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Zhang Y, Wu Z, Feng M, Chen J, Qin M, Wang W, Bao Y, Xu Q, Ye Y, Ma C, Jiang CZ, Gan SS, Zhou H, Cai Y, Hong B, Gao J, Ma N. The circadian-controlled PIF8-BBX28 module regulates petal senescence in rose flowers by governing mitochondrial ROS homeostasis at night. THE PLANT CELL 2021; 33:2716-2735. [PMID: 34043798 PMCID: PMC8408477 DOI: 10.1093/plcell/koab152] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 05/19/2021] [Indexed: 05/20/2023]
Abstract
Reactive oxygen species (ROS) are unstable reactive molecules that are toxic to cells. Regulation of ROS homeostasis is crucial to protect cells from dysfunction, senescence, and death. In plant leaves, ROS are mainly generated from chloroplasts and are tightly temporally restricted by the circadian clock. However, little is known about how ROS homeostasis is regulated in nonphotosynthetic organs, such as petals. Here, we showed that hydrogen peroxide (H2O2) levels exhibit typical circadian rhythmicity in rose (Rosa hybrida) petals, consistent with the measured respiratory rate. RNA-seq and functional screening identified a B-box gene, RhBBX28, whose expression was associated with H2O2 rhythms. Silencing RhBBX28 accelerated flower senescence and promoted H2O2 accumulation at night in petals, while overexpression of RhBBX28 had the opposite effects. RhBBX28 influenced the expression of various genes related to respiratory metabolism, including the TCA cycle and glycolysis, and directly repressed the expression of SUCCINATE DEHYDROGENASE 1, which plays a central role in mitochondrial ROS (mtROS) homeostasis. We also found that PHYTOCHROME-INTERACTING FACTOR8 (RhPIF8) could activate RhBBX28 expression to control H2O2 levels in petals and thus flower senescence. Our results indicate that the circadian-controlled RhPIF8-RhBBX28 module is a critical player that controls flower senescence by governing mtROS homeostasis in rose.
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Affiliation(s)
- Yi Zhang
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Zhicheng Wu
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ming Feng
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Jiwei Chen
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Meizhu Qin
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Wenran Wang
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Bao
- Faculty of Life Science, Tangshan Normal University, Tangshan, 063000, Hebei, China
| | - Qian Xu
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Ying Ye
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Chao Ma
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Cai-Zhong Jiang
- United States Department of Agriculture, Crop Pathology and Genetic Research Unit, Agricultural Research Service, University of California, Davis, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Su-Sheng Gan
- Plant Biology Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, USA
| | - Hougao Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225, China
| | - Youming Cai
- Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Bo Hong
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Junping Gao
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
| | - Nan Ma
- Department of Ornamental Horticulture, State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, College of Horticulture, China Agricultural University, Beijing, 100193, China
- Author for correspondence:
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Shalaby NA, Pinzon JH, Narayanan AS, Jin EJ, Ritz MP, Dove RJ, Wolfenberg H, Rodan AR, Buszczak M, Rothenfluh A. JmjC domain proteins modulate circadian behaviors and sleep in Drosophila. Sci Rep 2018; 8:815. [PMID: 29339751 PMCID: PMC5770425 DOI: 10.1038/s41598-017-18989-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 12/20/2017] [Indexed: 12/23/2022] Open
Abstract
Jumonji (JmjC) domain proteins are known regulators of gene expression and chromatin organization by way of histone demethylation. Chromatin modification and remodeling provides a means to modulate the activity of large numbers of genes, but the importance of this class of predicted histone-modifying enzymes for different aspects of post-developmental processes remains poorly understood. Here we test the function of all 11 non-lethal members in the regulation of circadian rhythms and sleep. We find loss of every Drosophila JmjC gene affects different aspects of circadian behavior and sleep in a specific manner. Together these findings suggest that the majority of JmjC proteins function as regulators of behavior, rather than controlling essential developmental programs.
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Affiliation(s)
- Nevine A Shalaby
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Institute for Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Jorge H Pinzon
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.,Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Anjana S Narayanan
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | | | - Morgan P Ritz
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Rachel J Dove
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Heike Wolfenberg
- Institute for Biology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Aylin R Rodan
- Department of Internal Medicine - Division of Nephrology, Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112, USA.,Molecular Medicine Program, University of Utah, Salt Lake City, Utah, 84112, USA
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Adrian Rothenfluh
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA. .,Molecular Medicine Program, University of Utah, Salt Lake City, Utah, 84112, USA. .,Department of Psychiatry, Department of Neurobiology and Anatomy, Department of Human Genetics, University of Utah, Salt Lake City, Utah, 84112, USA.
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Sinha S, Raxwal VK, Joshi B, Jagannath A, Katiyar-Agarwal S, Goel S, Kumar A, Agarwal M. De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). FRONTIERS IN PLANT SCIENCE 2015; 6:932. [PMID: 26579175 PMCID: PMC4626631 DOI: 10.3389/fpls.2015.00932] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/15/2015] [Indexed: 05/07/2023]
Abstract
Low temperature is a major abiotic stress that impedes plant growth and development. Brassica juncea is an economically important oil seed crop and is sensitive to freezing stress during pod filling subsequently leading to abortion of seeds. To understand the cold stress mediated global perturbations in gene expression, whole transcriptome of B. juncea siliques that were exposed to sub-optimal temperature was sequenced. Manually self-pollinated siliques at different stages of development were subjected to either short (6 h) or long (12 h) durations of chilling stress followed by construction of RNA-seq libraries and deep sequencing using Illumina's NGS platform. De-novo assembly of B. juncea transcriptome resulted in 133,641 transcripts, whose combined length was 117 Mb and N50 value was 1428 bp. We identified 13,342 differentially regulated transcripts by pair-wise comparison of 18 transcriptome libraries. Hierarchical clustering along with Spearman correlation analysis identified that the differentially expressed genes segregated in two major clusters representing early (5-15 DAP) and late stages (20-30 DAP) of silique development. Further analysis led to the discovery of sub-clusters having similar patterns of gene expression. Two of the sub-clusters (one each from the early and late stages) comprised of genes that were inducible by both the durations of cold stress. Comparison of transcripts from these clusters led to identification of 283 transcripts that were commonly induced by cold stress, and were referred to as "core cold-inducible" transcripts. Additionally, we found that 689 and 100 transcripts were specifically up-regulated by cold stress in early and late stages, respectively. We further explored the expression patterns of gene families encoding for transcription factors (TFs), transcription regulators (TRs) and kinases, and found that cold stress induced protein kinases only during early silique development. We validated the digital gene expression profiles of selected transcripts by qPCR and found a high degree of concordance between the two analyses. To our knowledge this is the first report of transcriptome sequencing of cold-stressed B. juncea siliques. The data generated in this study would be a valuable resource for not only understanding the cold stress signaling pathway but also for introducing cold hardiness in B. juncea.
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Affiliation(s)
- Somya Sinha
- Department of Botany, University of DelhiNew Delhi, India
| | - Vivek K. Raxwal
- Department of Botany, University of DelhiNew Delhi, India
- Department of Plant Molecular Biology, Central European Institute of TechnologyBrno, Czech Republic
| | - Bharat Joshi
- Department of Botany, University of DelhiNew Delhi, India
| | - Arun Jagannath
- Department of Botany, University of DelhiNew Delhi, India
| | | | | | - Amar Kumar
- Department of Botany, University of DelhiNew Delhi, India
| | - Manu Agarwal
- Department of Botany, University of DelhiNew Delhi, India
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Temperature influences histone methylation and mRNA expression of the Jmj-C histone-demethylase orthologues during the early development of the oyster Crassostrea gigas. Mar Genomics 2015; 19:23-30. [DOI: 10.1016/j.margen.2014.09.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 09/03/2014] [Accepted: 09/04/2014] [Indexed: 01/08/2023]
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Bauerfeind MA, Winkelmann T, Franken P, Druege U. Transcriptome, carbohydrate, and phytohormone analysis of Petunia hybrida reveals a complex disturbance of plant functional integrity under mild chilling stress. FRONTIERS IN PLANT SCIENCE 2015; 6:583. [PMID: 26284099 PMCID: PMC4517316 DOI: 10.3389/fpls.2015.00583] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 07/13/2015] [Indexed: 05/05/2023]
Abstract
Cultivation of chilling-tolerant ornamental crops at lower temperature could reduce the energy demands of heated greenhouses. To provide a better understanding of how sub-optimal temperatures (12°C vs. 16°C) affect growth of the sensitive Petunia hybrida cultivar 'SweetSunshine Williams', the transcriptome, carbohydrate metabolism, and phytohormone homeostasis were monitored in aerial plant parts over 4 weeks by use of a microarray, enzymatic assays and GC-MS/MS. The data revealed three consecutive phases of chilling response. The first days were marked by a strong accumulation of sugars, particularly in source leaves, preferential up-regulation of genes in the same tissue and down-regulation of several genes in the shoot apex, especially those involved in the abiotic stress response. The midterm phase featured a partial normalization of carbohydrate levels and gene expression. After 3 weeks of chilling exposure, a new stabilized balance was established. Reduced hexose levels in the shoot apex, reduced ratios of sugar levels between the apex and source leaves and a higher apical sucrose/hexose ratio, associated with decreased activity and expression of cell wall invertase, indicate that prolonged chilling induced sugar accumulation in source leaves at the expense of reduced sugar transport to and reduced sucrose utilization in the shoot. This was associated with reduced levels of indole-3-acetic acid and abscisic acid in the apex and high numbers of differentially, particularly up-regulated genes, especially in the source leaves, including those regulating histones, ethylene action, transcription factors, and a jasmonate-ZIM-domain protein. Transcripts of one Jumonji C domain containing protein and one expansin accumulated in source leaves throughout the chilling period. The results reveal a dynamic and complex disturbance of plant function in response to mild chilling, opening new perspectives for the comparative analysis of differently tolerant cultivars.
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Affiliation(s)
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Leibniz Universität HannoverHannover, Germany
| | - Philipp Franken
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental CropsErfurt, Germany
| | - Uwe Druege
- Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental CropsErfurt, Germany
- *Correspondence: Uwe Druege, Department of Plant Propagation, Leibniz Institute of Vegetable and Ornamental Crops, Kuehnhaeuser Straße 101, 99090 Erfurt, Germany,
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Liew LC, Singh MB, Bhalla PL. An RNA-seq transcriptome analysis of histone modifiers and RNA silencing genes in soybean during floral initiation process. PLoS One 2013; 8:e77502. [PMID: 24147010 PMCID: PMC3797736 DOI: 10.1371/journal.pone.0077502] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2013] [Accepted: 09/09/2013] [Indexed: 11/19/2022] Open
Abstract
Epigenetics has been recognised to play vital roles in many plant developmental processes, including floral initiation through the epigenetic regulation of gene expression. The histone modifying proteins that mediate these modifications involve the SET domain-containing histone methyltransferases, JmjC domain-containing demethylase, acetylases and deacetylases. In addition, RNA interference (RNAi)-associated genes are also involved in epigenetic regulation via RNA-directed DNA methylation and post-transcriptional gene silencing. Soybean, a major crop legume, requires a short day to induce flowering. How histone modifications regulate the plant response to external cues that initiate flowering is still largely unknown. Here, we used RNA-seq to address the dynamics of transcripts that are potentially involved in the epigenetic programming and RNAi mediated gene silencing during the floral initiation of soybean. Soybean is a paleopolyploid that has been subjected to at least two rounds of whole genome duplication events. We report that the expanded genomic repertoire of histone modifiers and RNA silencing genes in soybean includes 14 histone acetyltransferases, 24 histone deacetylases, 47 histone methyltransferases, 15 protein arginine methyltransferases, 24 JmjC domain-containing demethylases and 47 RNAi-associated genes. To investigate the role of these histone modifiers and RNA silencing genes during floral initiation, we compared the transcriptional dynamics of the leaf and shoot apical meristem at different time points after a short-day treatment. Our data reveal that the extensive activation of genes that are usually involved in the epigenetic programming and RNAi gene silencing in the soybean shoot apical meristem are reprogrammed for floral development following an exposure to inductive conditions.
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Affiliation(s)
- Lim Chee Liew
- Plant Molecular Biology and Biotechnology Laboratory, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, the University of Melbourne, Parkville, Victoria, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, the University of Melbourne, Parkville, Victoria, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, ARC Centre of Excellence for Integrative Legume Research, Melbourne School of Land and Environment, the University of Melbourne, Parkville, Victoria, Australia
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Misiak B, Frydecka D, Piotrowski P, Kiejna A. The multidimensional nature of metabolic syndrome in schizophrenia: lessons from studies of one-carbon metabolism and DNA methylation. Epigenomics 2013; 5:317-29. [DOI: 10.2217/epi.13.22] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Large data sets indicate that the prevalence of metabolic syndrome (MetS) is significantly higher in patients with schizophrenia in comparison with the general population. Given that interactions between genes and the environment may underlie the etiology of MetS in subjects with schizophrenia, it is feasible that epigenetic phenomena can serve as the etiological consensus between genetic and environmental factors. However, there is still a striking scarcity of studies aimed at investigating the role of aberrant DNA methylation in the development of MetS in this group of patients. This article provides an update on the epigenetics of schizophrenia and reviews studies on the role of one-carbon metabolism and aberrant DNA methylation in the development of MetS.
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Affiliation(s)
- Blazej Misiak
- Department of Psychiatry, Wroclaw Medical University, Pasteura 10, 51-367 Wroclaw, Poland.
| | - Dorota Frydecka
- Department of Psychiatry, Wroclaw Medical University, Pasteura 10, 51-367 Wroclaw, Poland
| | - Patryk Piotrowski
- Department of Psychiatry, Wroclaw Medical University, Pasteura 10, 51-367 Wroclaw, Poland
| | - Andrzej Kiejna
- Department of Psychiatry, Wroclaw Medical University, Pasteura 10, 51-367 Wroclaw, Poland
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Aiese Cigliano R, Sanseverino W, Cremona G, Ercolano MR, Conicella C, Consiglio FM. Genome-wide analysis of histone modifiers in tomato: gaining an insight into their developmental roles. BMC Genomics 2013; 14:57. [PMID: 23356725 PMCID: PMC3567966 DOI: 10.1186/1471-2164-14-57] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 01/22/2013] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Histone post-translational modifications (HPTMs) including acetylation and methylation have been recognized as playing a crucial role in epigenetic regulation of plant growth and development. Although Solanum lycopersicum is a dicot model plant as well as an important crop, systematic analysis and expression profiling of histone modifier genes (HMs) in tomato are sketchy. RESULTS Based on recently released tomato whole-genome sequences, we identified in silico 32 histone acetyltransferases (HATs), 15 histone deacetylases (HDACs), 52 histone methytransferases (HMTs) and 26 histone demethylases (HDMs), and compared them with those detected in Arabidopsis (Arabidopsis thaliana), maize (Zea mays) and rice (Oryza sativa) orthologs. Comprehensive analysis of the protein domain architecture and phylogeny revealed the presence of non-canonical motifs and new domain combinations, thereby suggesting for HATs the existence of a new family in plants. Due to species-specific diversification during evolutionary history tomato has fewer HMs than Arabidopsis. The transcription profiles of HMs within tomato organs revealed a broad functional role for some HMs and a more specific activity for others, suggesting key HM regulators in tomato development. Finally, we explored S. pennellii introgression lines (ILs) and integrated the map position of HMs, their expression profiles and the phenotype of ILs. We thereby proved that the strategy was useful to identify HM candidates involved in carotenoid biosynthesis in tomato fruits. CONCLUSIONS In this study, we reveal the structure, phylogeny and spatial expression of members belonging to the classical families of HMs in tomato. We provide a framework for gene discovery and functional investigation of HMs in other Solanaceae species.
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Affiliation(s)
- Riccardo Aiese Cigliano
- CNR, National Research Council of Italy, Institute of Plant Genetics, Research Division Portici, Via Università 133, 80055 Portici, Italy
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Eckel-Mahan K, Sassone-Corsi P. Epigenetic Regulation of the Molecular Clockwork. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2013; 119:29-50. [DOI: 10.1016/b978-0-12-396971-2.00002-6] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Rosa BA, Jiao Y, Oh S, Montgomery BL, Qin W, Chen J. Frequency-based time-series gene expression recomposition using PRIISM. BMC SYSTEMS BIOLOGY 2012; 6:69. [PMID: 22703599 PMCID: PMC3464900 DOI: 10.1186/1752-0509-6-69] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 06/15/2012] [Indexed: 11/30/2022]
Abstract
Background Circadian rhythm pathways influence the expression patterns of as much as 31% of the Arabidopsis genome through complicated interaction pathways, and have been found to be significantly disrupted by biotic and abiotic stress treatments, complicating treatment-response gene discovery methods due to clock pattern mismatches in the fold change-based statistics. The PRIISM (Pattern Recomposition for the Isolation of Independent Signals in Microarray data) algorithm outlined in this paper is designed to separate pattern changes induced by different forces, including treatment-response pathways and circadian clock rhythm disruptions. Results Using the Fourier transform, high-resolution time-series microarray data is projected to the frequency domain. By identifying the clock frequency range from the core circadian clock genes, we separate the frequency spectrum to different sections containing treatment-frequency (representing up- or down-regulation by an adaptive treatment response), clock-frequency (representing the circadian clock-disruption response) and noise-frequency components. Then, we project the components’ spectra back to the expression domain to reconstruct isolated, independent gene expression patterns representing the effects of the different influences. By applying PRIISM on a high-resolution time-series Arabidopsis microarray dataset under a cold treatment, we systematically evaluated our method using maximum fold change and principal component analyses. The results of this study showed that the ranked treatment-frequency fold change results produce fewer false positives than the original methodology, and the 26-hour timepoint in our dataset was the best statistic for distinguishing the most known cold-response genes. In addition, six novel cold-response genes were discovered. PRIISM also provides gene expression data which represents only circadian clock influences, and may be useful for circadian clock studies. Conclusion PRIISM is a novel approach for overcoming the problem of circadian disruptions from stress treatments on plants. PRIISM can be integrated with any existing analysis approach on gene expression data to separate circadian-influenced changes in gene expression, and it can be extended to apply to any organism with regular oscillations in gene expression patterns across a large portion of the genome.
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Affiliation(s)
- Bruce A Rosa
- Department of Biology, Lakehead University, ON, Canada
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Lu SX, Webb CJ, Knowles SM, Kim SH, Wang Z, Tobin EM. CCA1 and ELF3 Interact in the control of hypocotyl length and flowering time in Arabidopsis. PLANT PHYSIOLOGY 2012; 158:1079-88. [PMID: 22190341 PMCID: PMC3271744 DOI: 10.1104/pp.111.189670] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Accepted: 12/16/2011] [Indexed: 05/18/2023]
Abstract
The circadian clock is an endogenous oscillator with a period of approximately 24 h that allows organisms to anticipate, and respond to, changes in the environment. In Arabidopsis (Arabidopsis thaliana), the circadian clock regulates a wide variety of physiological processes, including hypocotyl elongation and flowering time. CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is a central clock component, and CCA1 overexpression causes circadian dysfunction, elongated hypocotyls, and late flowering. EARLY FLOWERING3 (ELF3) modulates light input to the clock and is also postulated to be part of the clock mechanism. elf3 mutations cause light-dependent arrhythmicity, elongated hypocotyls, and early flowering. Although both genes affect similar processes, their relationship is not clear. Here, we show that CCA1 represses ELF3 by associating with its promoter, completing a CCA1-ELF3 negative feedback loop that places ELF3 within the oscillator. We also show that ELF3 acts downstream of CCA1, mediating the repression of PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5 in the control of hypocotyl elongation. In the regulation of flowering, our findings show that ELF3 and CCA1 either cooperate or act in parallel through the CONSTANS/FLOWERING LOCUS T pathway. In addition, we show that CCA1 represses GIGANTEA and SUPPRESSOR OF CONSTANS1 by direct interaction with their promoters, revealing additional connections between the circadian clock and the flowering pathways.
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