Arabidopsis thaliana
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-60835
PROVIDER: PRJNA259643 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs. Total of twelve samples, two treatments and three genotypes, and each have three replicates.
2015-03-19 | E-GEOD-60835 | biostudies-arrayexpress
Project description:Arabidopsis seedlings undergo photomorphogenic development even in darkness when the function of De-etiolated 1 (DET1), a repressor of photomorphogenesis, is disrupted. Our results indicate that DET1 directly interacts with a group of transcription factors known as the phytochrome-interacting factors (PIFs). Furthermore, our results suggest that DET1 positively regulates PIF protein levels primarily by stabilizing PIF proteins in the dark. Genomic analysis also revealed that DET1 may control the expression of light-regulated genes to mediate photomorphogenesis partially through PIFs.
2015-03-19 | GSE60835 | GEO
Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.
2019-03-28 | GSE115584 | GEO
Project description:Etiolated Arabidopsis seedlings open their cotyledons and halt rapid elongation of hypocotyl when exposed to light (de-etiolation). Major light responsive components in this process have been identified and signaling pathways revealed, yet how the organ-specific light responses are achieved remains unknown. Here we report that a developmental regulator TCP4 (TEOSINTE BRANCHED1, CYCLOIDEA, and PCF) participates in photomorphogenesis and facilitates light-induced cotyledon-opening. We demonstrate that TCP4-like transcriptional factors, which predominantly express in cotyledons of both light and dark seedlings, activate SAUR16 and SAUR50 in response to light. Light repressor PIF3 (or PIFs, phytochrome-interacting factors), which accumulates in etiolated seedlings and rapidly declines upon light exposure, inhibits TCP4 promoter-binding and prevents activation of SAUR16/50 in darkness. Our study reveals how an interplay between light responsive factors and developmental regulators leads to signal-dependent and tissue-specific regulation of gene expressions, which ultimately resulted in organ-specific light responses during de-etiolation.
2019-03-28 | GSE115358 | GEO
Project description:Light-induced phosphorylation is necessary and essential for the degradation of phytochrome-interacting factors (PIFs), the central repressors of photomorphogenesis. Although the kinases responsible for PIF phosphorylation have been extensively studied, the phosphatases underlying PIF dephosphorylation are largely unknown. Here, we real that mutation of FyPP1 and FyPP3, two catalytic subunits of PP6 phosphatases, promoted photomorphogenesis of seedlings in the dark. PP6 and PIFs functioned synergistically to repress photomorphogenesis. FyPP1 and FyPP3 directly interacted with and dephosphorylated PIF3 and PIF4. The light-induced degradation of PIF4 and the PIF transcriptional activities were dependent on PP6 activity. These data demonstrate that PP6 phosphatases repress photomorphogenesis through regulation of PIF phosphorylation, protein stability and transcriptional activity.
2019-09-04 | GSE128498 | GEO
Project description:The developmental switch from skotomorphogenesis to photomorphogenesis is critical for the survival and growth of plants, but its regulatory mechanism remains unclear. Here, we report that the steroid hormone brassinosteroids (BRs) play crucial roles in the transition from skotomorphogenesis to photomorphogenesis by regulating chlorophyll biosynthesis to promote the greening of etiolated seedlings upon light exposure. Seedlings of BR-deficient mutant det2-1 accumulated excess protochlorophyllide when grown in darkness, resulting in photo-oxidative damage upon exposure to light. Conversely, the gain-of-function mutant bzr1-1D suppressed the protochlorophyllide-accumulated phenotype of det2-1, thereby promoting greening of etiolated seedlings. Genetic analysis indicated that phytochrome-interacting factors (PIFs) were required for BZR1-promoted seedlings greening. Furthermore, we revealed that the GROWTH REGULATING FACTOR 7 (GRF7) and GRF8 were induced by BZR1 and PIF4 to repress the chlorophyll biosynthesis and promote seedling greening. Suppression the functions of GRFs by overexpressing microRNA396a (miR396a) caused the high-accumulated photochlorophyllide in darkness and more serious photobleach upon light exposure. Additionally, BZR1, PIF4 and GRF7 interact with each other and precisely regulate the expression of chlorophyll biosynthetic genes. Our findings revealed an essential role of brassinosteroid in promoting seedling development and survival during the critical initial emergence of seedlings from subterranean darkness to sunlight.
2020-06-01 | GSE149834 | GEO
Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations
2010-05-01 | GSE19843 | GEO
Project description:The hemera (hmr) mutant was identified as the first photomorphogenetic mutant with the combination of long hypocotyl and albino phenotypes in the light. Phytochrome-Interacting bHLH transcription Factors (PIFs), which are repressors of photomorphogenesis accumulate in darkness and are degraded in the light in a phytochrome-dependent manner. Two PIFs, PIF1 and PIF3 accumulated in the light in hmr mutants. In order to determine the gene expression of PIF-dependent genes in hmr mutants in the light, we have performed whole-genome expression analysis on two hmr mutants: a null allele, hmr-5; and a weak allele, hmr-22. Wild-type (Col-0) and hmr mutant seeds were surface-sterilized and plated on half-strength Murashige and Skoog (MS) growth medium without sucrose. The seeds were stratified in the dark at 4ºC for 4d. Seedlings were grown in constant red light (Rc, 10?mol/m2/s) at 21°C for 4d.
2014-06-01 | E-GEOD-43311 | biostudies-arrayexpress
Project description:rs09-01_det1 - photomorphogenesis - - Identification of the genes deregulated in det1-1 when seedlings grow in light or in dark (dark increase morphological differences between det1-1 and wild-type) - Expression profile of seedlings grown in dark then exposed to light - etiolated seedlings (5days) are briefly exposed to light to induce developmental transition between skoto- and photomorphogenesis without visible change in plant morphology and differences between col0 and the mutant det1-1 grown in light or in dark Keywords: treatment variations 6 dye-swap - CATMA arrays
2010-04-30 | E-GEOD-19843 | biostudies-arrayexpress
Project description:Light, an important environmental factor regulates most of plant physiology and development. In the photomorphogenic stage, light globally enhances translation status in de-etiolating Arabidopsis seedlings. More than 1500 genes showed increased translation but not transcription in this developmental process. This implies these mRNAs are translationally repressed in dark-grown seedlings. Through transcriptome and translatome comparisons, we revealed that p-bodies attenuate the translation of mRNAs in the etiolated seedlings. We found hundreds of mRNAs accumulated and also increased translation for thousands of genes in dark-grown dcp5-1, including genes known to regulate the transition from skotomorphogenesis to photomorphogenesis. Our data reports p-bodies regulate both RNA stability and attenuation of translation for specific mRNAs in the dark.
2019-06-20 | GSE107892 | GEO