Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Xu Gao

PROVIDER: E-GEOD-60835 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Publications

Arabidopsis DE-ETIOLATED1 represses photomorphogenesis by positively regulating phytochrome-interacting factors in the dark.

Dong Jie J Tang Dafang D Gao Zhaoxu Z Yu Renbo R Li Kunlun K He Hang H Terzaghi William W Deng Xing Wang XW Chen Haodong H

The Plant cell 20140923 9

Arabidopsis thaliana seedlings undergo photomorphogenic development even in darkness when the function of DE-ETIOLATED1 (DET1), a repressor of photomorphogenesis, is disrupted. However, the mechanism by which DET1 represses photomorphogenesis remains unclear. 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 sta ...[more]

PMID: 25248553

Similar Datasets

Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis.

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

Arabidopsis De-etiolated 1 Represses Photomorphogenesis by Positively Regulating Phytochrome Interacting Factors in the Dark

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

Analyses of blue light (BL) and CRY-regualted genes and genes dependent on auxin receptors by RNA-seq

Project description:Total RNA was extracted from samples including dark-grown WT and tir1 afb123, blue light-grown WT and cry1 cry2 seedlings in continuous conditions for 4.5 days and subjected to high throughput sequencing. Light and auxin co-regulate a variety of developmental processes. This study reveals the molecular basis for light and auxin crosstalk by analyzing gene expression profile under control of both signals. mRNA from dark-grown WT, BL-grown WT, BL-grown BL photoreceptors, and dark-grown auxin receptors was sequenced to analyze the genes regulated by CRY-mediated BL signaling and TIR1/AFBs-mediated auxin signaling.

2016-06-15 | E-GEOD-58552 | biostudies-arrayexpress

Analyses of genes regulated by the N-terminal photolyase homology region (CNT1/PHR) of CRY1 by RNA-seq

Project description:Total RNA was extracted from samples including 35S::CNT1-NLS-YFP;cry1 and 35S::CNT1-G283E-NLS-YFP;cry1 seedlings grown in continuous blue light and subjected to high throughput sequencing. Previous studies reported that the C-terminal domain of CRY1 regulates hypocotyl elongation and blue light-regulated genes. This study reveals that CNT1 overexpression also regulates blue light-regulated genes, supporting the role of CNT1 in hypocotyl elongation at transcriptomic level. mRNA from blue light-grown CNT1 or CNT1 variant (G283E) overexpressors was sequenced to analyze the genes regulated by CNT1.

2016-07-25 | E-GEOD-59763 | biostudies-arrayexpress

Gene expression in hemera mutants in red light condition

2014-06-01 | GSE43311 | GEO

Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis.

Project description:Arabidopsis PP6 phosphatases dephosphorylate PIF proteins to repress photomorphogenesis.

| PRJNA527851 | ENA

Gene expression in hemera mutants in red light condition

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

SKIP Confers Salt Tolerance through Controlling Gene Alternative Splicing in Arabidopsis

Project description:A better understanding of the mechanisms for plant in response to abiotic stresses is key for the improvement of plant to resistant to the stresses. Much has been known for the regulation of gene expression in response to salt stress at transcriptional level, however, little is known at posttranscriptional level for this response. Recently, we identified that SKIP is a component of spliceosome and is necessary for the regulation of alternative splicing and mRNA maturation of clock genes. In this study, we observed that skip-1 is hypersensitive to salt stress. SKIP is necessary for the alternative splicing and mRNA maturation of several salt tolerance genes, e.g. NHX1, CBL1, P5CS1, RCI2A, and PAT10. Genome-wide analysis reveals that SKIP mediates the alternative splicing of many genes under salt stress condition, most of the new alternative splicing events in skip-1 is intron retention, which leads to the premature termination codon in their mRNA. SKIP also controls the alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt stress condition. Therefore, this study addresses a fundamental question on how the mRNA splicing machinery contributes to salt response at a posttranscriptional level. Totally six samples, two treatments and two genotypes, and each have two replicats.

2015-04-01 | E-GEOD-55632 | biostudies-arrayexpress

Transcriptome-wide analysis of gene expression in dark-grown WT and pif mutant seedlings

Project description:We sequenced mRNA from WT and PhytochromeInteractingFactor (pif) mutant seedlings grown for 2d in darkness. Transcriptome profiles of the wild-type (WT), pif1, pif3, pif, pif5 monogenic mutants, pif3pif4pif5 (pif345), pif1pif4pif5(pif145), pif1pif3pif5 (pif135) and pif1pif3pif4 (pif134) triple mutants and pif1pif3pif4pif5 (pifq) quadruple mutant seedlings. Biological triplicate samples were analyzed from libraries constructed using a 3'-capture, 5' to 3' directional method.

2014-10-02 | E-GEOD-42665 | biostudies-arrayexpress

RNA-Seq Transcriptome Profiling Reveals Differentially Expressed Genes Involved in Sex Expression in Melon (Cucumis melo L.)

Project description:RNA-Seq was conducted among sergeant bulks of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg), a total of about 105 million reads were generated from the melon transcriptome using Solexa sequencing.Totally 79,698 unigenes were generated and 75,537 unigenes were mapped to 11,805 annotated proteins in assembled melon genome (Garcia-Mas et al., 2012). Transcripts related to photomorphogenesis and flower development in plants were found, Most of the genes encoding plant hormone metabolism related protein, others related to flora development including Tasselseeds and male sterility genes which in phytohormones pathway were also detected. Comparison each two bulks (AAGG:AAgg, AAGG:aaGG, aagg:AAgg and aaGG:aagg ) exhibited different profiles of putative genes (include 745, 1342, 858 and 571 different expression genes, respectively). mRNA profiles of four sex types of melon flowers, namely monoecious (AAGG), gynoecious (AAgg), hermaphrodite (aaGG), and andromonoecious (aagg) were were generated by deep sequencing using Illumina Hiseq 2000.

2014-06-15 | E-GEOD-57580 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data