Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize
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PROVIDER: PRJNA705177 | ENA |
REPOSITORIES: ENA
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Project description:This was a comparative transcriptome analysis by using high throughput sequencing. To assess the effects of heat stress on maize alternative splicing we used a controlled environment facility called the Enviratron to simulate field conditions. For our experiments, maize plants were subjected to conditions simulating normal diurnal rhythms of light and temperature, with increasing maximal daily temperature (MDT). Maize plants were grown continuously under four different temperature regimes with simulated morning temperatures ramped up over 6 hr to the MDT of 31°C, 33°C, 35°C or 37°C and simulated evening/night time temperatures ramped down over 8 hr to 10°C below the MDT. We tracked the alternative splicing events of maize W22 seedlings grow under different temperatures (MDT of 31°C, 33°C, 35°C or 37°C) to evaluate how different MDTs affect the program of gene alternative splicing in maize. RNA was extracted from small strips of leaf lamina excised from the first fully expanded leaf of V4 and V5 W22 plants (at 20 and 27 DAG, respectively). Plants were sampled in triplicates.
2021-02-27 | GSE167670 | GEO
Project description:Elevated temperatures enhance alternative RNA splicing in maize (Zea mays) with the potential to expand the repertoire of plant responses to heat stress. Alternative RNA splicing generates multiple RNA isoforms for many maize genes, and here we observed changes in the pattern of RNA isoforms with temperature changes. Increases in maximum daily temperature elevated the frequency of the major modes of alternative splices (AS), in particular retained introns and skipped exons. The genes most frequently targeted by increased AS with temperature encode factors involved in RNA processing and plant development. Genes encoding regulators of alternative RNA splicing were themselves among the principal AS targets in maize. Under controlled environmental conditions, daily changes in temperature comparable to field conditions altered the abundance of different RNA isoforms, including the RNAs encoding the splicing regulator SR45a, a member of the SR45 gene family. We established an "in protoplast" RNA splicing assay to show that during the afternoon on simulated hot summer days, SR45a RNA isoforms were produced with the potential to encode proteins efficient in splicing model substrates. With the RNA splicing assay, we also defined the exonic splicing enhancers that the splicing-efficient SR45a forms utilize to aid in the splicing of model substrates. Hence, with rising temperatures on hot summer days, SR45a RNA isoforms in maize are produced with the capability to encode proteins with greater RNA splicing potential.
| S-EPMC8195531 | biostudies-literature
Project description:The circadian clock drives daily changes of physiology, including sleep-wake cycles, by regulating transcription, protein abundance and function. Circadian phosphorylation controls cellular processes in peripheral organs, but little is known about its role in brain function and synaptic activity. We applied advanced quantitative phosphoproteomics to mouse forebrain synaptoneurosomes isolated across 24h, accurately quantifying almost 8,000 phosphopeptides. Remarkably, half of the synaptic phosphoproteins, including numerous kinases, had large-amplitude rhythms peaking at rest-activity and activity-rest transitions. Bioinformatic analyses revealed global temporal control of synaptic function via phosphorylation, including synaptic transmission, cytoskeleton reorganization and excitatory/inhibitory balance. Remarkably, sleep deprivation abolished 98% of all phosphorylation cycles in synaptoneurosomes, indicating that sleep-wake cycles rather than circadian signals are main drivers of synaptic phosphorylation, responding to both sleep and wake pressures.
2019-10-14 | PXD010697 | Pride
Project description:In mammals body temperature fluctuates diurnally around a mean value of 36-37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, in, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of Cold- Inducible RNA-Binding Protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles Cirbp mRNA oscillates about 3-fold in abundance, as it does in mouse liver. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cells’ circadian clocks. Here, we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide “approach-to-steady-kinetics”, this posttranscriptional mechanism is wide-spread in the temperature-dependent control of gene expression.
2016-08-13 | GSE85553 | GEO
Project description:The daily organisation of most mammalian cellular functions is attributed to circadian regulation of clock-controlled protein expression, driven by daily cycles of CRYPTOCHROME-dependent transcriptional feedback repression. To test this, we used quantitative mass spectrometry to compare wild type and CRY-deficient fibroblasts under constant conditions. In CRY-deficient cells, we found that temporal variation in protein, phosphopeptide, and K+ abundance was at least as great as wild type controls. Most strikingly. the extent of temporal variation within either genotype was much smaller than overall differences in proteome composition between WT and CRY-deficient cells. This proteome imbalance in CRY-deficient cells and tissues was associated with increased susceptibility to proteotoxic stress, which impairs circadian robustness, and may contribute to the wide-ranging phenotypes of CRY-deficient mice. Rather than generating largescale daily variation in proteome composition, we suggest it is plausible that the various transcriptional and post-translational functions of CRY proteins ultimately act to promote protein and osmotic homeostasis against daily perturbation.
2021-11-19 | PXD019499 | Pride
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: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:In mammals body temperature fluctuates diurnally around a mean value of 36-37°C. Despite the small differences between minimal and maximal values, body temperature rhythms can drive robust cycles in gene expression in cultured cells and, likely, in, animals. Here we studied the mechanisms responsible for the temperature-dependent expression of Cold- Inducible RNA-Binding Protein (CIRBP). In NIH3T3 fibroblasts exposed to simulated mouse body temperature cycles Cirbp mRNA oscillates about 3-fold in abundance, as it does in mouse liver. This daily mRNA accumulation cycle is directly controlled by temperature oscillations and does not depend on the cellsâ circadian clocks. Here, we show that the temperature-dependent accumulation of Cirbp mRNA is controlled primarily by the regulation of splicing efficiency, defined as the fraction of Cirbp pre-mRNA processed into mature mRNA. As revealed by genome-wide âapproach-to-steady-kineticsâ, this posttranscriptional mechanism is wide-spread in the temperature-dependent control of gene expression. Cultured NIH3T3 cells seeded and kept at 37C degree for 4 hours before being switched to 33C and 38C. After 16 hours of incubation the temperature was shifted to 38C and 33C, respectively. Sample were then taken at 0, 1, 3, 6 and 9 hour after the temperature shift. Paired-end, strand-specific, total RNA-seq was performed over the samples at the respective time points using the Illumina HiSeq2500 platform.
2016-08-13 | E-GEOD-85553 | biostudies-arrayexpress
Project description:It is well known that host-microbes and immunity interactions are influenced by dietary patterns, as well as daily environmental light-dark (LD) cycles that entrain circadian rhythms in the host. Emerging data has highlighted the importance of diet patterns and timing on the interaction among circadian rhythms, gut microbiome, and immunity, however, their impacts on LD cycles are less reported. Therefore, we aim to study how LD cycles regulate the homeostatic crosstalk between gut microbiome, hypothalamic and hepatic circadian clock oscillations and immunity. We hypothesized that different environmental LD cycles: (1) constant darkness, LD0/24; (2) short light, LD8/16; (3) normal LD cycle, LD12/12; (4) long light, LD16/8; and (5) constant light, LD24/0, may affect immunity and metabolism to varying degrees. Therefore, 240 mice were managed with chow diets (CD) and antibiotics treatments (ABX) under five different LD cycles for 42 days. The colonic (co) and cecum (ce) contents were obtained for studying their impacts on gut microbiome using 16S rRNA sequencing.
2023-03-10 | GSE226852 | GEO
Project description:Mammalian body temperature oscillates with the time of the day and is altered in diverse pathological conditions. We recently identified a body temperature-sensitive thermometer-like kinase, which alters SR protein phosphorylation and thereby globally controls alternative splicing (AS). AS can generate unproductive variants which are recognized and degraded by diverse mRNA decay pathways – including nonsense-mediated decay (NMD). Here we show extensive coupling of body temperature-controlled AS to mRNA decay, leading to global control of temperature-dependent gene expression (GE). Temperature-controlled, decay-inducing splicing events are evolutionarily conserved and pervasively found within RNA-binding proteins, including most SR proteins. AS-coupled poison exon inclusion is essential for rhythmic GE of SR proteins and has a global role in establishing temperature-dependent rhythmic GE profiles, both, in mammals under circadian body temperature cycles and in plants in response to ambient temperature changes. Together, these data identify body temperature-driven AS coupled mRNA decay as an evolutionary ancient, core clock-independent mechanism to generate rhythmic GE.
2020-11-01 | GSE158882 | GEO