Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

MiRNA profiling by Illumina sequencing technology

ABSTRACT: miRNAs are 19-25 nucleotides long small RNAs now well-known for their regulatory roles in the development and diseases through post-transcriptional and translational controls in a wide range of species. Mammalian hibernation is a physiological process involving dramatic metabolic suppression and cellular reorganization, during which miRNAs may play an important role. We systematically analyzed the miRNAs in the liver of an extreme hibernating species, arctic ground squirrels (Spermophilus parryii), during two stages of hibernation compared to non-hibernating animals by massively parallel Illumina sequencing technology. We identified more than 200 ground squirrel miRNAs including novel miRNAs specific to ground squirrel and a fast-evolving miRNA cluster that also showed significant differential expression during hibernation. Integrating with Agilent miRNA microarray and Real-time PCR results, we identified that mir-211, mir-378, mir-184, mir-200a, and mir-320 were significantly under-expressed during hibernation, whereas mir-144, mir-486, mir-451, mir-142-5p, and mir-1 were over-expressed. Analyses of the their target genes suggested that these miRNAs could play an important role to suppress tumor progression and cell growth during hibernation. Investigation of microRNA changes in arctic ground squirrel livers during Early Arousal(EA), Late Topor(LT), and Post-Reproduction(PR) stages.

ORGANISM(S): Urocitellus parryii

SUBMITTER: Wenchao Hu

PROVIDER: E-GEOD-19807 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel.

Liu Yuting Y Hu Wenchao W Wang Haifang H Lu Minghua M Shao Chunxuan C Menzel Corinna C Yan Zheng Z Li Ying Y Zhao Sen S Khaitovich Philipp P Liu Mofang M Chen Wei W Barnes Brian M BM Yan Jun J

Physiological genomics 20100504 1

MicroRNAs (miRNAs) are 19- to 25-nucleotide-long small and noncoding RNAs now well-known for their regulatory roles in gene expression through posttranscriptional and translational controls. Mammalian hibernation is a physiological process involving profound changes in set-points for food consumption, body mass and growth, body temperature, and metabolic rate in which miRNAs may play important regulatory roles. In an initial study, we analyzed miRNAs in the liver of an extreme hibernating specie ...[more]

PMID: 20442247

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Project description:Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional program underlying molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screening in hind limb muscles comparing hibernating and summer active black bears and arctic ground squirrels by the use of custom 9,600 probe cDNA microarrays. The molecular pathway analysis showed an elevated proportion of overexpressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during hibernation that implies induction of translation at different hibernation states. The induction of protein biosynthesis likely contributes to attenuation of disuse muscle atrophy through prolonged periods of immobility and starvation. This adaptive mechanism allows hibernating mammals to maintain full musculoskeletal function and preserve mobility during and immediately after hibernation, thus promoting survival. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter. Coordinated reduction of multiply genes involved in oxidation reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation. Arctic ground squirrels sampled during winter hibernation were compared with the animals sampled during summer. Muscle was hybridized on a custom 9,600 probes nylon membrane microarray platform. Ten in late torpor, four in early arousal, then in late arousal were studied in experiments.

Project description:Hibernation is energy saving adaptation involving suppression of activity to survive in highly seasonal environments. Immobility and disuse generate muscle loss in most mammalian species. In contrast to other mammals, bears and ground squirrels demonstrate limited muscle atrophy over the physical inactivity of winter hibernation. This suggests that hibernating mammals have adaptive mechanisms to prevent disuse muscle atrophy. To identify common transcriptional program underlying molecular mechanisms preventing muscle loss, we conducted a large-scale gene expression screening in hind limb muscles comparing hibernating and summer active black bears and arctic ground squirrels by the use of custom 9,600 probe cDNA microarrays. The molecular pathway analysis showed an elevated proportion of overexpressed genes involved in all stages of protein biosynthesis and ribosome biogenesis in muscle of both species during hibernation that implies induction of translation at different hibernation states. The induction of protein biosynthesis likely contributes to attenuation of disuse muscle atrophy through prolonged periods of immobility and starvation. This adaptive mechanism allows hibernating mammals to maintain full musculoskeletal function and preserve mobility during and immediately after hibernation, thus promoting survival. The lack of directional changes in genes of protein catabolic pathways does not support the importance of metabolic suppression for preserving muscle mass during winter. Coordinated reduction of multiply genes involved in oxidation reduction and glucose metabolism detected in both species is consistent with metabolic suppression and lower energy demand in skeletal muscle during inactivity of hibernation. Black bears sampled during winter hibernation were compared with the animals sampled during summer. Muscle tissue were hybridized on a custom 12,800 cDNA probe nylon membrane microarray platform . Six hibernating and six summer active bears were studied in the experiment.

Project description:Mammalian hibernation is a dramatic physiological transition that involves the controlled reduction of regulated body temperature and the consequent depression of all physiological processes. The resulting reduction of metabolism and associated energy expenditure permits survival during extended periods of poor food availability in winter. To date our understanding of the molecular events that give rise to the hibernating phenotype is fragmentary and incomplete. Here, we present a large-scale gene expression screen to explore the transcriptional changes that are associated with the torpid phenotype of the hibernating golden-mantled ground squirrel, Spermophilus lateralis. Expression profiles for liver, cardiac tissue, and brain isolated from summer active, torpid, and interbout aroused animals were generated by hybridization to a squirrel microarray composed of >12,000 cDNA probes. We reveal that the transcriptional changes associated with torpor are modest and generally involve less than 2-fold changes in mRNA level. By profiling the distribution of gene ontological terms in the lists of differentially expressed genes we were able to identify the functional themes that distinguish the summer awake and hibernating phenotypes. In all tissues, the pattern of differential gene expression is consistent with a switch to lipid metabolism during hibernation. In liver, we detected an expression signature suggestive of a profound depression in urea metabolism and detoxification pathways. This expression signature was reproduced in transcript data collected from liver of the13-lined ground squirrel, S. tridecemlineatus, suggesting that this phenotype is conserved between closely related species. The transcriptional changes in cardiac tissue were interpreted as a component of the bradycardia associated with torpor. The function of the differentially expressed transcripts in brain is less transparent, likely due to heterogeneity among the responses of different cell populations in this complex organ.

Dataset Information

MiRNA profiling by Illumina sequencing technology

Publications

Genomic analysis of miRNAs in an extreme mammalian hibernator, the Arctic ground squirrel.

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