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Transcriptome-wide analysis of gene expression in 4-day-old WT and athb1-1 mutant seedlings grown under short day conditions

ABSTRACT: To understand which genes acts downstream AtHB1 affecting hypocotyl growth in Arabidopsis thaliana, we performed transcriptional profiles of 4-day-old seedlings grown in a short-day regime comparing wild-type with athb1-1 mutant plants. These results show that some of the AtHB1-regulated genes modulate cell elongation, particularly cell wall composition and elongation, or encode proteins that serve as a source of carbon, nitrogen, and sulfur for early seedling growth.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE66666 | GEO | 2015/04/01

SECONDARY ACCESSION(S): PRJNA277695

REPOSITORIES: GEO

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Transcriptome-wide analysis of gene expression in 4-day-old WT and athb1-1 mutant seedlings grown under short day conditions

Project description:To understand which genes acts downstream AtHB1 affecting hypocotyl growth in Arabidopsis thaliana, we performed transcriptional profiles of 4-day-old seedlings grown in a short-day regime comparing wild-type with athb1-1 mutant plants. These results show that some of the AtHB1-regulated genes modulate cell elongation, particularly cell wall composition and elongation, or encode proteins that serve as a source of carbon, nitrogen, and sulfur for early seedling growth. RNA-Seq data for 4-day-old wild-type (Col-0) and athb1-1 mutant seedlings grown under short-day conditions. Biological triplicates were performed for each genotype analyzed.

2015-04-01 | E-GEOD-66666 | biostudies-arrayexpress

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

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]

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Proteomics Analysis of Soybean Hypocotyl during Recovery after Flooding Stress

Project description:Soybean (Glycine max L. cv Enrei) seeds were sterilized with 2% sodium hypochlorite solution and then thoroughly rinsed in water. The sterilized seeds were sown 4 cm inside surface of sand in 450 mL of quartz seedling cases wetted with 150 mL water and grown at 25°C and 70% humidity in a growth chamber (Sanyo, Tokyo, Japan) under white fluorescent light (160 μmol m-2 s-1, 16 h light period/day). Two-day-old soybeans were flooded for 2 days and hypocotyl samples were collected at the day of removal of flooding and then at 2 more points during the 4-day recovery period.

2015-05-26 | PXD001567 | Pride

Transcription profiling of Arabidopsis seedlings grown under light or dark conditions in a time series

Project description:Arabidopsis seedling were grown 3 days in complete darkness then put into normal light regime for 24 h<br>Seedling were harvesrted at 15 min, 1, 2, 4, 8, 24h

2011-01-05 | E-MEXP-2543 | biostudies-arrayexpress

Auxin signaling in the epidermis regulates stem growth via interactions with the brassinosteroid pathway

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. We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.

2016-06-30 | E-GEOD-79881 | biostudies-arrayexpress

Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

2011-03-31 | GSE21684 | GEO

Transcriptome analysis of the effect of far-red light on hypocotyl elongation of pumpkin

Project description:The mechanism of hypocotyl elongation in pumpkin mediate by end of day far red was analyzed by transcriptome analysis

2021-04-28 | GSE173421 | GEO

Expression data from Arabidopsis pifq seedlings grown in short days (SD) and in free running (LL) conditions.

Project description:Members of the PIF quartet (PIFq) (PIF1, PIF3, PIF4, and PIF5) collectively contribute to induce growth in Arabidopsis seedlings under short day (SD) conditions, specifically promoting elongation at dawn. Their action involves the direct regulation of growth-related and hormone-associated genes. The objective of this genomic analysis was to define a comprehensive set of SD-regulated genes at dawn compared to free-running (LL) conditions in the wild type, followed by identification of those SD-regulated genes whose expression depends on the presence of PIFq. By using this sequential strategy, our aim was to identify PIF/SD-coregulated genes.

2016-08-31 | GSE81813 | GEO

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