Gene expression time series during natural senescence of Arabidopsis thaliana leaves under short-day growth conditions
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PROVIDER: PRJNA633142 | ENA |
REPOSITORIES: ENA
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Project description:This experiment profiled a time series of gene expression in leaf 7 of Arabidopsis thaliana plants grown in a controlled environment under 8 h light: 16 h dark (i.e. short days) to compare to the profiles analysed in Breeze et al. (2011) Plant Cell 23(3):873-94 under long day conditions.
2023-02-28 | GSE150678 | GEO
Project description:A gene expression analysis of the changes in in popolulus tremula during the autumn sensencece. Leaves were analyzed from late summer and late into autumn. Cytokinins are plant hormones that typically block or delay leaf senescence. We profiled 34 different cytokinins/cytokinin metabolites (including precursors, conjugates and degradation products) in leaves of a free-growing mature aspen (Populus tremula) before and after the initiation of autumnal senescence over three consecutive years. The levels and profiles of individual cytokinin species, or classes/groups, varied greatly between years, despite the fact that the onset of autumn senescence was at the same time each year, and senescence was not associated with depletion of either active or total cytokinin levels. Levels of aromatic cytokinins (topolins) were low and changed little over the autumn period. Diurnal variations and weather-dependent variations in cytokinin content were relatively limited. We also followed the expression patterns of all aspen genes implicated as having roles in cytokinin metabolism or signaling, but neither the pattern of regulation of any group of genes nor the expression of any particular gene supported the notion that decreased cytokinin signaling could explain the onset of senescence. Based on the results from this tree, we therefore suggest that cytokinin depletion is unlikely to explain the onset of autumn leaf senescence in aspen.
2016-12-11 | GSE86960 | GEO
Project description:Telomere shortening rates must be regulated to prevent premature replicative senescence. TERRA R-loops become stabilized at critically short telomeres to promote their elongation through homology-directed repair (HDR), thereby counteracting senescence onset. Using a non-bias proteomic approach to identify telomere binding factors, we identified Npl3, an RNA-binding protein previously implicated in multiple RNA biogenesis processes. Using Chromatin- and RNA immunoprecipitation, we demonstrate that Npl3 interacts with TERRA and telomeres. Furthermore, we show that Npl3 associates to telomeres in an R-loop dependent manner, as changes in R-loop levels, e.g. at short telomeres, modulate the recruitment of Npl3 to chromosome ends. Through a series of genetic and biochemical approaches we demonstrate that Npl3 binds to TERRA and stabilizes R-loops at short telomeres, which in turn promotes HDR and prevents premature replicative senescence onset. This may have implications for diseases associated with excessive telomere shortening.
2020-01-31 | PXD016772 | Pride
Project description:Although senescence has long been implicated in aging-associated pathologies, it is not clearly understood how senescent cells are linked to these diseases. To address this knowledge gap, we profiled cellular senescence phenotypes and mRNA expression patterns during replicative senescence in human diploid fibroblasts. We identified a sequential order of gain-of-senescence phenotypes: low levels of reactive oxygen species, cell mass/size increases with delayed cell growth, high levels of reactive oxygen species with increases in senescence-associated M-NM-2-galactosidase activity (SA-M-NM-2-gal), and high levels of SA-M-NM-2-gal activity. Gene expression profiling revealed four distinct modules in which genes were prominently expressed at certain stages of senescence, allowing us to divide the process into four stages: early, middle, advanced, and very advanced. Interestingly, the gene expression modules governing each stage supported the development of the associated senescence phenotypes. Senescence-associated secretory phenotype-related genes also displayed a stage-specific expression pattern with three unique features during senescence: differential expression of interleukin isoforms, differential expression of interleukins and their receptors, and differential expression of matrix metalloproteinases and their inhibitory proteins. The analysis of time series gene expression level during replicaive senescence.
2013-04-24 | E-GEOD-41714 | biostudies-arrayexpress
Project description:We measured time series transcriptome level in mouse eyes kept under short day and cool (SC), winter-like conditions, and long day and warm (LW), summer-like conditions.
2021-01-18 | GSE156141 | GEO
Project description:The profiling was conducted with the 385K Microarray manufactured at NimbleGen, Inc (http://www.nimblegen.com/) designed from 30,386 genes of Arabidopsis (TAIR v.6). RNA samples of leaves of S1 (100% green leaf from 40 days plant) and S3 (more than 50% yellow leaf) senescence stages from senescence-inducible LEC2 transgenic plant, OIL21 were subjected for analysis of Arabidopsis 385K transcriptome. Expression of 3,025 genes were significantly changed with log2 ratios greater than 1.0 or less than -1.0 in S1 or S3 stage (p value <0.05), among which 1491 were up-regulated and 1534 were down regulated. Gene annotation revealed that 7.4% genes, 223 out of 3,025 changed by LEC2 were encoded transcription factors (TF). 106 TFs were up-regulated and 115 TFs were down-regulated. A total of 9 chips were used for microarray. Total RNAs were extracted from senescence leaves at S1 and S3 stages of wild-type and senescence-inducible LEC2 transgenic Arabidopsis. Experiments were triplicated.
2012-12-05 | E-GEOD-38489 | biostudies-arrayexpress
Project description:Various physiological processes and behaviours are controlled by changing daylength. To dissect genes involved in the photoperiodic changes in physiology and behaviour, global expression analysis was performed using quail kept under short and long day conditions. Experiment Overall Design: The mediobasal hypothalamus (MBH) of quail kept under short day condition (6h light:18h dark) or long day condition (20h light:4h dark) were collected for RNA extraction. Pooled total RNA from three MBHs was labelled and hybridized on Affymetrix microarrays. Samples were collected from 6 birds every 4h during a 24 h cycle and were analyzed in duplicate set of array (two biological replicates).
2008-11-06 | E-GEOD-8018 | biostudies-arrayexpress
Project description:Various physiological processes and behaviours are controlled by changing daylength. To dissect genes involved in the photoperiodic changes in physiology and behaviour, global expression analysis was performed using quail kept under short and long day conditions. Keywords: time course
2008-03-11 | GSE8018 | GEO
Project description:Senescence (or aging) is the final stage of plant development; senescence involves a complex programmed process that is closely related to biotic and abiotic stresses and is regulated by fine-tuned molecular mechanisms. Postharvest vegetative organs undergo a series of physiological and biochemical changes during senescence. However, if postharvest plant organs were not scientifically processed or cured, there would be a great loss in their commercial value during curing or storage. Thus, studying the molecular mechanisms underlying senescence of plant organs will enhance understanding of such a fundamental biological process and might provide new insights into controlling senescence and improving commercial value during curing or storage. However, few studies have focused specifically on the molecular mechanism of leaf senescence affecting tobacco quality at the proteomic level during the yellowing stage. The main objectives of this work were to determine the protein profile changes associated with different curing stages and to establish links between protein profile changes and senescence physiology to provide a more in-depth understanding of the mechanism of senescence in postharvest tobacco leaves under oxidation, heat/high temperature, dehydration and starvation stresses at the proteomic level. This study provides new insights into the postharvest physiology and molecular mechanism of senescence at the proteomic level in postharvest leaves of tobacco, a model solanaceous plant, in response to curing and senescence during the yellowing stage.
2020-01-06 | PXD016941 |
Project description:Although senescence has long been implicated in aging-associated pathologies, it is not clearly understood how senescent cells are linked to these diseases. To address this knowledge gap, we profiled cellular senescence phenotypes and mRNA expression patterns during replicative senescence in human diploid fibroblasts. We identified a sequential order of gain-of-senescence phenotypes: low levels of reactive oxygen species, cell mass/size increases with delayed cell growth, high levels of reactive oxygen species with increases in senescence-associated β-galactosidase activity (SA-β-gal), and high levels of SA-β-gal activity. Gene expression profiling revealed four distinct modules in which genes were prominently expressed at certain stages of senescence, allowing us to divide the process into four stages: early, middle, advanced, and very advanced. Interestingly, the gene expression modules governing each stage supported the development of the associated senescence phenotypes. Senescence-associated secretory phenotype-related genes also displayed a stage-specific expression pattern with three unique features during senescence: differential expression of interleukin isoforms, differential expression of interleukins and their receptors, and differential expression of matrix metalloproteinases and their inhibitory proteins.
2013-04-24 | GSE41714 | GEO