid nitrogen inside the FR chamber. Seedlings were grown under continuous far-red illumination for 7 d.

2013-03-01 | E-GEOD-38989 | biostudies-arrayexpress

SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days [RNA-seq]

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

SUPPRESSOR OF PHYTOCHROME B4#3 reduces the expression of PIF-activated genes and increases expression of growth repressors to regulate hypocotyl elongation in short days [ChIP-seq]

2022-08-24 | GSE189262 | GEO

Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

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

Expression data from epidermis specific phytochrome B or global phytochrome B line comparing to phyB-9 mutant.

Project description:Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.

2017-02-08 | GSE87591 | GEO

Two bHLH Transcription Factors, bHLH48 and bHLH60, Associate with PHYTOCHROME INTERACTING FACTOR 7 to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Project description:A ChIP-Seq was performed using 35S::PIF7-Flash and 35S::bHLH60-Flag transgenic plants after 1 hr shade treatment. Approximately 6374 peaks (5262 genes) were considered as high-confidence of PIF7 binding peaks (Fold change > 2, q-value < 0.05). And 2278 peaks (2143 genes) were considered as high-confidence of bHLH60 binding peaks. The bound genes of PIF7 significantly overlapped with bHLH60-bound genes. And, the transcriptional levels of PIF7 and bHLH60 co-bound genes were also regulated by PIF7 and bHLH48/60. Our results indicated PIF7 and bHLH60 form a heterodimer to bind to promoters of the common target genes and regulate their expressions.

2021-12-08 | GSE156584 | GEO

Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

2011-03-31 | GSE21684 | GEO

phytochrome A-mediated shade avoidance responses

Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.

2019-12-21 | GSE55899 | GEO

Downstream effectors of light- and phytochrome-dependent regulation of hypocotyl elongation in Arabidopsis thaliana.

Project description: Not available

| S-EPMC3597320 | biostudies-literature

Two bHLH Transcription Factors, bHLH48 and bHLH60, Associate with PHYTOCHROME INTERACTING FACTOR 7 to Regulate Hypocotyl Elongation in Arabidopsis thaliana

Project description:Two bHLH Transcription Factors, bHLH48 and bHLH60, Associate with PHYTOCHROME INTERACTING FACTOR 7 to Regulate Hypocotyl Elongation in Arabidopsis thaliana

| PRJNA658378 | ENA

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