Identifying Y candidate genes
Ontology highlight
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: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: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: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: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:The plant pathogenic fungus Verticillium dahliae has homologs of the clock genes [Cascant-Lopez et al., 2020], which are well described in Neurospora crassa [Diernfellner et al., 2020]. In N. crassa, frequency (Frq) and the Frq-interacting RNA helicase (Frh) interact and form the Frq-Frh complex [Cheng et al., 2005]. Formation of this complex was described to be still possible but weakened by a single amino acid exchange of arginine 806 of Frh to histidine (Frh^R806H) [Shi et al., 2010; Conrad et al., 2016]. We found that both FRQ and wild-type FRH were required for enhanced conidiation and the light-dependent repression of microsclerotia formation in V. dahliae, but were dispensable for disease induction in tomato plants. Strikingly, the FRH^R806H mutant strain grew similar to the FRQ deletion strain, although transcript and protein levels of Frq were not significantly affected by the FRH^R806H mutation when compared with the wild-type. Therefore, we hypothesized that V. dahliae Frq and Frh form the Frq-Frh complex to regulate V. dahliae development, and that this complex formation is abolished upon the amino acid exchange in the Frh. By the use of protein pull-downs, potential interactions of Frh-GFP or Frh^R806H-GFP with Frq were investigated. While we found evidence for a direct interaction of Frh-GFP and Frq, no proteins were significantly co-enriched with Frh^R806H-GFP. References: Cascant-Lopez, E.; Crosthwaite, S.K.; Johnson, L.J.; Harrison, R.J. No evidence that homologs of key circadian clock genes direct circadian programs of development or mRNA abundance in Verticillium dahliae. Front Microbiol 2020, 11, 1977, doi:10.3389/fmicb.2020.01977. Diernfellner, A.C.R.; Brunner, M. Phosphorylation timers in the Neurospora crassa circadian clock. J Mol Biol 2020, 432, 3449–3465, doi:10.1016/j.jmb.2020.04.004. Cheng, P.; He, Q.; He, Q.; Wang, L.; Liu, Y. Regulation of the Neurospora circadian clock by an RNA helicase. Genes Dev 2005, 19, 234–241, doi:10.1101/gad.1266805. Shi, M.; Collett, M.; Loros, J.J.; Dunlap, J.C. FRQ-interacting RNA helicase mediates negative and positive feedback in the Neurospora circadian clock. Genetics 2010, 184, 351–361, doi:10.1534/genetics.109.111393. Conrad, K.S.; Hurley, J.M.; Widom, J.; Ringelberg, C.S.; Loros, J.J.; Dunlap, J.C.; Crane, B.R. Structure of the frequency‐interacting RNA helicase: a protein interaction hub for the circadian clock. EMBO J 2016, 35, 1707–1719, doi:10.15252/embj.201694327.
2023-07-12 | PXD041716 | Pride
Project description:Disruption of the circadian rhythm is associated with inflammatory diseases, metabolic syndrome and cancer. In mice, the time of day strongly influences lethality in response to LPS, with survival greatest at the beginning compared to the end of the light cycle (Halberg et al. 1960; Marpegan et al. 2009; Nguyen et al. 2013). Myeloid-cell intrinsic circadian clock components control inflammatory cytokine production (Gibbs et al. 2012; Curtis et al. 2015; Bellet et al. 2013), and metabolic inputs influence lethality in response to LPS (Wang et al. 2016; Weis et al. 2017; Traba et al. 2017), but the relative contributions of these inputs to daily changes in sepsis susceptibility are not known. Here we show that feeding, rather than light, controls time of day dependent LPS sensitivity. Mortality following LPS administration after 12 hours of food deprivation was associated with hypoglycemia, rather than inflammatory cytokine production, independent of the clock regulator BMAL1 expressed in myeloid cells. Deletion of BMAL1 in hepatocytes globally disrupted the transcriptional response to the feeding cycle in the liver and resulted in constitutively high LPS sensitivity. These results show that food, rather than light, is the ‘zeitgeber’ for acute mortality in response to LPS, with a critical role for the hepatocyte-intrinsic circadian clock in integrating nutritional cues to regulate survival in response to innate immune stimuli. Understanding the hepatic molecular programs operational in response to fasting versus fed cues could identify novel pathways that may be targeted to enhance resistance to endotoxemia.
2020-12-31 | GSE123909 | GEO
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:Previous studies have shown that a considerable proportion of the Arabidopsis genome cycles under circadian and/or diurnal conditions (Edwards et al., 2006 PMID: 16473970, Blaesing et al., 2005 PMID 16299223). It is likely that the correct phasing of gene expression plays an important role in improving the growth of the model plant (Dodd et al., 2005 PMID: 16040710). A key question is whether similar regulation is occurring in other higher plant species. In this study we measure the diurnal expression pattern of genes in the T89 clone of the hybrid aspen (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark). Time-points were labelled relative to dawn (time 0) on the first day of sampling. T89 was selected as it has routinely been used for genetic modification since 1992 (Nilsson et al.) and is the genetic background for a large number of transgenic trees created in order to investigate the function of aspen genes, providing potential for genetic manipulations during our further studies. We also measured the diurnal expression pattern of genes in trees with a compromised circadian clock. Trees with less expressed LATE ELONGATED HYPOCOTYL 1 (LHY1) and LHY2 by RNA interference (lhy) line that was created in T89 clone of the aspen hybrid (Populus tremula L. x P. tremuloides Michx.) using the Affymetrix Poplar array. Samples (leaf blades) were taken at 4h intervals over the course of 2 diurnal cycles (18h Light: 6h Dark) as described above. Thus, time-points are labelled relative to dawn (time 0) on the first day of sampling. The data obtained from using a RNAi line in central Clock components complements the study of wild type T89, since they were grown and sampled at the same time under the same conditions.
2018-03-13 | E-MTAB-4516 | biostudies-arrayexpress