Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1139359 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29936972_1.fastq.gz | Fastqsanger.gz | |||
| SRR29936972_2.fastq.gz | Fastqsanger.gz | |||
| SRR29936973_1.fastq.gz | Fastqsanger.gz | |||
| SRR29936973_2.fastq.gz | Fastqsanger.gz | |||
| SRR29936974_1.fastq.gz | Fastqsanger.gz |
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Project description:Changes in gene regulation have long been though to underlie most phenotypic differences between species. Subterranean rodents, and in particular the naked mole-rat (NMR), have attracted substantial attention due to their proposed phenotypic adaptations, which include hypoxia tolerance, metabolic changes and cancer resistance. However, it is largely unknown what regulatory changes may associate with these phenotypic traits, and whether these are unique to the NMR, the mole-rat clade or also present in other mammals. Here, we undertook a comparative genomics approach to identify genome-wide promoter and enhancer regions harbouring epigenomic hallmarks of regulatory activity, in heart and liver from two mole-rat species (NMR and DMR) and two rodent outgroups. To identify promoters and enhancers displaying robust shifts in regulatory activity in the mole-rat clade, we adapted and applied a phylogenetic modeling approach to quantitatively compare epigenomic signals at orthologous locations, while accounting for phylogenetic distance and inter-species variation. This method identified thousands of orthologous promoter and enhancer regions with increased activity in ancestral or single-species mole-rat branches, as well as hundreds of promoters and enhancers with reduced activity in mole-rats versus other rodents. These elements underlie both shared tissue-specific changes in gene regulation associated with mole-rat evolution, which include metabolic and functional adaptations in heart and liver. Moreover, by comparing mole-rat specific changes in promoters and enhancers between ancestral and single-species branches, our data revealed a number of candidate pathways with stepwise regulatory changes during mole-rat evolution. Lastly, we analysed the genomic properties of non-alignable promoters and enhancers in mole-rats, and report (i) their overlap with specific repetitive elements and transcription factor binding sites; and (ii) their association with metabolic gene functions. On the whole, these comparative analyses reveal mole-rat specific epigenomic changes across orthologous and non-mappable promoters and enhancers - which inform previously reported mole-rat adaptations from a gene regulation perspective.
2023-08-21 | GSE222972 | GEO
Project description:We performed RNAseq, metabolomics and pathway enrichment analysis on cardiac tissue from naked mole-rats (Heterocephalus glaber) and from seven other members of African mole rat genera, Cape mole-rat (Georychus capensis), Cape dune mole-rat (Bathyergus suillus), Common mole-rat (Cryptomys hottentotus hottentotus), Natal mole-rat (C. h. natalenesis), Mahali mole rat (C. h. mahali), Highveld mole-rat (C. h. pretoriae) and Damaraland mole-rats (Fukomys damarensis) representing differing burrow and soil types, degrees of sociality, lifespan and hypoxia tolerance. In addition, we include the evolutionarily highly divergent hottentot golden mole (Ambysomus hottentotus), an Afrotherian subterranean, solitary mammal, and the C57/BL6 laboratory mouse as a standard mammal control. After RNA sequencing, we removed the reads mapped to rRNAs and get rawdata, then we filtered the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads. These are the data uploaded.
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Project description:An Infinium microarray platform (GPL28271, HorvathMammalMethylChip40) was used to generate DNA methylation data from many tissues of 3 species of mole rats: Cape mole rat (Georychus capensis), Damaraland mole rat (Cryptomys damarensis), Naked mole rat (Heterocephalus glaber). We generated DNA methylation data from n=94 tissues from 3 species: Cryptomys damarensis (n=10), Georychus capensis (n=6), Heterocephalus glaber (n=78). All tissues ewere obtained from frozen tissue collection that were euthanized for other studies. Kidney (n=6), liver (n=61), skin (n=27). The tissues used in this study were obtained from post-mortem specimens from animals free from disease in compliance. Sample collection was from post-mortem material. Tissue samples were snap frozen in liquid nitrogen following dissection and transferred for storage at -80ºC. Genomic DNA was extracted using Qiagen DNeasy Blood and Tissue kit and quantified using Nanodrop and Qubit.als
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Project description:We generated single cell transcriptomes from full thickness skin biopsies in naked mole-rat to quantify the skin cell types found in this species (control samples). To study if and how naked mole-rat skin changes upon exposure to a carcinogen, we performed a classical two-stage skin carcinogenesis experiment traditionally performed in mice, wherein cancer is initiated by a single application of 7,12-dimethylbenz[a]-anthracene (DMBA) followed by repeated treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA) to drive cell proliferation. After 12 weeks, full thickness skin biopsies were collected and used to generate single cell transcriptomes (treatment samples).
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Project description:We generated single cell transcriptomes from full thickness skin biopsies in naked mole-rat to quantify the skin cell types found in this species (control samples). To study if and how naked mole-rat skin changes upon exposure to a carcinogen, we performed a classical two-stage skin carcinogenesis experiment traditionally performed in mice, wherein cancer is initiated by a single application of 7,12-dimethylbenz[a]-anthracene (DMBA) followed by repeated treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA) to drive cell proliferation. After 12 weeks, full thickness skin biopsies were collected and used to generate single cell transcriptomes (treatment samples).
2023-11-21 | E-MTAB-12459 | biostudies-arrayexpress
Project description:We generated single cell transcriptomes from full thickness skin biopsies in naked mole-rat to quantify the skin cell types found in this species (control samples). To study if and how naked mole-rat skin changes upon exposure to a carcinogen, we performed a classical two-stage skin carcinogenesis experiment traditionally performed in mice, wherein cancer is initiated by a single application of 7,12-dimethylbenz[a]-anthracene (DMBA) followed by repeated treatment with 12-O-tetradecanoylphorbol-13-acetate (TPA) to drive cell proliferation. After 12 weeks, full thickness skin biopsies were collected and used to generate single cell transcriptomes (treatment samples).
2023-11-21 | E-MTAB-12451 | biostudies-arrayexpress
Project description:Transcriptome of long-lived naked-mole rat (NMR) oligodendrocyte progenitor cells (OPCs) were compared with OPCs of other species.
2022-03-31 | E-MTAB-9160 | biostudies-arrayexpress
Project description:The goal was to find genes which are differentially expressed between the naked mole-rat (Heterocephalus glaber) and the wild-type mice liver tissue. The genes which are most differentially expressed may provide a clue for the remarkable differences between naked mole-rat and mouse in terms of longevity, cancer resistance and adaptation to subterranean environments. Analysis of 2 mRNA samples, one pooled from 3 wild-type mice liver tissue and another pooled from 3 naked mole-rat liver tissue.
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Project description:We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse.
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