Genomewide identification of LHY binding targets
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE103785 | GEO | 2018/09/13
REPOSITORIES: GEO
Similar Datasets
Project description:The plant circadian enables plants to adjust their physiology and modulate their developmental responses in anticipation of diurnal and seasonal changes in environmental conditions. Thus, it makes an important contribution to overall fitness. The complex regulatory network underlying the oscillatory mechanism of the clock is now well characterised, but we still know relatively little about how downstream processes are controlled. In order to investigate this question we identified genes that are under direct control of one of the oscillator components, a MYB transcription factor known as LATE ELONGATED HYPOCOTYL (LHY).
2014-03-01 | GSE52175 | GEO
Project description:The plant circadian enables plants to adjust their physiology and modulate their developmental responses in anticipation of diurnal and seasonal changes in environmental conditions. Thus, it makes an important contribution to overall fitness. The complex regulatory network underlying the oscillatory mechanism of the clock is now well characterised, but we still know relatively little about how downstream processes are controlled. In order to investigate this question we identified genes that are under direct control of one of the oscillator components, a MYB transcription factor known as LATE ELONGATED HYPOCOTYL (LHY). 2-week-old wild-type (Ws) and LHY knock-out (lhy-21) seedlings were harvested 2 h after dawn. Tissue was cross-linked using 1% formaldehyde for 10 min. Chromatin was extracted and used for immunoprecipitation using an antibody to the full-length LHY protein. The immunoprecipitated DNA was sequenced using Illumina technology. LHY binding regions were identified as genomic regions that showed over-representation of reads in the wild-type sample as compared to the LHY knock-out sample.
2014-03-01 | E-GEOD-52175 | biostudies-arrayexpress
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
Project description:This a model from the article:
Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana.
Locke JC, Kozma-Bognár L, Gould PD, Fehér B, Kevei E, Nagy F, Turner MS, Hall A, Millar AJ
Mol. Syst. Biol.2006;Volume:2;Page:59
17102804,
Abstract:
Our computational model of the circadian clock comprised the feedback loop between LATE ELONGATED HYPOCOTYL (LHY), CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) and TIMING OF CAB EXPRESSION 1 (TOC1), and a predicted, interlocking feedback loop involving TOC1 and a hypothetical component Y. Experiments based on model predictions suggested GIGANTEA (GI) as a candidate for Y. We now extend the model to include a recently demonstrated feedback loop between the TOC1 homologues PSEUDO-RESPONSE REGULATOR 7 (PRR7), PRR9 and LHY and CCA1. This three-loop network explains the rhythmic phenotype of toc1 mutant alleles. Model predictions fit closely to new data on the gi;lhy;cca1 mutant, which confirm that GI is a major contributor to Y function. Analysis of the three-loop network suggests that the plant clock consists of morning and evening oscillators, coupled intracellularly, which may be analogous to coupled, morning and evening clock cells in Drosophila and the mouse.
The model describes a three loops model of the Arabidopsis circadian clock. It provides initial conditions, parameter values and reactions for the production rates of the following species: LHY mRNA (cLm), cytoplasmic LHY (cLc), nuclear LHY (cLn), TOC1 mRNA (cTm), cytoplasmic TOC1 (cTc), nuclear TOC1 (cTn), X mRNA (cXm), cytoplasmic X (cXc), nuclear X (cXn), Y mRNA (cYm), cytoplasmic Y (cYc), nuclear Y (cYn), nuclear P (cPn), APRR7/9 mRNA, cytoplasmic APRR7/9, and nuclear APRR7/9.
The paper describes the behaviour of the model in constant light (LL) and day-night cycle (LD). However, the current model only contains the LL cycle. Some parameter values should be changed from the wild-type (WT) ones in order to simulate the effect of mutations. These changes are listed in the notes of relevant parameters.
This model originates from BioModels Database: A Database of Annotated Published Models. It is copyright (c) 2005-2009 The BioModels Team.For more information see the terms of use.To cite BioModels Database, please use Le Novère N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., Hucka M. (2006) BioModels Database: A Free, Centralized Database of Curated, Published, Quantitative Kinetic Models of Biochemical and Cellular Systems Nucleic Acids Res., 34: D689-D691.
2024-09-02 | BIOMD0000000089 | BioModels
Project description:Plants are continuously exposed to varying environmental conditions; some anticipated diurnal changes in light and temperature and others far less predictable. Key to adaptation to a diurnal environment is the anticipation provided by the circadian clock, which coordinates broad changes in gene expression with a period of about 24 h.Here we present the analysis of RNA sequencing to measure transcript abundance over time in Brachypodium distachyon entrained in photo- and thermocycles then transferred to photocycles or thermocycles alone, or constant light and temperature conditions.
2019-05-19 | E-MTAB-7950 | biostudies-arrayexpress
Project description:Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs). Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids. Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids. Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth. Consistently, repressing the stress genes in diploids increased growth vigor. We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor. Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids. Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids. Examination of gene expression in Arabidopsis thaliana F1 hybrids between Col and C24 and 3 time points using mRNA-seq
2015-05-31 | E-GEOD-51578 | biostudies-arrayexpress
Project description:The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies. ChIP-Seq of CCA1-GFP plants under control of the CCA1 promoter in continuous light and diel conditions
2015-07-26 | E-GEOD-70533 | biostudies-arrayexpress
Project description:Circadian clocks are gene networks producing 24-h oscillations at the level of clock gene expression that is synchronized to environmental cycles via light signals. The ELONGATED HYPOCOTYL 5 (HY5) transcription factor is a signalling hub acting downstream of several photoreceptors and is a key regulator of photomorphogenesis. Here we describe a mechanism by which light quality could modulate the pace of the circadian clock through controlling abundance of HY5. We show that hy5 mutants display remarkably shorter period rhythms in blue but not in red light or darkness and blue light is more efficient than red to induce accumulation of HY5 at transcriptional and post-transcriptional levels. We demonstrate that the pattern and level of HY5 accumulation modulates its binding to specific promoter elements of majority of clock genes, but only a few of these show altered transcription in the hy5 mutant. Mathematical modelling suggests that the direct effect of HY5 on the apparently non-responsive clock genes could be masked by feed-back from the clock gene network. We conclude that the information on the ratio of blue and red components of the white light spectrum is decoded and relayed to the circadian oscillator, at least partially, by HY5.
2018-09-05 | GSE117797 | GEO
Project description:The plant circadian clock exerts a critical role in the regulation of multiple biological processes including responses to biotic and abiotic stresses. It is estimated that the clock regulates up to 80% of the transcriptome in Arabidopsis, thus understanding the molecular mechanisms that control this rhythmic transcriptome requires identification of the targets of each clock component. The Arabidopsis core clock is partially comprised of a transcriptional regulatory loop between the MYB domain containing transcription factors CIRCADIAN CLOCK ASSOCIATED1 (CCA1) and LATE ELONGATED HYPOCOTYL (LHY), and TIMING OF CAB EXPRESSION1 (TOC1). As a key component of the clock, CCA1 is able to initiate and set the phase of clock-controlled rhythms. CCA1 regulates the transcription of several genes by directly binding to the evening element (EE) motif primarily found in the promoters of evening expressed genes. Using a genome-wide approach we have identified direct targets of CCA1 in plants grown in constant (LL) and driven conditions (LD). These CCA1 targets are enriched for a myriad of biological processes and stress responses. While many of these target genes are evening phased and contain the EE in their promoter regions, a significant subset is morning phased and lack an EE. Furthermore, several CCA1 targets do not cycle in either LL or LD or both. Expression analysis in CCA1 overexpressing plants confirms CCA1 regulation of analyzed targets. Our results emphasize an expanded role for the circadian clock in regulation of key pathways in Arabidopsis, and provide a comprehensive and solid resource for future functional studies.
2015-07-26 | GSE70533 | GEO
Project description:Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs). Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids. Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids. Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth. Consistently, repressing the stress genes in diploids increased growth vigor. We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor. Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids. Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids.
2015-05-31 | GSE51578 | GEO