Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

H3K27me3 and H3K4me3 profiles in chr4/pkr1 and WT [RNA-seq]

ABSTRACT: Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that act in the shoot apical meristem to mediate the floral transition. Many characterized mutations impair environmental flowering responses, however downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant in which several environmental pathways are impaired and showed that its flowering responses to changes in photoperiod and ambient temperature are almost abolished. Analysis of the quintuple mutant by RNA-seq showed that expression of gibberellin biosynthetic genes and transcription factors that contribute to the age pathway correlate with flowering. Mutagenesis of the quintuple mutant recovered two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The causal genes were identified by isogenic mapping and transgenic complementation. The qem1 mutation was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, qem2 is in CHROMATIN REMODELING 4 (CHR4), which was not previously genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 plays important roles in the inflorescence meristem to promote floral identity.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE140726 | GEO | 2020/02/14

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Role of CHR4 during floral transition

Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that mediate floral transition in the shoot apical meristem. Many characterized mutations disrupt these environmental responses, but downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant impaired in several environmental pathways and showed that it possesses severely reduced flowering responses to changes in photoperiod and ambient temperature. RNA-seq analysis of the quintuple mutant showed that the expression of genes encoding gibberellin biosynthesis enzymes and transcription factors involved in the age pathway correlates with flowering. Mutagenesis of the quintuple mutant generated two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The mutated genes were identified by isogenic mapping and transgenic complementation. The qem1 mutant was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, the qem2 mutation is in CHROMATIN REMODELING 4 (CHR4), which has not been genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 mediates the response to endogenous flowering pathways in the inflorescence meristem to promote floral identity.

2020-03-02 | PXD016457 | Pride

H3K27me3 and H3K4me3 profiles in chr4/pkr1 and WT [ChIP-seq]

Project description:Several pathways conferring environmental flowering responses in Arabidopsis converge on developmental processes that act in the shoot apical meristem to mediate the floral transition. Many characterized mutations impair environmental flowering responses, however downstream developmental processes have been more refractory to mutagenesis. We constructed a quintuple mutant in which several environmental pathways are impaired and showed that its flowering responses to changes in photoperiod and ambient temperature are almost abolished. Analysis of the quintuple mutant by RNA-seq showed that expression of gibberellin biosynthetic genes and transcription factors that contribute to the age pathway correlate with flowering. Mutagenesis of the quintuple mutant recovered two late-flowering mutants, quintuple ems 1 (qem1) and qem2. The causal genes were identified by isogenic mapping and transgenic complementation. The qem1 mutation was an allele of ga20ox2, confirming the importance of gibberellin for flowering in the absence of environmental responses. By contrast, qem2 is in CHROMATIN REMODELING 4 (CHR4), which was not previously genetically implicated in floral induction. Using co-immunoprecipitation, RNA-seq and ChIP-seq, we show that CHR4 interacts with transcription factors involved in floral meristem identity and affects expression of key floral regulators. We conclude that CHR4 plays important roles in the inflorescence meristem to promote floral identity.

2020-02-14 | GSE140727 | GEO

Transcription profiling of Arabidopsis micro-dissected apical tissue harvested 0, 3, 5, and 7 days after the shift to LD from SD

Project description:Floral transition and flower development are regulated by numerous environmental and endogenous signals, which are integrated at a relatively small number of floral integrators, such as FLOWERING LOCUS T (FT) and SUPPRESSOR OF CONSTANS OVEREXPRESSION 1 (SOC1). Of the environmental factors, photoperiod is regarded the most important one in promoting floral transition in Arabidopsis thaliana and most labstrains will flower earlier under long day (LD) conditions than under short day (SD) conditions. Arabidopsis is therefore considered a facultative LD plant. To monitor gene expression changes during floral transition and early flower development plants were grown under SD (9 hr light, 15 hr dark) for 30 days. Plants were then shifted to LD (16 hr light, 8 hr dark) conditions to induce flowering. RNA was isolated from micro-dissected apical tissue harvested 0, 3, 5, and 7 days after the shift to LD and double-stranded cDNA was synthesized. Biotinylated cRNA probes were prepared and hybridized to the Affymetrix ATH1 array in duplicate (biological replicates). To study floral transition, we not only analyzed response of wildtype Landsberg erecta (Ler) plants, but also the effect of mutants in the flowering time genes CONSTANS (CO; co-2) and FT (ft-2). Early flower development was analyzed by comparing Col-0 wildtype plants with the meristem identity mutant lfy-12 (Col-0).

2022-11-20 | E-AFMX-8 | biostudies-arrayexpress

Global transcriptome analysis identifies genes regulated by FDP

Project description:Flowering of Arabidopsis is induced at the shoot meristem by environmental and endogenous signals. FLOWERING LOCUS T (FT) protein is a systemic signal that induces rapid flowering in response to long summer days (LDs) whereas gibberellin (GA) growth regulators trigger flowering by default in short days (SDs). Mutations in the bZIP transcription factor FDP, which physically interacts to FT, cause late flowering and dwarfism. In order to study the genetic pathways affected by FDP, we compared the global transcriptome changes of Col-0 plants carrying a fusion of the strong ubiquitously expressed CaMV35S promoter to an FDP DsRNAi construct (35S::FDP dsRNA).

2019-12-31 | GSE48948 | GEO

Transcriptional responses analysis of the inflorescence meristems in Jatropha curcas following gibberellin treatment

Project description:Our results showed that 951 differentially expressed genes (DEGs) were obtained to response to gibberellin treatment. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide signaling transduction pathways were repressed after exogenous GA3 treatment. However, the DEGs (JcAHP1, JcHK3, and JcMYC2, JcMYC4) which were respectively associated with cytokinin and jasmonic acid signaling were up-regulation for 24-h time point following GA3 treatment. In addition, the floral meristem determinacy genes (JcLFY and JcSOC1) and floral organ identity genes (JcAP3, JcPI, and JcSEP1-3) were significantly up-regulated, but their negative factor (JcSVP) was down-regulated after GA3 treatment.

2021-12-31 | GSE107561 | GEO

Transcriptome analysis of the shoot apical meristem (SAM) of WT tomato and the late termination (ltm) mutant [exp2]

Project description:Enlargement and doming of the shoot apical meristem (SAM) is a hallmark of the transition from vegetative growth to flowering. While this change is widespread, its role in the flowering process is unknown. The late termination (ltm) tomato mutant shows severely delayed flowering and precocious doming of the vegetative SAM. LTM encodes a kelch domain-containing protein, with no link to known meristem maintenance or flowering time pathways. LTM interacts with the TOPLESS (TPL) corepressor and with several transcription factors, providing specificity for its repressive functions. A sub-group of flowering-associated genes are precociously upregulated in vegetative stages of ltm SAMs, among them, the antiflorigen gene SELF PRUNING (SP). A mutation in SP restored the structure of vegetative SAMs in ltm sp double mutants and late flowering was partially suppressed, suggesting LTM functions to suppress SP in the vegetative SAM. In agreement, SP-overexpressing wild type plants exhibited precocious doming of vegetative SAMs combined with late flowering, as found in ltm plants. Strong flowering signals can result in termination of the SAM, usually by its differentiation into a flower. We propose that activation of a floral antagonist that promotes SAM growth in concert with floral transition protects it from such terminating effects.

2017-04-08 | GSE95114 | GEO

Transcriptome analysis of the shoot apical meristem (SAM) of WT tomato and the late termination (ltm) mutant [exp1]

2017-04-08 | GSE95110 | GEO

Analysis of PHOTOPERIOD SENSITIVITY5 Sheds Light on the Role of Phytochromes in Photoperiodic Flowering in Rice

Project description:A great majority of plants synchronize flowering with day length. In rice, the most important environmental cue that triggers flowering is the photoperiod. Here, we show that the s73 mutant, identified in a gamma irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the SE5 gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants showed a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of Hd3a, the most important floral integrator. Ehd1, an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds implies that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering affecting both Hd1 and Ehd1 flowering pathways.

2009-12-31 | GSE16796 | GEO

Comparison of gene expression in wild-type and rpl-1 Arabidopsis inflorescence apices

Project description:The Arabidopsis thaliana REPLUMLESS gene (RPL), also known as PENNYWISE (PNY) and BELLRINGER (BLR) encodes a BEL1-like TALE homeodomain (BLH) transcription factor that controls multiple aspects of meristem and floral development, including meristem maintenance, phyllotaxis, the transition to flowering, stem development and floral organ patterning [1-3]. As part of a screen for genes that mediate the function of RPL in the processes above, we compared gene expression in inflorescence apices of wild-type (Landsberg-erecta) and the rpl-1 mutant [2]. 1. Byrne, M.E., Groover, A.T., Fontana, J.R., and Martienssen, R.A. (2003). Development 130, 3941-3950. 2. Roeder, A.H.K., Ferrandiz, C., and Yanofsky, M.F. (2003). Current Biology 13, 1630-1635. 3. Smith, H.M.S., and Hake, S. (2003). Plant Cell 15, 1717-1727.

2016-09-22 | GSE78511 | GEO

Identification of genes regulated by GIGANTEA (GI), the CYCLING DOF FACTORS (CDFs) and the GI-CDF module

Project description:Plants monitor and integrate temperature, photoperiod and light quality signals to respond to continuous changes in their environment. The GIGANTEA (GI) protein is central in diverse signaling pathways, including photoperiodic, sugar and light signaling pathways, stress responses and circadian clock regulation. Previously, GI was shown to activate expression of the key floral regulators CONSTANS (CO) and FLOWERING LOCUS T (FT) by facilitating degradation of a family of CYCLING DOF FACTOR (CDF) transcriptional repressors. However, whether CDFs are implicated in other processes regulated by GI remains unclear. We investigated the contribution of the GI-CDF module to traits that depend on GI. Transcriptome profiling indicated that mutations in GI and the CDFs have antagonistic effects on expression of a wider set of genes than CO and FT, whilst other genes are regulated by GI independently of the CDFs. Detailed expression studies followed by phenotypic assays showed that the CDFs function downstream of GI to control responses to freezing temperatures and growth, but are not necessary for proper clock function. Thus GI-mediated regulation of CDFs contributes to several processes in addition to flowering, but is not implicated in all of the phenotypes influenced by GI. Seedlings of Col-0, the cdf1-R cdf2-1 cdf3-1 cdf5-1 quadruple mutant, gi-100 and gi-100 cdf1-R cdf2-1 cdf3-1 cdf5-1 quintuple mutant were grown for 10 days under LD conditions (16h light/8h dark). The aerial part of the seedlings was collected at ZT12 and RNA was prepared from three biological replicas

2015-07-31 | E-GEOD-59996 | 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