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Constraint and divergence of global gene expression in the mammalian embryo

ABSTRACT: We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis.

ORGANISM(S): Mus musculus

PROVIDER: GSE62967 | GEO | 2015/04/14

SECONDARY ACCESSION(S): PRJNA266316

REPOSITORIES: GEO

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Constraint and divergence of global gene expression in the mammalian embryo

Project description:We profiled genome-wide gene expression of 170 individual mid-gestation (embryonic day 11.5) whole mouse embryos derived from a 2-generation interspecies mouse cross and asked to what extent genetic variation drives four important parameters of regulatory architecture: allele-specific expression (ASE), imprinting, trans-regulatory effects, and maternal effect. The inbred strain C57BL/6J and wild-derived inbred strain CAST/EiJ were used in reciprocal crosses to generate F1 embryos. F1 progeny were backcrossed to C57BL/6J in reciprocal crosses to generate 154 N2 embryos. We employed a backcross design, in which N2 offspring have genotypically distinct parents, to enable comparison of gene expression for offspring from each side of the reciprocal cross. Our findings demonstrate that genetic variation contributes to widespread gene expression differences during mammalian embryogenesis. Transcriptome analysis of E11.5 mouse embryos: 16 F1 embryos from reciprocally crossed C57BL/6J and CastEi/J parents; and 154 N2 embryos from reciprocal backcross of F1s to the C57BL/6J parent.

2015-04-14 | E-GEOD-62967 | biostudies-arrayexpress

The direction of cross affects obesity after puberty in male but not female offspring

Project description:We investigated parent-of-origin and allele-specific expression effects on obesity and hepatic gene expression in reciprocal crosses between the Berlin Fat Mouse Inbred line (BFMI) and C57Bl/6NCrl (B6N). We sequenced mRNA extracted from liver tissue of 10 M. Musculus individuals. 4 liver samples were collected from 10 week old inbred strains (1 male and 1 female Berlin Fat Mouse Inbred line (BFMI), 1 male and 1 female C57Bl/6NCrl (B6N)) and 6 liver samples collected from 10 week old F1 males using a reciprocal cross design (3 paternal BFMI (patBFMI) vs 3 maternal BFMI (matBFMI)). Reciprocal crosses were generated from the Berlin Fat Mouse Inbred line BFMI860-12/Hber (BFMI) and C57BL/6NCrl (B6N). Seven BFMI males were mated with seven B6N females and six B6N males with six BFMI860 females to generate 48 F1 animals (deemed patBFMI and matBFMI, respectively). Each reciprocal F1 offspring groups consisted of 12 males and 12 females. From these animals three F1 males from three BFMI females and three F1 males from three B6N females were used for RNA-seq measurements. One high fat diet raised male and female from each inbred parental strain (BFMI and B6N) were used as parental strain control animals and measured via RNA-seq as well.

2015-11-11 | E-GEOD-74889 | biostudies-arrayexpress

The direction of cross affects obesity after puberty in male but not female offspring

2015-11-11 | GSE74889 | GEO

Compensatory cis-trans regulation of mouse liver gene expression

Project description:Two inbred mouse strains, C57BL/6J and CAST/EiJ, were crossed to generate both initial and reciprocal F1 crosses. For each genetically distinct class of mice (F0 C57BL/6J, F0 CAST/EiJ, F1i - C57BL/6J x CAST/EiJ, F1r - CAST/EiJ x C57BL/6J, where the male parent is listed first), samples were collected from a single lobe of the liver from 6 male mice between the ages of 4 and 6 months. The 24 samples were then processed to generate strand-specific RNA-seq libraries, which were sequenced on the Illumina GAII platform using 72bp paired-end reads.

2012-09-07 | E-MTAB-1091 | biostudies-arrayexpress

Widespread over-expression of the X chromosome in sterile F1 hybrid mice

Project description:We used a reciprocal cross of Mus musculus and M. domesticus in which F1 males are sterile in one direction and fertile in the other direction, in order to associate expression differences with sterility. Four different crosses were performed. A cross between two strains within each mouse species (M. musculus, PWK/PhJ and CZECHII/EiJ; M. domesticus, LEWES/EiJ and WSB/EiJ). And two reciprocal crosses between a domesticus (LEWES/EiJ) and a musculus (PWK/PhJ) strain. The cross between a musculus female and a domesticus male produces sterile male offspring - whereas all other crosses produced fertile male offspring. Testis tissue from three male mice (60 days old) from all four crosses were analysed on the Affymetrix MG 430.2. Array.

2010-10-05 | E-GEOD-17684 | biostudies-arrayexpress

High resolution analysis of genomic imprinting in the embryonic and adult mouse brain AND Sex-specific imprinting in the mouse brain

Project description:Genomic imprinting results in the preferential expression of the paternal, or maternal allele of certain genes. We have performed a genome-wide characterization of imprinting in the mouse embryonic and adult brain using F1 hybrid mice generated from reciprocal crosses of CASTEiJ and C57BL/6J mice. We also uncovered genes associated with sex specific parental effects in the adult mouse brain. Our study identified preferential selection of the maternally inherited X chromosome in glutamatergic neurons of the female cortex. Examination of allele specific expression in the brains of reciprocal crosses of F1 hybrid mice from CASTEiJ and C57BL/6J crosses. Processed data files (GenomicAligned, SNP_calls, TranscriptomeAligned, fRNAdbAligned) and README file linked below as supplementary files.

2010-07-08 | E-GEOD-22131 | biostudies-arrayexpress

RNA-Seq of mESCs based on sex chromosome complement

Project description:RNA-Seq was performed on mESCs generated from F1 hybrids from reciprocal crosses of C57BL/6J and CAST/EiJ, denoted B and C hereafter; cell lines are designated as BC or CB, with the maternal line symbolized first

2017-09-15 | GSE90516 | GEO

Strain differences in e11.5 XY gonad transcriptome suggest a mechanism for the sensitivity of C57BL/6J to sex reversal

Project description:Transcriptional profiling of individual mouse embryonic (e11.5) XY gonads comparing inbred strains that are sensitive (C57BL/6J) and resistant (129S1/SvImJ) to XY sex reversal, and their reciprocal F1 hybrids.

2009-10-30 | GSE16917 | GEO

Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

Project description:Heterosis occurs where F1 offspring display superior characteristics to the parents. Heterosis is usually considered to result from crosses of genetically distinct (e.g. homozygous inbred) parents producing heterozygous F1 offspring. Most mechanistic models for heterosis require genetically heterozygous F1 hybrid offspring harbouring allelic diversity. Epigenetic or dosage models for heterosis could allow for heterosis effects in F1 offspring that display no allelic diversity with their parents. Reciprocal inter-ploidy crosses between diploid (2x) and tetraploid (4x) lines in the same genetic background generates genetically identical F1 triploids (3x). Such reciprocal F1 triploids differ according to whether the additional chromosome set is either maternally (maternal excess) or paternally inherited (paternal excess). Biomass accumulation and abiotic stress tolerance between the parental (2x and 4x) and reciprocal F1 triploid (3x) offspring of Arabidopsis thaliana accession C24 reveals a strong parental genome-dosage induced heterosis in the paternal-excess triploid F1 plants. In these F1 triploids, the circadian clock related genes CCA1 and TOC1, and the growth factors PIF4 and PIF5, display different expression levels compared to the non-heterotic maternal excess F1 triploid siblings. Whole transcriptome profiling reveals a paternal genome dosage effect on gene expression levels with strong enrichment for dysregulated abiotic stress-related genes in the paternal excess F1 triploids. This study demonstrates that heterosis can be triggered without allelic diversity in F1 triploid plants. Heterosis without heterozygosity in plants can be induced via an epigenetic “chromosome imprinting” like parental genome dosage effect requiring paternal transmission of an additional chromosome set

2014-08-01 | GSE52885 | GEO

Transcriptome profiling of an autopolyploidy series of Arabidopsis thaliana

2014-08-01 | E-GEOD-52885 | biostudies-arrayexpress

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