Identifying Y candidate genes
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE19263 | GEO | 2009/12/10
SECONDARY ACCESSION(S): PRJNA120931
REPOSITORIES: GEO
Similar Datasets
Project description:The circadian clock generates biological rhythms with a period of approximately 24 hours. Using microarray experiments, we have previously shown that approximately 16% of the Arabidopsis genome is regulated in a circadian manner (Edwards et al., 2006). Previous work from our lab in modelling the molecular oscillator of Arabidopsis introduced a hypothetical component Y into an evening loop of the clock gene network (Locke et al., 2005). GIGANTEA (GI) was suggested as a strong candidate for Y based on genetic evidence and its close matching of the expression profile predicted by the mathematical modelling. Recent experimental evidence suggests that GI may only partially account for the function of Y. Thus, we are undertaking a genomics approach to identify other candidate genes that match the predicted expression profile of Y. Samples were taken from wild type and lhy cca1 double mutant seedlings from 4 timepoints around the night to day transition (-15mins, +15mins, +30mins and +60mins) after 9 days of growth in 18:6 light dark cycles. We aim to identify genes showing the light induction response predicted for Y around dawn. 16 samples were used in this experiment.
2009-12-09 | E-GEOD-19263 | biostudies-arrayexpress
Project description:Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Hence: 13 RNA samples on 13 chips in total. METHOD: Seed was sown on MS agar plates with 3% sucrose, imbibed at 4 C for 96 hours. Seed was then entrained for 7 days at 22C, in cycles of 12 hours white light, 12 hours darkness. After 7 days they were transferred to constant white light at 22 C: this is time 0h. Tissue harvested at the time points shown after time 0. Experimenter name = Kieron Edwards; Experimenter phone = 024 7652 8374; Experimenter fax = 024 7652 3701; Experimenter department = Department of Biological Sciences; Experimenter institute = University of Warwick; Experimenter address = Department of Biological Sciences; Experimenter address = University of Warwick; Experimenter address = Gibbet Hill Road; Experimenter address = Coventry; Experimenter zip/postal_code = CV4 7AL; Experimenter country = UK Experiment Overall Design: 13 samples were used in this experiment
2008-06-13 | E-GEOD-5612 | biostudies-arrayexpress
Project description:GIGANTEA (GI) is an important modulator of plant circadian system. Recent studies have reported that protein GI is localized in both nucleus and cytosol, and nuclear and cytosolic GI exert differential effect on plant circadian clock. We first generated GI-null mutants and transgenic Arabidopsis plants that expressed GI fused to green fluorescent protein gene (GIpro::GI-GFP) and GI-GFP with a nuclear localization signal (GIpro::GI-GFP-NLS) or with a nuclear export signal (GIpro::GI-GFP-NES) under the control of native promoter in GI-null mutants. To investigate differential roles of nuclear and cytosolic GI in regulating plant circadian clock, we performed genome-wide gene expression profiling for wild-type plants and the GI-transgenic plants at morning and evening, and analyzed complementation patterns of gi-2 lesion by nuclear and cytosolic GI. As a result, we identified four complementation patterns representing genes affected by only nuclear GI (GIN) or cytosolic GI (GIC), those by either GIN or GIC, and those by the action of both GIN and GIC. Furthermore, we compared the transgenic plants expressing GIpro::GI-GFP with WT and the other GI-transgenic plants to confirm whether abnormally expressed genes by the gi-2 mutation can be complemented by restoring protein GI. Wild-type plants (Col), GI-null mutants (gi-2), and the other transgenic gi-2 plants expressing GIpro::GI-GFP (called GI plants), GIpro::GI-GFP-NLS (called GI-NLS plants), and GIpro::GI-GFP-NES (called GI-NES plants) were grown for seven days under conditions of 16 h light and 8 h dark (LD) and harvested at 1h (ZT1) and 16 hr (ZT16) after the light is turned on, representing morning and evening, respectively. mRNA levels were measured from three biological replicates of Col, gi-2, GI-NLS, GI-NES, and GI.
2013-09-01 | E-GEOD-47169 | biostudies-arrayexpress
Project description:Our aim is to study the circadian expression of genes to aid in our attempt of modelling the Arabidopsis circadian clock. Circadian microarray data have previously been published for plants after white light (WL)-dark cycles, using the 8k chip (Harmer et al. 2000). We intend to repeat this experiment using the 26k chips and are coordinating with Dr. Harmer, who is pursuing complementary experiments in UC Davis. Plants will be transferred to continuous WL after entrainment to 12h:12h light dark cycles. RNAs will be harvested every 4 hours over two days, with the same accession and sampling intervals used previously by Harmer et al. The two days of sampling provide internal replication. Our experience shows that this is the most economical design: it is easier to identify rhythms over a two-day timecourse than in two replicates of a single day. Hence: 13 RNA samples on 13 chips in total. METHOD: Seed was sown on MS agar plates with 3% sucrose, imbibed at 4 C for 96 hours. Seed was then entrained for 7 days at 22C, in cycles of 12 hours white light, 12 hours darkness. After 7 days they were transferred to constant white light at 22 C: this is time 0h. Tissue harvested at the time points shown after time 0. Experimenter name = Kieron Edwards Experimenter phone = 024 7652 8374 Experimenter fax = 024 7652 3701 Experimenter department = Department of Biological Sciences Experimenter institute = University of Warwick Experimenter address = Department of Biological Sciences Experimenter address = University of Warwick Experimenter address = Gibbet Hill Road Experimenter address = Coventry Experimenter zip/postal_code = CV4 7AL Experimenter country = UK Keywords: time_series_design, growth_condition_design
2007-01-08 | GSE5612 | GEO
Project description:Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth. The genetic interactions between GI and ELF4 could be time-dependent functional dominance along a day, called temporal dominance hereafter. To test this hypothesis, we performed gene expression profiling of WT, gi-2, elf4 and gi elf4 plants at dawn (ZT1) and dusk (ZT16).
2012-06-30 | E-GEOD-32938 | biostudies-arrayexpress
Project description:Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional, unrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters. This research has been described more fully in Schaffer R et al.(2001) Plant Cell 13:113-123 Keywords = circadian rhythm Keywords: other
2001-07-20 | GSE4 | GEO
Project description:The circadian clock is comprised of proteins that form negative feedback loops, which regulate the timing of global gene expression in a coordinated 24 hour cycle. As a result, the plant circadian clock is responsible for regulating numerous physiological processes central to growth and survival. To date, most plant circadian clock studies have relied on diurnal transcriptome changes to elucidate molecular connections between the circadian clock and observable phenotypes in wild-type plants. Here, we have combined high-throughput RNA-sequencing and mass spectrometry to comparatively characterize the lhycca1, prr7prr9, gi and toc1 circadian clock mutant rosette transcriptome and proteome at the end-of-day and end-of-night.
2018-01-02 | PXD004763 | Pride
Project description:Plants use their endogenous clock to regulate many physiological processes related to their survival and adaptability. GIGANTEA (GI), one of the clock proteins, contributes to the maintenance of circadian period length and amplitude and also regulates flowering time and hypocotyl growth in response to day length. In addition to GI, EARLY FLOWERING 4 (ELF4), another clock regulator, also contributes to these processes. However, little is known about the overall interactions between GI and ELF4 in Arabidopsis. In this study, we investigated the genetic interactions between GI and ELF4 in circadian output regulation. The results show that GI is dominant to ELF4 in flowering time determination, but ELF4 is dominant to GI in hypocotyl growth regulation. Moreover, GI and ELF4 have a synergistic effect on endogenous clock regulation. Further, gene expression profiling of gi-2, elf4, and gi-2 elf4 mutants confirmed that GI and ELF4 had differential dominant effects on circadian physiological outputs at dawn and dusk, respectively. This differential dominance of GI and ELF4 provides a potential means to achieve the diversity in the regulation of circadian physiological outputs including flowering time and hypocotyl growth.
2012-07-01 | GSE32938 | GEO
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
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.
2015-07-31 | GSE59996 | GEO