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Contrasting patterns of expression divergence in early and late stages of population divergence in mice

ABSTRACT: We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. Keywords: multi-species comparison

ORGANISM(S): Mus musculus Mus spretus

PROVIDER: GSE2597 | GEO | 2006/12/13

SECONDARY ACCESSION(S): PRJNA92009

REPOSITORIES: GEO

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Contrasting patterns of expression divergence in early and late stages of population divergence in mice

Project description:We compared gene expression differences in the polytypic species complex Mus musculus (Mus musculus musculus, Mus musculus domesticus, Mus musculus castaneus and Mus musculus ssp) with that of Mus spretus via oligonucleotide microarrays representing more than 20,000 genes. Analysis of the results by two way ANOVA statistics suggests that the most genes with significant differences in expression levels among the subspecies are found in liver and kidney and the least in testis. This picture is different when one compares with Mus spretus, where the largest number of differences is found in testis. The design we employed is a reference design. All tissues were hybridized against a pool of that same tissue from 9 C57BL6 mice. All mice were roughly 12 weeks of age. To control for biological variation, we have used several individual males from each sub-species. RNA was isolated from three different organs, namely brain, liver/kidney and testis.

2010-06-30 | E-GEOD-2597 | biostudies-arrayexpress

ChIP-Seq analysis of CCCTC-binding factor (CTCF) binding in rodents

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Variation in mouse chemical signals is genetically controlled and environmentally modulated

Project description:Urine proteomes of the house mouse (Mus musculus musculus, M. m. domesticus, M. m. castaneus).

2023-07-20 | PXD037086 | Pride

Transcription profiling of mouse subspecies and their F1 hybrids for 3 tissues (brain, liver, testis)

Project description:We have studied different subspecies of the house mouse (M. m. musculus, M. m. domesticus and M. m. castaneus) and their reciprocal F1 hybrids to estimate the within-locus mode of inheritance for subspecies differences in gene expression in three tissues (brain, liver, testis) of male mice. This study investigates mode of inheritance in crosses at a larger taxonomic distance than have been previously systematically investigated. We found the vast majority of transcripts to be additively expressed with only a few transcripts showing dominance or overdominance in expression, except for one direction of one cross, which showed large mis-expression in the testis. Experiment Overall Design: Wild-derived inbred lines of M. m. musculus, M. m. domesticus and M. m. castaneus were used to generate reciprocal crosses of M. m. musculus x M. m. domesticus and M. m. musculus x M. m. castaeneus. The gene expression profile of 2 males each of the hybrids and the pure parental subspecies were analyzed by using the Affymetrix GeneChip 430 2.0 to obtain evidence about the within-locus mode of inheritance of genes. First, we studied all transcripts that are differentially expressed between the parental subspecies and assessed additivity vs. nonadditivity of expression of these transcripts in the F1 hybrids. Second, we investigated those transcripts which do not differ in expression between the parental lines, but which are expressed differently in the F1 hybrids relative to both of their parents.

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Expression data from Mus musculus subspecies and their F1 hybrids for 3 tissues (brain, liver, testis)

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Differential expression in testis in 4 house mouse species

Project description:RNA from testis from 4 mus musculus species was hybridized on affymetrix gene chip U74Av2. Subspecies-specific differences in expression level were then extracted by conditioning on outcomes to cases where the expression in one subspecies differed significantly from all others but these did not differ significantly among each other. Keywords: other

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Genome-wide map of H3K4me3 and PRDM9-binding in 12 day post-partum mouse spermatocytes

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DNA Methylation Divergence and Tissue Specialization in the Developing Mouse Placenta

Project description:The placental epigenome plays a vital role in regulating mammalian growth and development. Aberrations in placental DNA methylation are linked to several disease states, including intrauterine growth restriction and preeclampsia. Studying the evolution and development of the placental epigenome is critical to understanding the origin and progression of such diseases. Although high resolution studies have found substantial variation between placental methylomes of different species, the nature of methylome variation has yet to be characterized within any individual species. We conducted a study of placental DNA methylation at high resolution in multiple strains and closely related species of house mice (Mus musculus musculus, Mus m. domesticus, and M. spretus), across developmental timepoints (embryonic days 15 to 18), and between the labyrinthine transport and junctional endocrine layers. We observed substantial genome-wide methylation heterogeneity in mouse placenta compared to other differentiated tissues. Species-specific methylation profiles were concentrated in retrotransposon subfamilies, specifically RLTR10 and RLTR20 subfamilies. Regulatory regions such as gene promoters and CpG islands displayed cross-species conservation, but showed strong differences between layers and developmental timepoints. Partially methylated domains exist in the mouse placenta and widen during development. Taken together, our results characterize the mouse placental methylome as a highly heterogeneous and deregulated landscape globally, intermixed with actively regulated promoter and retrotransposon sequences.

2017-04-12 | GSE84350 | GEO

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