Genome-wide DNA methylation maps of Arabidopsis thaliana in two seasons
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE38991 | GEO | 2013/07/21
SECONDARY ACCESSION(S): PRJNA170183
REPOSITORIES: GEO
Similar Datasets
Project description:DNA methylation is involved in many biological processes during plant growth and development. Here, we report a novel annual growth rhythm that is found in cotton plants grown in different time-of-year. To further study this rhythm in other plants, we use Arabidopsis thaliana for genome-wide bisulfite sequencing. Two A. thaliana DNA samples were extracted from 20 days old whole plant in Feburary and August for bisulphite treatment and further Illumina sequencing.
2013-07-21 | E-GEOD-38991 | biostudies-arrayexpress
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93066 | GEO
Project description:Seasonal cycles of light, temperature and precipitation provide signals that set the timing of gene expression and growth for trees. Conifers possess evergreen needles to sense and respond to year-round external signals. We monitored gene activity in Douglas-fir needles for one year and found that gene expression is dependent on light at daily and annual scales. The majority of rhythmic genes achieve maximum activity +/- 2 hours from sunrise and sunset, and +/- 20 days from the winter and summer solstices. Remarkably, the dormant period is characterized by significant gene activation, with thousands of genes achieving peak activity. This study identifies annual gene rhythms in conifers needles, and provides a framework for identifying genes that respond to other environmental cues. Background: Perennial growth in plants is the product of interdependent cycles of daily and annual stimuli that induce cycles of growth and dormancy. In conifers, needles are the key perennial organ that integrates daily and seasonal signals from light, temperature, and water availability. To understand the relationship between seasonal rhythms and seasonal gene expression responses in conifers, we examined diurnal and circannual needle mRNA accumulation in Douglas-fir (Pseudotsuga menziesii) needles at diurnal and circannual scales. Using mRNA sequencing, we sampled 6.1x10^9 microreads from 19 trees and constructed a de novo pan-transcriptome reference that includes 173,882 tree-derived transcripts. Using this reference, we mapped RNA-Seq reads from 179 samples that capture daily, seasonal, and annual variation. Results: We identified 12,042 diurnally-cyclic transcripts, 9,299 of which showed homology to annotated genes from other plant genomes, including angiosperm core clock genes. Annual analysis revealed 21,225 annually-cyclic transcripts, 17,335 of which showed homology to annotated genes from other plant genomes. The timing of maximum gene expression is associated with light quality at diurnal and photoperiod at annual scales, with two-thirds of transcripts reaching maximum expression +/- 2 hours from sunrise and sunset, and half reaching maximum expression +/- 20 days from winter and summer solstices. Comparison to published microarray-based gene expression studies in spruce (Picea) show that the rank order of expression for 760 putatively orthologous genes was significantly preserved, highlighting the generality of our findings. Conclusions: This finding highlights the extensive annual and seasonal transcriptome variability demonstrated in conifer needles. At these temporal scales, 29% of expressed transcripts showed a significant diurnal rhythm, and 58.7% showed a significant circannual rhythm. Remarkably, thousands of genes reach their annual peak activity during winter dormancy, a time of metabolic stasis. Photoperiod appears to be a dominant driver of annual transcription patterns in Douglas-fir, and these results may be general for predicting rhythmic transcription patterns in emerging gymnosperm models.
2017-01-04 | GSE93067 | GEO
Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file.
2011-07-01 | GSE27697 | GEO
Project description:Photoperiodic Time Measurement (PPTM) is the ability of plants and animals to measure differences in day/night-length (photoperiod, PP) and use that information to anticipate seasonal changes in key environmental factors such as annual changes in average temperature. This timekeeping phenomenon, which is well documented for higher organisms, enables processes such as gonadal growth/regression, flowering, hibernation, and diapause to optimally adapt to annual transformations of the environment. We discovered PPTM capability in cyanobacteria, which is unexpected since cyanobacteria are unicellular prokaryotes with generation times as short as 5-6 hours. Therefore PPTM is not confined to eukaryotes with long generation times. Here we show that cyanobacteria can distinguish between short and long daylengths (photoperiods) and respond to short winter-like days by developing an enhanced resistance to cold. This capability develops over several cycles of photoperiod, and therefore they harbor a “photoperiodic counter” that is a common characteristic of PPTM in higher organisms. These photoperiodic responses are dependent on the presence of the kaiABC genes that encode the central circadian clockwork in cyanobacteria. Short days that herald winter stimulated desaturation of membrane lipids, which is a seasonally adaptive response to lower temperatures. Long vs. short days evoke differential programs of gene transcription, including differential expression of stress response genes, suggesting that PPTM originally evolved from stresses that recur seasonally. Therefore, PPTM is a property of much simpler organisms than previously appreciated, with important implications for the evolution of biological timekeeping mechanisms.
2024-06-01 | GSE252562 | GEO
Project description:Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. The 35nt sequence tags from sequencing went through data cleaning first, which included getting rid of the low-quality tags and several kinds of contaminants from the 35nt tags. All clean tag sequences with copy numbers were then summarized into a fasta format file. Fiber samples from different seasons were used for small RNA sequencing and data processing.
2011-07-01 | E-GEOD-27697 | biostudies-arrayexpress
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response
2009-12-18 | GSE16467 | GEO
Project description:Cotton (Gossypium hirsutum L) is an important crop world wide that provides fiber for the textile industry. Cotton is a perennial plant that stores starch in stems and roots to provide carbohydrates for growth in subsequent seasons. These reserves are not available to produce seed and fiber when cotton is usually grown as an annual crop. Analysis of developing cotton plants indicated that starch levels peaked about the time of first anthesis then began to decline. An earlier peak of levels of starch was occasionally observed and in some greenhouse-grown samples starch increased 2 week after first bloom. Microarray analyses compared gene expression in tissues containing low levels of starch with tissues rapidly accumulating starch. Statistical analysis of differentially expressed genes indicated increased expression among genes associated with carbohydrate metabolism, transcription activity and the proteasome. Genes associated with starch synthesis, starch degradation, sucrose metabolism, hexose metabolism, raffinose synthesis and trehalose synthesis increased in expression in starch accumulating tissues. The anticipated changes in these sugars were largely confirmed by measuring soluble sugars in relevant tissues. We propose that altering expressions of genes and pathways identified in this work could be used to more efficiently mobilize stored carbohydrate to fiber production. Keywords: starch accumulating, stem, root
2009-01-04 | GSE8973 | GEO
Project description:A cDNA library from 0-10 day post anthesis cotton ovules was established to study genes expressed in cotton ovule during initiation and quickly elongation period. We randomly sequenced over 100,000 ESTs from this library and acquired a gene pool of more than 28,000 UniESTs. The cotton UniESTs were then PCR-amplified and printed onto microarray. This array is comprised of about 28000 high-quality cotton cDNAs (with average length>750bp) and external controls. To study the different growth potential of cotton fibers in a one-year cycle, we then hybridized the array with RNA samples derived from +7 DPA wild-type upland cotton fibers in four different seasons, respectively.
2010-06-01 | GSE16802 | GEO
Project description:Global gene expression was compared between roots of cotton plants (variety Sicot 71) flooded for 4 hours and roots of unflooded cotton plants. Global gene expression was also compared between leaves of cotton plants (variety Sicot 71) flooded for 24 hours and leaves of unflooded cotton plants. Waterlogging stress causes yield reductions in cotton (Gossypium hirsutum L.). A major component of waterlogging stress is the lack of oxygen available to submerged tissues. While changes in expressed protein, gene transcription and metabolite levels have been studied in response to low oxygen stress, little research has been done on molecular responses to waterlogging in cotton. We assessed cotton growth responses to waterlogging and assayed global gene transcription responses in root and leaf cotton tissues of partially submerged plants. Waterlogging causes significant reductions in stem elongation, shoot mass, root mass, and leaf number. At the global gene expression level waterlogging significantly alters the expression of 1012 genes (4.2% of genes assayed) in root tissue as early as 4h after flooding. Many of these genes are associated with cell wall modification and growth pathways, glycolysis, fermentation, mitochondrial electron transport and nitrogen metabolism. Waterlogging of plant roots also altered global leaf gene expression, significantly changing the expression of 1305 genes (5.4% of genes assayed) after 24h of flooding. Genes associated with cell wall growth and modification, tetrapyrrole synthesis, hormone response, starch metabolism and nitrogen metabolism were affected in leaf tissues of waterlogged plants. Implications of these results for the development of waterlogging tolerant cotton are discussed. Keywords: Stress Response Plants of cotton cultivar Sicot 71 were grown to the two-leaf stage in tubs. For stress treatments plants were either watered as normal or flooded with water to completely submerge the root system. At four and twenty-four hours post-flooding samples of root or leaf tissue were taken from control and flooded plants. Total RNA was extracted from each tissue sample and assayed on cotton Affymetrix chips. Two biological replications were used for each comparison.
2010-05-17 | E-GEOD-16467 | biostudies-arrayexpress