Mus musculus breed:C57BL/6J, 129, CAST/EiJ, SPRET/EiJ
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA390071 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5678390_1.fastq.gz | Fastqsanger.gz | |||
| SRR5678390_2.fastq.gz | Fastqsanger.gz | |||
| SRR5678400_1.fastq.gz | Fastqsanger.gz | |||
| SRR5678400_2.fastq.gz | Fastqsanger.gz | |||
| SRR5678410_1.fastq.gz | Fastqsanger.gz |
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Project description:Here we introduce a test for lineage-specific selection of cis-regulation that can be applied to any gene set of interest. Applying the test to hundreds of gene sets in two diverged subspecies of mouse, we find evidence for selection acting on the cis-regulation of several functional classes, including those involved in both physiology (e.g. mitochondria-related genes and growth regulators) and behavior (e.g. locomotory-related genes and memory-related genes). These positively selected gene sets implicate potential targets of positive selection that are supported by quantitative trait loci, and accurately predict a number of phenotypic differences between the two subspecies, suggesting that the divergence in these traits may have been driven by adaptive evolution.
2009-08-31 | GSE16227 | GEO
Project description:OBJECTIVE:Low-density lipoprotein receptor (LDLR) and proprotein convertase subtilisin/kexin type 9 (PCSK9) are opposing regulators of plasma LDL-cholesterol levels. The PCSK9 gene exhibits many single or compound polymorphisms within or among mammalian species. This is case between the SPRET/EiJ (SPRET) and C57BL/6J (B6) mouse strains. We examined whether these polymorphisms could be associated with differential expression and activity of their respective PCSK9 molecules. METHODS:Liver expression of LDLR and PCSK9 transcripts were assessed by RT-PCR, and that of their corresponding proteins by immunoblotting. Purified recombinant PCSK9 proteins were assayed for their ability to degrade LDLR. Pcsk9 gene proximal promoters were tested for activation of a luciferase reporter gene. RESULTS:SPRET and B6 mice carried comparable levels of plasma cholesterol in spite of the fact that SPRET mice expressed less PCSK9 and more LDLR in liver. There were indels and single-base differences between their Pcsk9 cDNA and promoter sequences. Ex vivo, SPRET PCSK9 protein was less secreted but was more active at degrading LDLR. Its gene promoter was more active at driving expression of the luciferase reporter. CONCLUSIONS:Collectively, these results suggest that, compared to the B6 mouse, the SPRET mouse may represent an example of absence of direct correlation between PCSK9 and cholesterol levels in plasma, due to genetic variations leading to reduced secretion of PCSK9 associated with greater LDLR-degrading activity.
| S-EPMC5155046 | biostudies-literature
Project description:In a nutrient self-selection study, CAST/EiJ mice consumed more carbohydrate than fat while C57BL/6J (B6) mice showed the opposite preference. The present study revealed similar strain differences in preferences for isocaloric fat (Intralipid) and carbohydrate (sucrose, maltodextrin) solutions in chow-fed mice. In initial 2-day choice tests, percent fat intakes of CAST and B6 mice were 4-9% and 71-81% respectively. In subsequent nutrient vs. water tests, CAST mice consumed considerably less fat but not carbohydrate compared to B6 mice. Orosensory rather than postoral factors are implicated in the very low fat preference and intake of CAST mice. This is supported by results of a choice test with Intralipid mixed with non-nutritive sweeteners vs. non-sweet maltodextrin. The preference of CAST mice for sweetened fat exceeded that of B6 mice (94 vs. 74%) and absolute fat intakes were similar in the two strains. When given unsweetened Intralipid vs. water tests at ascending fat concentrations CAST mice displayed reduced fat preferences at 0.1-5% and reduced intakes at 0.5-5% concentrations, compared to B6 mice. The differential fat preferences of CAST and B6 mice may reflect differences in fat taste sensing or in central neural processes related to fat selection.
| S-EPMC6082157 | biostudies-literature
Project description:Study objectiveWe have previously established that CAST/EiJ (CAST) mice differ from normal mice, such as C57BL/6J (B6), in the timing of wheel-running onset relative to light/dark cycles. These mice provide an animal model for studies of the genetic and neurobiological basis for circadian phase misalignment in humans. Neither differences in endogenous circadian period nor the shape of the photic phase response curve explain the difference in the timing of activity onset between CAST and B6 mice, suggesting a mechanism downstream of the circadian clock. Here, we further test the hypothesis that the two strains differ with respect to circadian oscillations at the molecular level.DesignSleep/wake cycles were examined and rhythms of Period1 (Per1) and Period2 (Per2) expression were measured in the cerebral cortex, suprachiasmatic nucleus (SCN), and other hypothalamic regions.SettingBasic sleep and molecular research laboratory.Patients or participantsMale mice of the B6 and CAST inbred strains.InterventionsNone.Measurements and resultsSleep/wake cycles were advanced by approximately 4 h in CAST mice relative to B6 mice. This was paralleled by phase-advanced rhythms of Per1 and Per2 expression, as measured byin situ hybridization, in the cerebral cortex of CAST relative to B6. By contrast, the timing of circadian oscillations and the photic induction ofPer1 and Per2 expression in the SCN were unaffected by strain.ConclusionThe advanced phase of wheel running and sleep/wake cycles in CAST mice relative to B6 mice is apparently not associated with differences in molecular oscillations in the SCN clock itself, but most likely in mechanisms downstream of the SCN clock. CAST mice may therefore provide a model system to investigate circadian downstream mechanisms underlying unusual patterns of entrainment to the ambient photoperiod.CitationJiang P; Franklin KM; Duncan MJ; O'Hara BF; Wisor JP. Distinct phase relationships between suprachiasmatic molecular rhythms, cerebral cortex molecular rhythms, and behavioral rhythms in early runner (CAST/EiJ) and nocturnal (C57BL/6J) mice. SLEEP 2012;35(10):1385-1394.
| S-EPMC3443765 | biostudies-literature
Project description:We explored the relationship between the evolutionary dynamics of CTCF binding and the functional stability of higher order genome structures, by performing ChIP-seq experiments in closely related Mus species or strains and intersecting with Hi-C-derived topologically associating domains (TADs) and expression data. All experiments were performed in adult male liver samples in 3 biological replicates and with an input control set. We also generated RAD21 (cohesin subunit) ChIP-seq from a replicate of adult male mouse (C57BL/6J) liver to determine localization of cohesin with respect to CTCF.
2019-11-20 | E-MTAB-8014 | biostudies-arrayexpress
Project description:We have identified candidate genes from the Feml2 QTL influencing femur length through allele specific expression analysis of growth plates in C57BL/6J x CAST/EiJ F1 hybrids. This work provides the foundation to identify novel genes affecting bone geometry.
2016-11-19 | GSE90055 | GEO
Project description:Sequencing files provided here are mouse liver RNA-seq in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes DNase-seq and H3K27ac ChIP-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.
2021-10-27 | GSE130913 | GEO
Project description:BACKGROUNDThe damaging effects of exposure to environmental toxicants differentially affect genetically distinct individuals, but the mechanisms contributing to these differences are poorly understood. Genetic variation affects the establishment of the gene regulatory landscape and thus gene expression, and we hypothesized that this contributes to the observed heterogeneity in individual responses to exogenous cellular insults.OBJECTIVESWe performed an in vivo study of how genetic variation and chromatin organization may dictate susceptibility to DNA damage, and influence the cellular response to such damage, caused by an environmental toxicant.MATERIALS AND METHODSWe measured DNA damage, messenger RNA (mRNA) and microRNA (miRNA) expression, and genome-wide chromatin accessibility in lung tissue from two genetically divergent inbred mouse strains, C57BL/6J and CAST/EiJ, both in unexposed mice and in mice exposed to a model DNA-damaging chemical, 1,3-butadiene.RESULTSOur results showed that unexposed CAST/EiJ and C57BL/6J mice have very different chromatin organization and transcription profiles in the lung. Importantly, in unexposed CAST/EiJ mice, which acquired relatively less 1,3-butadiene-induced DNA damage, we observed increased transcription and a more accessible chromatin landscape around genes involved in detoxification pathways. Upon chemical exposure, chromatin was significantly remodeled in the lung of C57BL/6J mice, a strain that acquired higher levels of 1,3-butadiene-induced DNA damage, around the same genes, ultimately resembling the molecular profile of CAST/EiJ.CONCLUSIONSThese results suggest that strain-specific changes in chromatin and transcription in response to chemical exposure lead to a "compensation" for underlying genetic-driven interindividual differences in the baseline chromatin and transcriptional state. This work represents an example of how chemical and environmental exposures can be evaluated to better understand gene-by-environment interactions, and it demonstrates the important role of chromatin response in transcriptomic changes and, potentially, in deleterious effects of exposure. https://doi.org/10.1289/EHP1937.
| S-EPMC5944832 | biostudies-literature
Project description:Sequencing files provided here are mouse liver ChIP-seq for the activating histone mark H3K27ac in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes RNA-seq and DNase-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.
2021-10-27 | GSE130909 | GEO
Project description:Sequencing files provided here are mouse liver DNase-seq in two mouse strains: C57BL/6J and CAST/EiJ. This is part of a larger study published in PLoS Genetics (2021) "Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model" that includes RNA-seq and H3K27ac ChIP-seq in mouse liver from the same two strains. This allows us to identify strain-shared ("core") and strain-unique sex-biased genes and enhancers.
2021-10-27 | GSE130912 | GEO