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Activation of immediate early response genes initiates a restorative gene expression program during each arousal from torpor in hibernating 13-lined ground squirrels

ABSTRACT: Activation of immediate early response genes initiates a restorative gene expression program during each arousal from torpor in hibernating 13-lined ground squirrels

PROVIDER: PRJNA854159 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR19901702.fastq.gz	Fastqsanger.gz
	SRR19901703.fastq.gz	Fastqsanger.gz
	SRR19901704.fastq.gz	Fastqsanger.gz
	SRR19901705.fastq.gz	Fastqsanger.gz
	SRR19901706.fastq.gz	Fastqsanger.gz

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Similar Datasets

Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels

Project description:Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels

| PRJNA943230 | ENA

GRO-seq analysis of liver gene transcription in hibernating 13-lined ground squirrels

Project description:Hibernators dramatically lower metabolism to save energy while fasting for months. Prolonged fasting challenges metabolic homeostasis, yet small-bodied hibernators emerge each spring ready to resume all aspects of active life, including immediate reproduction. The liver is the body’s metabolic hub, processing and detoxifying macromolecules to provide essential fuels to brain, muscle and other organs throughout the body. Here we quantify changes in liver gene expression using RNA-seq to measure the steady-state transcriptome and GRO-seq to measure transcription across several distinct physiological states of hibernation in 13-lined ground squirrels. Our data capture key timepoints in both the seasonal and torpor-arousal cycles of hibernation. Strong positive correlation between transcription and the transcriptome indicates that transcriptional control dominates the known seasonal reprogramming of metabolic gene expression in liver for hibernation. During the torpor-arousal cycle, however, discordance develops between transcription and the steady-state transcriptome by at least two mechanisms: 1) although not transcribed during torpor, some liver transcripts are unusually stable, consistent with data from other tissues; and 2) unexpectedly, on some genes, we document continuing, slow elongation with a failure to terminate transcription across the torpor bout. While the steady-state RNAs corresponding to these readthrough transcripts did not increase during torpor, they did increase shortly after rewarming despite then low transcription. Both of these mechanisms assure the availability of functional transcripts immediately upon rewarming. Integration of transcriptional, post-transcriptional and RNA stability control mechanisms, all demonstrated in these data, likely initiate a serial gene expression program across the short euthermic period that restores the tissue and prepares the animal for the next bout of torpor.

2021-05-10 | GSE166370 | GEO

Platelet proteome dynamics in hibernating 13-lined ground squirrels

Project description:Hibernating mammals undergo a dramatic drop in temperature and blood flow during torpor and must suppress hemostasis to avoid stasis blood clotting. In addition, cold storage of most mammalian platelets induces cold storage lesions, resulting in rapid clearance following transfusion. 13-lined ground squirrels (Ictidomys tridecemlineatus) provide a model to study hemostasis and cold storage of platelets during hibernation because, even with a body temperature of 4-8C, their platelets are resistant to cold storage lesions. We quantified and systematically compared proteomes of platelets collected from ground squirrels at summer (activity), fall (entrance), and winter (topor) to elucidate how molecular-level changes in platelets may support hemostatic adaptations in torpor. Platelets were isolated from squirrel blood collected in June, October, and January. Platelet lysates from each animal were digested with trypsin prior to 11-plex tandem mass tag (TMT) labeling, followed by LC-MS/MS analysis for relative protein quantification. We found over 700 platelet proteins with significant changes over the course of entrance, torpor, and activity – including systems of proteins regulating translation, platelet degranulation, metabolism, complement, and coagulation cascades. We also noted species specific differences in hemostatic, secretory, and inflammatory regulators in ground squirrel platelets relative to human platelets. In addition to providing the first ever proteomic characterization of platelets from hibernating animals, our results support a model whereby systematic changes in metabolic, hemostatic, and other proteins support physiological adaptations in torpor. In addition, our results could translate into better methods to cold store human platelets, increasing their supply and quality for transfusions.

2021-12-08 | PXD026903 | Pride

Rapid microwave fixation of the brain reveals seasonal changes in the phosphoproteome of hibernating thirteen-lined ground squirrels

Project description:Hibernating mammals such as the thirteen-lined ground squirrel (Ictidomys tridecemlineatus) experience significant reductions in oxidative metabolism and body temperature when entering a state known as torpor. Animals entering or exiting torpor do not experience permanent loss of brain function or other injuries, and the processes that enable such neuroprotection are not well understood. To gain insight into changes in protein function that occur in dramatically different physiological states, we performed quantitative phosphoproteomics experiments on thirteen-lined ground squirrels that are summer active, winter torpid, and spring active. An important aspect of our approach was the use of focused microwave irradiation of the brain to sacrifice the animals and rapidly inactivate phosphatases and kinases to preserve the native phosphoproteome. Overall, our results showed pronounced changes in phosphorylated proteins for the transitions into and out of torpor, including for proteins involved in gene expression and DNA repair, cellular plasticity, and human disease. In contrast, the transition between active states showed minimal changes. This study offers valuable insight into the global changes of brain phosphorylation in hibernating mammals, the results of which may be relevant to the future therapeutic strategies for brain injury.

2025-01-23 | PXD054824 | Pride

Comparative transcriptomics of the garden dormouse hypothalamus during early torpor, late torpor and interbout arousal of hibernation

Project description:Comparative transcriptomics of the garden dormouse hypothalamus during early torpor, late torpor and interbout arousal of hibernation

2023-11-13 | GSE207494 | GEO

Mitochondrial microRNA profiles are altered in thirteen-lined ground squirrels (Ictidomys tridecemlineatus) during hibernation

Project description:Thirteen-lined ground squirrels (TLGS) are obligate hibernators that cycle between torpor (low metabolic rate and body temperature) and interbout euthermia (IBE; typical euthermic body temperature and metabolism) from late autumn to spring. Many physiological changes occur throughout hibernation, including a reduction in liver mitochondrial metabolism during torpor, which is reversed during arousal to interbout euthermia. Nuclear-encoded microRNA (small post-transcriptional regulator molecules) differ in abundance throughout TLGS hibernation and have been shown to regulate mitochondrial gene expression in mammalian cell culture (where they are referred to as mitomiRs). This study characterized differences in mitomiR profiles from TLGS liver mitochondria isolated during summer, torpor, and IBE, and predicted their mitochondrial targets. Using small RNA sequencing, differentially abundant mitomiRs were identified between hibernation states and, using qPCR analysis we quantified expression of predicted mitochondrial mRNA targets. Most differences in mitomiR abundances were seasonal (i.e. between summer and winter) with only one mitomiR differentially abundant between IBE and torpor. Multiple factor analysis revealed unique clustering of hibernation states, predominantly driven by mitomiR abundances, and nine of these differentially abundant mitomiRs had predicted mitochondrial RNA targets, including subunits of electron transfer system complexes I and IV, 12S rRNA and two tRNAs. Overall, mitomiRs were predicted to suppress expression of their mitochondrial targets and may have some involvement in regulating protein translation in mitochondria. This study found differences in mitomiR abundances between seasons and hibernation states of TLGS and suggests potential mechanisms in regulating the mitochondrial electron transfer system.

2024-07-31 | GSE254223 | GEO

13-lined ground squirrel (Spermophilus tridecemlineatus) hibernating liver transcriptome

Project description:This series represents the liver transcriptome for animals sampled during summer, interbout arousal, and late torpor Keywords = squirrel, liver, hibernation Keywords: other

2004-12-03 | GSE2021 | GEO

13-lined ground squirrel (Spermophilus tridecemlineatus) hibernating liver transcriptome

Project description:This series represents the liver transcriptome for animals sampled during summer, interbout arousal, and late torpor Keywords = squirrel, liver, hibernation

2010-06-05 | E-GEOD-2021 | biostudies-arrayexpress

Kidney gene expression dynamics during torpor-arousal cycles in hibernating 13-lined ground squirrels

Project description:RNA-seq libraries were prepared from replicate samples (n=5-6) from six physiolocial groups to capture key changes in circannual hibernation.

2024-06-01 | GSE227101 | GEO

StrokeofGenus: RNA-seq in five tissues of the hibernating 13-lined ground squirrel

Project description:Identify shifts in gene expression relevant to torpor phenotypes and recovery following torpor in five tissues of the 13-lined ground squirrel. Sampled tissues and time points overlap with prior hibernation RNA-seq studies in 13-lined ground squirrel and other species, allowing for the analysis of conserved gene expression patterns in torpor.

2024-10-23 | GSE248932 | GEO

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